5nrl: Difference between revisions

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<StructureSection load='5nrl' size='340' side='right' caption='[[5nrl]], [[Resolution|resolution]] 7.20&Aring;' scene=''>
<StructureSection load='5nrl' size='340' side='right' caption='[[5nrl]], [[Resolution|resolution]] 7.20&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[5nrl]] is a 58 chain structure with sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae], [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae_(strain_atcc_204508_/_s288c) Saccharomyces cerevisiae (strain atcc 204508 / s288c)] and [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae_(strain_yjm789) Saccharomyces cerevisiae (strain yjm789)]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5NRL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5NRL FirstGlance]. <br>
<table><tr><td colspan='2'>[[5nrl]] is a 58 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_18824 Atcc 18824], [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae] and [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae_ Saccharomyces cerevisiae ]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5NRL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5NRL FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=PSU:PSEUDOURIDINE-5-MONOPHOSPHATE'>PSU</scene></td></tr>
<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=PSU:PSEUDOURIDINE-5-MONOPHOSPHATE'>PSU</scene></td></tr>
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{{Large structure}}
{{Large structure}}
== Function ==
== Function ==
[[http://www.uniprot.org/uniprot/YSF3_YEAST YSF3_YEAST]] Involved in pre-mRNA splicing. Required for the SF3b integrity and prespliceosome assembly.<ref>PMID:16314500</ref>  [[http://www.uniprot.org/uniprot/MSL1_YEAST MSL1_YEAST]] Involved in pre-mRNA splicing. This protein is associated with snRNP U2. It binds stem loop IV of U2 snRNA.<ref>PMID:8649387</ref>  [[http://www.uniprot.org/uniprot/SP381_YEAST SP381_YEAST]] Component of the spliceosome and rRNA processing machinery. In association with the spliceosomal U4/U6.U5 tri-snRNP particle, required for splicing of pre-mRNA.<ref>PMID:9858581</ref>  [[http://www.uniprot.org/uniprot/LSM8_YEAST LSM8_YEAST]] Component of the nuclear LSM2-LSM8 complex, which is involved in splicing of nuclear mRNAs. LSM2-LSM8 associates with multiple snRNP complexes containing the U6 snRNA (U4/U6 snRNP, spliceosomal U4/U6.U5 snRNP, and free U6 snRNP). It binds directly to the U6 snRNA and plays a role in the biogenesis and stability of the U6 snRNP and U4/U6 snRNP complexes. It probably also is involved degradation of nuclear pre-mRNA by targeting them for decapping. LSM2-LSM8 probably is involved in processing of pre-tRNAs, pre-rRNAs and U3 snoRNA. LSM2 is required for processing of pre-tRNAs, pre-rRNAs and U3 snoRNA.<ref>PMID:12077351</ref> <ref>PMID:12438310</ref> <ref>PMID:15485930</ref>  [[http://www.uniprot.org/uniprot/RDS3_YEAST RDS3_YEAST]] Required for pre-mRNA splicing. Involved in regulation of drug sensitivity and may play a role in multidrug resistance.<ref>PMID:11943786</ref> <ref>PMID:14517302</ref>  [[http://www.uniprot.org/uniprot/LSM3_YEAST LSM3_YEAST]] Component of LSm protein complexes, which are involved in RNA processing and may function in a chaperone-like manner. Component of the cytoplasmic LSM1-LSM7 complex which is thought to be involved in mRNA degradation by activating the decapping step. Component of the nuclear LSM2-LSM8 complex, which is involved in splicing of nuclear mRNAs. LSM2-LSM8 associates with multiple snRNP complexes containing the U6 snRNA (U4/U6 snRNP, U4/U6.U5 snRNP, and free U6 snRNP). It binds directly to the U6 snRNA and plays a role in the biogenesis and stability of the U6 snRNP and U4/U6 snRNP complexes. It probably also is involved degradation of nuclear pre-mRNA by targeting them for decapping. LSM3 binds specifically to the 3'-terminal U-tract of U6 snRNA. LSM2-LSM8 probably is involved in processing of pre-tRNAs, pre-rRNAs and U3 snoRNA. LSM3, probably in a complex that contains LSM2-LSM7 but not LSM1 or LSM8, associates with the precursor of the RNA component of RNase P (pre-P RNA) and may be involved in maturing pre-P RNA. LSM3 is required for processing of pre-tRNAs, pre-rRNAs and U3 snoRNA.<ref>PMID:7744014</ref> <ref>PMID:10747033</ref> <ref>PMID:10761922</ref> <ref>PMID:12077351</ref> <ref>PMID:12438310</ref> <ref>PMID:15485930</ref>  [[http://www.uniprot.org/uniprot/PRP6_YEAST PRP6_YEAST]] Participates in pre-mRNA splicing. Part of the U4/U5/U6 tri-snRNP complex, one of the building blocks of the spliceosome. [[http://www.uniprot.org/uniprot/SNU13_YEAST SNU13_YEAST]] Common component of the spliceosome and rRNA processing machinery. In association with the spliceosomal U4/U6.U5 tri-snRNP particle, required for splicing of pre-mRNA. In association with box C/D snoRNPs, required for processing of pre-ribosomal RNA (rRNA) and site-specific 2'-O-methylation of substrate RNAs. Essential for the accumulation and stability of U4 snRNA, U6 snRNA, and box C/D snoRNAs.<ref>PMID:11081632</ref> <ref>PMID:12215523</ref> <ref>PMID:14730029</ref>  [[http://www.uniprot.org/uniprot/RU2A_YEAST RU2A_YEAST]] Involved in pre-mRNA splicing. Associates to U2 snRNA in a MSL1 dependent manner and is required for normal accumulation of U2 snRNA. Required for the spliceosome assembly and the efficient addition of U2 snRNP onto the pre-mRNA.<ref>PMID:9799242</ref>  [[http://www.uniprot.org/uniprot/LSM6_YEAS7 LSM6_YEAS7]] Component of LSm protein complexes, which are involved in RNA processing and may function in a chaperone-like manner, facilitating the efficient association of RNA processing factors with their substrates. Component of the cytoplasmic LSM1-LSM7 complex, which is thought to be involved in mRNA degradation by activating the decapping step in the 5'-to-3' mRNA decay pathway. In association with PAT1, LSM1-LSM7 binds directly to RNAs near the 3'-end and prefers oligoadenylated RNAs over polyadenylated RNAs. Component of the nuclear LSM2-LSM8 complex, which is involved in splicing of nuclear mRNAs. LSM2-LSM8 associates with multiple snRNP complexes containing the U6 snRNA (U4/U6 di-snRNP, spliceosomal U4/U6.U5 tri-snRNP, and free U6 snRNP). It binds directly to the 3'-terminal U-tract of U6 snRNA and plays a role in the biogenesis and stability of the U6 snRNP and U4/U6 snRNP complexes. LSM2-LSM8 probably also is involved degradation of nuclear pre-mRNA by targeting them for decapping, and in processing of pre-tRNAs, pre-rRNAs and U3 snoRNA. Component of a nucleolar LSM2-LSM7 complex, which associates with the precursor of the RNA component of RNase P (pre-P RNA) and with the small nucleolar RNA (snoRNA) snR5. It may play a role in the maturation of a subset of nucleolus-associated small RNAs (By similarity). [[http://www.uniprot.org/uniprot/PRP9_YEAST PRP9_YEAST]] mRNA splicing factors, PRP9, PRP11, and PRP21, are necessary for binding of the U2 snRNP to the pre-mRNA in an early step of spliceosome assembly. [[http://www.uniprot.org/uniprot/HSH49_YEAST HSH49_YEAST]] Possible SF3b-like factor. [[http://www.uniprot.org/uniprot/PRP11_YEAST PRP11_YEAST]] mRNA splicing factors, PRP9, PRP11, and PRP21, are necessary for addition of the U2 snRNP to the pre-mRNA in an early step of spliceosome assembly.<ref>PMID:9710584</ref>  [[http://www.uniprot.org/uniprot/SMD1_YEAST SMD1_YEAST]] Involved in pre-mRNA splicing. Binds snRNA U1, U2, U4 and U5 which contain a highly conserved structural motif called the Sm binding site. Also binds telomerase RNA and is required for its accumulation.<ref>PMID:10490028</ref> <ref>PMID:8430095</ref>  [[http://www.uniprot.org/uniprot/PRP3_YEAST PRP3_YEAST]] Participates in pre-mRNA splicing. Part of the U4/U5/U6 tri-snRNP complex, one of the building blocks of the spliceosome.<ref>PMID:9326489</ref>  [[http://www.uniprot.org/uniprot/PRP38_YEAST PRP38_YEAST]] Required for pre-mRNA splicing and maintenance of stable U6 small nuclear RNA levels. Implicated in the formation of stable and biologically active snRNP structures. As part of the U4/U6.U5 tri-snRNP particle, dispensible for spliceosome assembly, but required for conformational changes, which result in U4 snRNA release and the subsequent catalytic activation of the spliceosome.<ref>PMID:1508195</ref> <ref>PMID:9582287</ref>  [[http://www.uniprot.org/uniprot/CUS1_YEAST CUS1_YEAST]] Essential splicing protein required for U2 snRNP binding to pre-mRNA during spliceosome assembly. [[http://www.uniprot.org/uniprot/SN114_YEAST SN114_YEAST]] Component of the U5 snRNP complex required for pre-mRNA splicing. Binds GTP. [[http://www.uniprot.org/uniprot/RSMB_YEAST RSMB_YEAST]] Involved in pre-mRNA splicing. Binds snRNA U1, U2, U4 and U5 which contain a highly conserved structural motif called the Sm binding site. [[http://www.uniprot.org/uniprot/DIB1_YEAST DIB1_YEAST]] Essential role in pre-mRNA splicing. Also essential for entry into mitosis (G2/M progression) as well as for chromosome segregation during mitosis. [[http://www.uniprot.org/uniprot/LSM4_YEAST LSM4_YEAST]] Component of LSm protein complexes, which are involved in RNA processing and may function in a chaperone-like manner. Component of the cytoplasmic LSM1-LSM7 complex which is thought to be involved in mRNA degradation by activating the decapping step. Component of the nuclear LSM2-LSM8 complex, which is involved in splicing of nuclear mRNAs. LSM2-LSM8 associates with multiple spliceosome snRNP complexes containing the U6 snRNA (U4/U6 snRNP, U4/U6.U5 snRNP, and free U6 snRNP). It binds directly to the U6 snRNA and plays a role in the biogenesis and stability of the U6 snRNP and U4/U6 snRNP complexes. It probably also is involved degradation of nuclear pre-mRNA by targeting them for decapping. LSM4 binds specifically to the 3'-terminal U-tract of U6 snRNA. LSM2-LSM8 probably is involved in processing of pre-tRNAs, pre-rRNAs and U3 snoRNA. LSM4, probably in a complex that contains LSM2-LSM7 but not LSM1 or LSM8, associates with the precursor of the RNA component of RNase P (pre-P RNA) and may be involved in maturing pre-P RNA. LSM4 is required for processing of pre-tRNAs, pre-rRNAs and U3 snoRNA.<ref>PMID:10747033</ref> <ref>PMID:10761922</ref> <ref>PMID:12077351</ref> <ref>PMID:12438310</ref> <ref>PMID:15485930</ref>  [[http://www.uniprot.org/uniprot/SF3B1_YEAST SF3B1_YEAST]] Contacts pre-mRNA on both sides of the branch site early in spliceosome assembly. [[http://www.uniprot.org/uniprot/PRP31_YEAST PRP31_YEAST]] Promotes the association of the U4/U6.U5 tri-snRNP particle with pre-spliceosomes to form the mature spliceosomal complex.<ref>PMID:8604353</ref>  [[http://www.uniprot.org/uniprot/RSE1_YEAST RSE1_YEAST]] Involved in G2/M transition (By similarity). Required for pre-mRNA splicing and endoplasmic reticulum (ER) to Golgi secretion pathway. U2 snRNPs associated protein required for the pre-spliceosome assembly. The involvement in ER to Golgi secretion is probably indirect and due to the splicing of the pre-mRNA coding for SAR1, a small GTP-binding protein required for COPII vesicle formation from the ER.<ref>PMID:10369685</ref> <ref>PMID:9819400</ref>  [[http://www.uniprot.org/uniprot/PRP21_YEAST PRP21_YEAST]] mRNA splicing factors, PRP9, PRP11, and PRP21, are necessary for binding of the U2 snRNP to the pre-mRNA in an early step of spliceosome assembly. [[http://www.uniprot.org/uniprot/LSM7_YEAST LSM7_YEAST]] Component of LSm protein complexes, which are involved in RNA processing and may function in a chaperone-like manner. Component of the cytoplasmic LSM1-LSM7 complex which is thought to be involved in mRNA degradation by activating the decapping step. Component of the nuclear LSM2-LSM8 complex, which is involved in splicing of nuclear mRNAs. LSM2-LSM8 associates with multiple snRNP complexes containing the U6 snRNA (U4/U6 snRNP, spliceosomal U4/U6.U5 snRNP, and free U6 snRNP). It binds directly to the U6 snRNA and plays a role in the biogenesis and stability of the U6 snRNP and U4/U6 snRNP complexes. It probably also is involved degradation of nuclear pre-mRNA by targeting them for decapping. LSM7 binds specifically to the 3'-terminal U-tract of U6 snRNA. LSM2-LSM8 probably is involved in processing of pre-tRNAs, pre-rRNAs and U3 snoRNA. LSM7, probably in a complex that contains LSM2-LSM7 but not LSM1 or LSM8, associates with the precursor of the RNA component of RNase P (pre-P RNA) and may be involved in maturing pre-P RNA.<ref>PMID:10747033</ref> <ref>PMID:10761922</ref> <ref>PMID:15485930</ref>  [[http://www.uniprot.org/uniprot/RUXG_YEAST RUXG_YEAST]] Involved in pre-mRNA splicing. Binds snRNA U1, U2, U4 and U5 which contain a highly conserved structural motif called the Sm binding site. [[http://www.uniprot.org/uniprot/SMD3_YEAST SMD3_YEAST]] Involved in pre-mRNA splicing. Binds snRNA U1, U2, U4 and U5 which contain a highly conserved structural motif called the Sm binding site. Also binds telomerase RNA and is required for its accumulation.<ref>PMID:10490028</ref> <ref>PMID:7799953</ref>  [[http://www.uniprot.org/uniprot/BRR2_YEAST BRR2_YEAST]] RNA helicase that plays an essential role in pre-mRNA splicing as component of the U5 snRNP and U4/U6-U5 tri-snRNP complexes. Involved in spliceosome assembly, activation and disassembly. Mediates changes in the dynamic network of RNA-RNA interactions in the spliceosome. Catalyzes the ATP-dependent unwinding of U4/U6 RNA duplices, an essential step in the assembly of a catalytically active spliceosome.<ref>PMID:19098916</ref> <ref>PMID:23124065</ref> <ref>PMID:19716790</ref> <ref>PMID:19525970</ref>  [[http://www.uniprot.org/uniprot/SMD2_YEAST SMD2_YEAST]] Involved in pre-mRNA splicing. Binds snRNA U1, U2, U4 and U5 which contain a highly conserved structural motif called the Sm binding site. [[http://www.uniprot.org/uniprot/SNU66_YEAST SNU66_YEAST]] Component of the U4/U6.U5 tri-snRNP particle, one of the building blocks of the spliceosome. Required for pre-mRNA splicing.<ref>PMID:11290703</ref>  [[http://www.uniprot.org/uniprot/PRP4_YEAST PRP4_YEAST]] Involved in RNA splicing. Is required for the association of U4/U6 snRNP with U5 snRNP in an early step of spliceosome assembly. [[http://www.uniprot.org/uniprot/PRP8_YEAST PRP8_YEAST]] Required for pre-spliceosome formation, which is the first step of pre-mRNA splicing. This protein is associated with snRNP U5. Has a role in branch site-3' splice site selection. Associates with the branch site-3' splice 3'-exon region. Also has a role in cell cycle.<ref>PMID:2835658</ref> <ref>PMID:9150140</ref> <ref>PMID:12773561</ref> <ref>PMID:18779563</ref>  [[http://www.uniprot.org/uniprot/RUXF_YEAST RUXF_YEAST]] Involved in pre-mRNA splicing. Binds snRNA U1, U2, U4 and U5 which contain a highly conserved structural motif called the Sm binding site. [[http://www.uniprot.org/uniprot/LSM2_YEAST LSM2_YEAST]] Component of LSm protein complexes, which are involved in RNA processing and may function in a chaperone-like manner. Component of the cytoplasmic LSM1-LSM7 complex which is thought to be involved in mRNA degradation by activating the decapping step. Component of the nuclear LSM2-LSM8 complex, which is involved in splicing of nuclear mRNAs. LSM2-LSM8 associates with multiple snRNP complexes containing the U6 snRNA (U4/U6 snRNP, U4/U6.U5 snRNP, and free U6 snRNP). It binds directly to the U6 snRNA and plays a role in the biogenesis and stability of the U6 snRNP and U4/U6 snRNP complexes. It probably also is involved degradation of nuclear pre-mRNA by targeting them for decapping. LSM2 binds specifically to the 3'-terminal U-tract of U6 snRNA. LSM2-LSM8 probably is involved in processing of pre-tRNAs, pre-rRNAs and U3 snoRNA. LSM2, probably in a complex that contains LSM2-LSM7 but not LSM1 or LSM8, associates with the precursor of the RNA component of RNase P (pre-P RNA) and may be involved in maturing pre-P RNA. LSM2 is required for processing of pre-tRNAs, pre-rRNAs and U3 snoRNA.<ref>PMID:10747033</ref> <ref>PMID:12077351</ref> <ref>PMID:12438310</ref> <ref>PMID:14627812</ref> <ref>PMID:15485930</ref>  [[http://www.uniprot.org/uniprot/RUXE_YEAST RUXE_YEAST]] Involved in pre-mRNA splicing. Binds and is required for the stability of snRNA U1, U2, U4 and U5 which contain a highly conserved structural motif called the Sm binding site. Involved in cap modification.<ref>PMID:8918241</ref>  [[http://www.uniprot.org/uniprot/LSM5_YEAST LSM5_YEAST]] Component of LSm protein complexes, which are involved in RNA processing and may function in a chaperone-like manner. Component of the cytoplasmic LSM1-LSM7 complex which is thought to be involved in mRNA degradation by activating the decapping step. Component of the nuclear LSM2-LSM8 complex, which is involved in splicing of nuclear mRNAs. LSM2-LSM8 associates with multiple snRNP complexes containing the U6 snRNA (U4/U6 snRNP, U4/U6.U5 snRNP, and free U6 snRNP). It binds directly to the U6 snRNA and plays a role in the biogenesis and stability of the U6 snRNP and U4/U6 snRNP complexes. It probably also is involved degradation of nuclear pre-mRNA by targeting them for decapping. LSM5 binds specifically to the 3'-terminal U-tract of U6 snRNA. LSM2-LSM8 probably is involved in processing of pre-tRNAs, pre-rRNAs and U3 snoRNA. LSM5, probably in a complex that contains LSM2-LSM7 but not LSM1 or LSM8, associates with the precursor of the RNA component of RNase P (pre-P RNA) and may be involved in maturing pre-P RNA. LSM5 is required for processing of pre-tRNAs, pre-rRNAs and U3 snoRNA.<ref>PMID:10747033</ref> <ref>PMID:10761922</ref> <ref>PMID:12077351</ref> <ref>PMID:12438310</ref> <ref>PMID:15485930</ref>  [[http://www.uniprot.org/uniprot/SNU23_YEAST SNU23_YEAST]] Participates in pre-mRNA splicing. Part of the U4/U5/U6 tri-snRNP complex, one of the building blocks of the spliceosome.  
[[http://www.uniprot.org/uniprot/YSF3_YEAST YSF3_YEAST]] Involved in pre-mRNA splicing. Required for the SF3b integrity and prespliceosome assembly.<ref>PMID:16314500</ref>  [[http://www.uniprot.org/uniprot/MSL1_YEAST MSL1_YEAST]] Involved in pre-mRNA splicing. This protein is associated with snRNP U2. It binds stem loop IV of U2 snRNA.<ref>PMID:8649387</ref>  [[http://www.uniprot.org/uniprot/SP381_YEAST SP381_YEAST]] Component of the spliceosome and rRNA processing machinery. In association with the spliceosomal U4/U6.U5 tri-snRNP particle, required for splicing of pre-mRNA.<ref>PMID:9858581</ref>  [[http://www.uniprot.org/uniprot/LSM8_YEAST LSM8_YEAST]] Component of the nuclear LSM2-LSM8 complex, which is involved in splicing of nuclear mRNAs. LSM2-LSM8 associates with multiple snRNP complexes containing the U6 snRNA (U4/U6 snRNP, spliceosomal U4/U6.U5 snRNP, and free U6 snRNP). It binds directly to the U6 snRNA and plays a role in the biogenesis and stability of the U6 snRNP and U4/U6 snRNP complexes. It probably also is involved degradation of nuclear pre-mRNA by targeting them for decapping. LSM2-LSM8 probably is involved in processing of pre-tRNAs, pre-rRNAs and U3 snoRNA. LSM2 is required for processing of pre-tRNAs, pre-rRNAs and U3 snoRNA.<ref>PMID:12077351</ref> <ref>PMID:12438310</ref> <ref>PMID:15485930</ref>  [[http://www.uniprot.org/uniprot/RDS3_YEAST RDS3_YEAST]] Required for pre-mRNA splicing. Involved in regulation of drug sensitivity and may play a role in multidrug resistance.<ref>PMID:11943786</ref> <ref>PMID:14517302</ref>  [[http://www.uniprot.org/uniprot/PRP6_YEAST PRP6_YEAST]] Participates in pre-mRNA splicing. Part of the U4/U5/U6 tri-snRNP complex, one of the building blocks of the spliceosome. [[http://www.uniprot.org/uniprot/LSM3_YEAST LSM3_YEAST]] Component of LSm protein complexes, which are involved in RNA processing and may function in a chaperone-like manner. Component of the cytoplasmic LSM1-LSM7 complex which is thought to be involved in mRNA degradation by activating the decapping step. Component of the nuclear LSM2-LSM8 complex, which is involved in splicing of nuclear mRNAs. LSM2-LSM8 associates with multiple snRNP complexes containing the U6 snRNA (U4/U6 snRNP, U4/U6.U5 snRNP, and free U6 snRNP). It binds directly to the U6 snRNA and plays a role in the biogenesis and stability of the U6 snRNP and U4/U6 snRNP complexes. It probably also is involved degradation of nuclear pre-mRNA by targeting them for decapping. LSM3 binds specifically to the 3'-terminal U-tract of U6 snRNA. LSM2-LSM8 probably is involved in processing of pre-tRNAs, pre-rRNAs and U3 snoRNA. LSM3, probably in a complex that contains LSM2-LSM7 but not LSM1 or LSM8, associates with the precursor of the RNA component of RNase P (pre-P RNA) and may be involved in maturing pre-P RNA. LSM3 is required for processing of pre-tRNAs, pre-rRNAs and U3 snoRNA.<ref>PMID:7744014</ref> <ref>PMID:10747033</ref> <ref>PMID:10761922</ref> <ref>PMID:12077351</ref> <ref>PMID:12438310</ref> <ref>PMID:15485930</ref>  [[http://www.uniprot.org/uniprot/SNU13_YEAST SNU13_YEAST]] Common component of the spliceosome and rRNA processing machinery. In association with the spliceosomal U4/U6.U5 tri-snRNP particle, required for splicing of pre-mRNA. In association with box C/D snoRNPs, required for processing of pre-ribosomal RNA (rRNA) and site-specific 2'-O-methylation of substrate RNAs. Essential for the accumulation and stability of U4 snRNA, U6 snRNA, and box C/D snoRNAs.<ref>PMID:11081632</ref> <ref>PMID:12215523</ref> <ref>PMID:14730029</ref>  [[http://www.uniprot.org/uniprot/RU2A_YEAST RU2A_YEAST]] Involved in pre-mRNA splicing. Associates to U2 snRNA in a MSL1 dependent manner and is required for normal accumulation of U2 snRNA. Required for the spliceosome assembly and the efficient addition of U2 snRNP onto the pre-mRNA.<ref>PMID:9799242</ref>  [[http://www.uniprot.org/uniprot/LSM6_YEAS7 LSM6_YEAS7]] Component of LSm protein complexes, which are involved in RNA processing and may function in a chaperone-like manner, facilitating the efficient association of RNA processing factors with their substrates. Component of the cytoplasmic LSM1-LSM7 complex, which is thought to be involved in mRNA degradation by activating the decapping step in the 5'-to-3' mRNA decay pathway. In association with PAT1, LSM1-LSM7 binds directly to RNAs near the 3'-end and prefers oligoadenylated RNAs over polyadenylated RNAs. Component of the nuclear LSM2-LSM8 complex, which is involved in splicing of nuclear mRNAs. LSM2-LSM8 associates with multiple snRNP complexes containing the U6 snRNA (U4/U6 di-snRNP, spliceosomal U4/U6.U5 tri-snRNP, and free U6 snRNP). It binds directly to the 3'-terminal U-tract of U6 snRNA and plays a role in the biogenesis and stability of the U6 snRNP and U4/U6 snRNP complexes. LSM2-LSM8 probably also is involved degradation of nuclear pre-mRNA by targeting them for decapping, and in processing of pre-tRNAs, pre-rRNAs and U3 snoRNA. Component of a nucleolar LSM2-LSM7 complex, which associates with the precursor of the RNA component of RNase P (pre-P RNA) and with the small nucleolar RNA (snoRNA) snR5. It may play a role in the maturation of a subset of nucleolus-associated small RNAs (By similarity). [[http://www.uniprot.org/uniprot/PRP9_YEAST PRP9_YEAST]] mRNA splicing factors, PRP9, PRP11, and PRP21, are necessary for binding of the U2 snRNP to the pre-mRNA in an early step of spliceosome assembly. [[http://www.uniprot.org/uniprot/HSH49_YEAST HSH49_YEAST]] Possible SF3b-like factor. [[http://www.uniprot.org/uniprot/PRP11_YEAST PRP11_YEAST]] mRNA splicing factors, PRP9, PRP11, and PRP21, are necessary for addition of the U2 snRNP to the pre-mRNA in an early step of spliceosome assembly.<ref>PMID:9710584</ref>  [[http://www.uniprot.org/uniprot/SMD1_YEAST SMD1_YEAST]] Involved in pre-mRNA splicing. Binds snRNA U1, U2, U4 and U5 which contain a highly conserved structural motif called the Sm binding site. Also binds telomerase RNA and is required for its accumulation.<ref>PMID:10490028</ref> <ref>PMID:8430095</ref>  [[http://www.uniprot.org/uniprot/PRP38_YEAST PRP38_YEAST]] Required for pre-mRNA splicing and maintenance of stable U6 small nuclear RNA levels. Implicated in the formation of stable and biologically active snRNP structures. As part of the U4/U6.U5 tri-snRNP particle, dispensible for spliceosome assembly, but required for conformational changes, which result in U4 snRNA release and the subsequent catalytic activation of the spliceosome.<ref>PMID:1508195</ref> <ref>PMID:9582287</ref>  [[http://www.uniprot.org/uniprot/PRP3_YEAST PRP3_YEAST]] Participates in pre-mRNA splicing. Part of the U4/U5/U6 tri-snRNP complex, one of the building blocks of the spliceosome.<ref>PMID:9326489</ref> [[http://www.uniprot.org/uniprot/CUS1_YEAST CUS1_YEAST]] Essential splicing protein required for U2 snRNP binding to pre-mRNA during spliceosome assembly. [[http://www.uniprot.org/uniprot/SN114_YEAST SN114_YEAST]] Component of the U5 snRNP complex required for pre-mRNA splicing. Binds GTP. [[http://www.uniprot.org/uniprot/RSMB_YEAST RSMB_YEAST]] Involved in pre-mRNA splicing. Binds snRNA U1, U2, U4 and U5 which contain a highly conserved structural motif called the Sm binding site. [[http://www.uniprot.org/uniprot/DIB1_YEAST DIB1_YEAST]] Essential role in pre-mRNA splicing. Also essential for entry into mitosis (G2/M progression) as well as for chromosome segregation during mitosis. [[http://www.uniprot.org/uniprot/LSM4_YEAST LSM4_YEAST]] Component of LSm protein complexes, which are involved in RNA processing and may function in a chaperone-like manner. Component of the cytoplasmic LSM1-LSM7 complex which is thought to be involved in mRNA degradation by activating the decapping step. Component of the nuclear LSM2-LSM8 complex, which is involved in splicing of nuclear mRNAs. LSM2-LSM8 associates with multiple spliceosome snRNP complexes containing the U6 snRNA (U4/U6 snRNP, U4/U6.U5 snRNP, and free U6 snRNP). It binds directly to the U6 snRNA and plays a role in the biogenesis and stability of the U6 snRNP and U4/U6 snRNP complexes. It probably also is involved degradation of nuclear pre-mRNA by targeting them for decapping. LSM4 binds specifically to the 3'-terminal U-tract of U6 snRNA. LSM2-LSM8 probably is involved in processing of pre-tRNAs, pre-rRNAs and U3 snoRNA. LSM4, probably in a complex that contains LSM2-LSM7 but not LSM1 or LSM8, associates with the precursor of the RNA component of RNase P (pre-P RNA) and may be involved in maturing pre-P RNA. LSM4 is required for processing of pre-tRNAs, pre-rRNAs and U3 snoRNA.<ref>PMID:10747033</ref> <ref>PMID:10761922</ref> <ref>PMID:12077351</ref> <ref>PMID:12438310</ref> <ref>PMID:15485930</ref>  [[http://www.uniprot.org/uniprot/SF3B1_YEAST SF3B1_YEAST]] Contacts pre-mRNA on both sides of the branch site early in spliceosome assembly. [[http://www.uniprot.org/uniprot/PRP31_YEAST PRP31_YEAST]] Promotes the association of the U4/U6.U5 tri-snRNP particle with pre-spliceosomes to form the mature spliceosomal complex.<ref>PMID:8604353</ref>  [[http://www.uniprot.org/uniprot/RSE1_YEAST RSE1_YEAST]] Involved in G2/M transition (By similarity). Required for pre-mRNA splicing and endoplasmic reticulum (ER) to Golgi secretion pathway. U2 snRNPs associated protein required for the pre-spliceosome assembly. The involvement in ER to Golgi secretion is probably indirect and due to the splicing of the pre-mRNA coding for SAR1, a small GTP-binding protein required for COPII vesicle formation from the ER.<ref>PMID:10369685</ref> <ref>PMID:9819400</ref>  [[http://www.uniprot.org/uniprot/PRP21_YEAST PRP21_YEAST]] mRNA splicing factors, PRP9, PRP11, and PRP21, are necessary for binding of the U2 snRNP to the pre-mRNA in an early step of spliceosome assembly. [[http://www.uniprot.org/uniprot/LSM7_YEAST LSM7_YEAST]] Component of LSm protein complexes, which are involved in RNA processing and may function in a chaperone-like manner. Component of the cytoplasmic LSM1-LSM7 complex which is thought to be involved in mRNA degradation by activating the decapping step. Component of the nuclear LSM2-LSM8 complex, which is involved in splicing of nuclear mRNAs. LSM2-LSM8 associates with multiple snRNP complexes containing the U6 snRNA (U4/U6 snRNP, spliceosomal U4/U6.U5 snRNP, and free U6 snRNP). It binds directly to the U6 snRNA and plays a role in the biogenesis and stability of the U6 snRNP and U4/U6 snRNP complexes. It probably also is involved degradation of nuclear pre-mRNA by targeting them for decapping. LSM7 binds specifically to the 3'-terminal U-tract of U6 snRNA. LSM2-LSM8 probably is involved in processing of pre-tRNAs, pre-rRNAs and U3 snoRNA. LSM7, probably in a complex that contains LSM2-LSM7 but not LSM1 or LSM8, associates with the precursor of the RNA component of RNase P (pre-P RNA) and may be involved in maturing pre-P RNA.<ref>PMID:10747033</ref> <ref>PMID:10761922</ref> <ref>PMID:15485930</ref>  [[http://www.uniprot.org/uniprot/RUXG_YEAST RUXG_YEAST]] Involved in pre-mRNA splicing. Binds snRNA U1, U2, U4 and U5 which contain a highly conserved structural motif called the Sm binding site. [[http://www.uniprot.org/uniprot/SMD3_YEAST SMD3_YEAST]] Involved in pre-mRNA splicing. Binds snRNA U1, U2, U4 and U5 which contain a highly conserved structural motif called the Sm binding site. Also binds telomerase RNA and is required for its accumulation.<ref>PMID:10490028</ref> <ref>PMID:7799953</ref>  [[http://www.uniprot.org/uniprot/BRR2_YEAST BRR2_YEAST]] RNA helicase that plays an essential role in pre-mRNA splicing as component of the U5 snRNP and U4/U6-U5 tri-snRNP complexes. Involved in spliceosome assembly, activation and disassembly. Mediates changes in the dynamic network of RNA-RNA interactions in the spliceosome. Catalyzes the ATP-dependent unwinding of U4/U6 RNA duplices, an essential step in the assembly of a catalytically active spliceosome.<ref>PMID:19098916</ref> <ref>PMID:23124065</ref> <ref>PMID:19716790</ref> <ref>PMID:19525970</ref>  [[http://www.uniprot.org/uniprot/SMD2_YEAST SMD2_YEAST]] Involved in pre-mRNA splicing. Binds snRNA U1, U2, U4 and U5 which contain a highly conserved structural motif called the Sm binding site. [[http://www.uniprot.org/uniprot/SNU66_YEAST SNU66_YEAST]] Component of the U4/U6.U5 tri-snRNP particle, one of the building blocks of the spliceosome. Required for pre-mRNA splicing.<ref>PMID:11290703</ref>  [[http://www.uniprot.org/uniprot/PRP4_YEAST PRP4_YEAST]] Involved in RNA splicing. Is required for the association of U4/U6 snRNP with U5 snRNP in an early step of spliceosome assembly. [[http://www.uniprot.org/uniprot/RUXF_YEAST RUXF_YEAST]] Involved in pre-mRNA splicing. Binds snRNA U1, U2, U4 and U5 which contain a highly conserved structural motif called the Sm binding site. [[http://www.uniprot.org/uniprot/PRP8_YEAST PRP8_YEAST]] Required for pre-spliceosome formation, which is the first step of pre-mRNA splicing. This protein is associated with snRNP U5. Has a role in branch site-3' splice site selection. Associates with the branch site-3' splice 3'-exon region. Also has a role in cell cycle.<ref>PMID:2835658</ref> <ref>PMID:9150140</ref> <ref>PMID:12773561</ref> <ref>PMID:18779563</ref>  [[http://www.uniprot.org/uniprot/LSM2_YEAST LSM2_YEAST]] Component of LSm protein complexes, which are involved in RNA processing and may function in a chaperone-like manner. Component of the cytoplasmic LSM1-LSM7 complex which is thought to be involved in mRNA degradation by activating the decapping step. Component of the nuclear LSM2-LSM8 complex, which is involved in splicing of nuclear mRNAs. LSM2-LSM8 associates with multiple snRNP complexes containing the U6 snRNA (U4/U6 snRNP, U4/U6.U5 snRNP, and free U6 snRNP). It binds directly to the U6 snRNA and plays a role in the biogenesis and stability of the U6 snRNP and U4/U6 snRNP complexes. It probably also is involved degradation of nuclear pre-mRNA by targeting them for decapping. LSM2 binds specifically to the 3'-terminal U-tract of U6 snRNA. LSM2-LSM8 probably is involved in processing of pre-tRNAs, pre-rRNAs and U3 snoRNA. LSM2, probably in a complex that contains LSM2-LSM7 but not LSM1 or LSM8, associates with the precursor of the RNA component of RNase P (pre-P RNA) and may be involved in maturing pre-P RNA. LSM2 is required for processing of pre-tRNAs, pre-rRNAs and U3 snoRNA.<ref>PMID:10747033</ref> <ref>PMID:12077351</ref> <ref>PMID:12438310</ref> <ref>PMID:14627812</ref> <ref>PMID:15485930</ref>  [[http://www.uniprot.org/uniprot/RUXE_YEAST RUXE_YEAST]] Involved in pre-mRNA splicing. Binds and is required for the stability of snRNA U1, U2, U4 and U5 which contain a highly conserved structural motif called the Sm binding site. Involved in cap modification.<ref>PMID:8918241</ref>  [[http://www.uniprot.org/uniprot/LSM5_YEAST LSM5_YEAST]] Component of LSm protein complexes, which are involved in RNA processing and may function in a chaperone-like manner. Component of the cytoplasmic LSM1-LSM7 complex which is thought to be involved in mRNA degradation by activating the decapping step. Component of the nuclear LSM2-LSM8 complex, which is involved in splicing of nuclear mRNAs. LSM2-LSM8 associates with multiple snRNP complexes containing the U6 snRNA (U4/U6 snRNP, U4/U6.U5 snRNP, and free U6 snRNP). It binds directly to the U6 snRNA and plays a role in the biogenesis and stability of the U6 snRNP and U4/U6 snRNP complexes. It probably also is involved degradation of nuclear pre-mRNA by targeting them for decapping. LSM5 binds specifically to the 3'-terminal U-tract of U6 snRNA. LSM2-LSM8 probably is involved in processing of pre-tRNAs, pre-rRNAs and U3 snoRNA. LSM5, probably in a complex that contains LSM2-LSM7 but not LSM1 or LSM8, associates with the precursor of the RNA component of RNase P (pre-P RNA) and may be involved in maturing pre-P RNA. LSM5 is required for processing of pre-tRNAs, pre-rRNAs and U3 snoRNA.<ref>PMID:10747033</ref> <ref>PMID:10761922</ref> <ref>PMID:12077351</ref> <ref>PMID:12438310</ref> <ref>PMID:15485930</ref>  [[http://www.uniprot.org/uniprot/SNU23_YEAST SNU23_YEAST]] Participates in pre-mRNA splicing. Part of the U4/U5/U6 tri-snRNP complex, one of the building blocks of the spliceosome.  
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== Publication Abstract from PubMed ==
== Publication Abstract from PubMed ==
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__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Atcc 18824]]
[[Category: RNA helicase]]
[[Category: RNA helicase]]
[[Category: Saccharomyces cerevisiae]]
[[Category: Saccharomyces cerevisiae]]

Revision as of 11:08, 21 March 2018

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Structure of a pre-catalytic spliceosomeStructure of a pre-catalytic spliceosome

Structural highlights

5nrl is a 58 chain structure with sequence from Atcc 18824, Saccharomyces cerevisiae and Saccharomyces cerevisiae . Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:,
NonStd Res:
Activity:RNA helicase, with EC number 3.6.4.13
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT
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Function

[YSF3_YEAST] Involved in pre-mRNA splicing. Required for the SF3b integrity and prespliceosome assembly.[1] [MSL1_YEAST] Involved in pre-mRNA splicing. This protein is associated with snRNP U2. It binds stem loop IV of U2 snRNA.[2] [SP381_YEAST] Component of the spliceosome and rRNA processing machinery. In association with the spliceosomal U4/U6.U5 tri-snRNP particle, required for splicing of pre-mRNA.[3] [LSM8_YEAST] Component of the nuclear LSM2-LSM8 complex, which is involved in splicing of nuclear mRNAs. LSM2-LSM8 associates with multiple snRNP complexes containing the U6 snRNA (U4/U6 snRNP, spliceosomal U4/U6.U5 snRNP, and free U6 snRNP). It binds directly to the U6 snRNA and plays a role in the biogenesis and stability of the U6 snRNP and U4/U6 snRNP complexes. It probably also is involved degradation of nuclear pre-mRNA by targeting them for decapping. LSM2-LSM8 probably is involved in processing of pre-tRNAs, pre-rRNAs and U3 snoRNA. LSM2 is required for processing of pre-tRNAs, pre-rRNAs and U3 snoRNA.[4] [5] [6] [RDS3_YEAST] Required for pre-mRNA splicing. Involved in regulation of drug sensitivity and may play a role in multidrug resistance.[7] [8] [PRP6_YEAST] Participates in pre-mRNA splicing. Part of the U4/U5/U6 tri-snRNP complex, one of the building blocks of the spliceosome. [LSM3_YEAST] Component of LSm protein complexes, which are involved in RNA processing and may function in a chaperone-like manner. Component of the cytoplasmic LSM1-LSM7 complex which is thought to be involved in mRNA degradation by activating the decapping step. Component of the nuclear LSM2-LSM8 complex, which is involved in splicing of nuclear mRNAs. LSM2-LSM8 associates with multiple snRNP complexes containing the U6 snRNA (U4/U6 snRNP, U4/U6.U5 snRNP, and free U6 snRNP). It binds directly to the U6 snRNA and plays a role in the biogenesis and stability of the U6 snRNP and U4/U6 snRNP complexes. It probably also is involved degradation of nuclear pre-mRNA by targeting them for decapping. LSM3 binds specifically to the 3'-terminal U-tract of U6 snRNA. LSM2-LSM8 probably is involved in processing of pre-tRNAs, pre-rRNAs and U3 snoRNA. LSM3, probably in a complex that contains LSM2-LSM7 but not LSM1 or LSM8, associates with the precursor of the RNA component of RNase P (pre-P RNA) and may be involved in maturing pre-P RNA. LSM3 is required for processing of pre-tRNAs, pre-rRNAs and U3 snoRNA.[9] [10] [11] [12] [13] [14] [SNU13_YEAST] Common component of the spliceosome and rRNA processing machinery. In association with the spliceosomal U4/U6.U5 tri-snRNP particle, required for splicing of pre-mRNA. In association with box C/D snoRNPs, required for processing of pre-ribosomal RNA (rRNA) and site-specific 2'-O-methylation of substrate RNAs. Essential for the accumulation and stability of U4 snRNA, U6 snRNA, and box C/D snoRNAs.[15] [16] [17] [RU2A_YEAST] Involved in pre-mRNA splicing. Associates to U2 snRNA in a MSL1 dependent manner and is required for normal accumulation of U2 snRNA. Required for the spliceosome assembly and the efficient addition of U2 snRNP onto the pre-mRNA.[18] [LSM6_YEAS7] Component of LSm protein complexes, which are involved in RNA processing and may function in a chaperone-like manner, facilitating the efficient association of RNA processing factors with their substrates. Component of the cytoplasmic LSM1-LSM7 complex, which is thought to be involved in mRNA degradation by activating the decapping step in the 5'-to-3' mRNA decay pathway. In association with PAT1, LSM1-LSM7 binds directly to RNAs near the 3'-end and prefers oligoadenylated RNAs over polyadenylated RNAs. Component of the nuclear LSM2-LSM8 complex, which is involved in splicing of nuclear mRNAs. LSM2-LSM8 associates with multiple snRNP complexes containing the U6 snRNA (U4/U6 di-snRNP, spliceosomal U4/U6.U5 tri-snRNP, and free U6 snRNP). It binds directly to the 3'-terminal U-tract of U6 snRNA and plays a role in the biogenesis and stability of the U6 snRNP and U4/U6 snRNP complexes. LSM2-LSM8 probably also is involved degradation of nuclear pre-mRNA by targeting them for decapping, and in processing of pre-tRNAs, pre-rRNAs and U3 snoRNA. Component of a nucleolar LSM2-LSM7 complex, which associates with the precursor of the RNA component of RNase P (pre-P RNA) and with the small nucleolar RNA (snoRNA) snR5. It may play a role in the maturation of a subset of nucleolus-associated small RNAs (By similarity). [PRP9_YEAST] mRNA splicing factors, PRP9, PRP11, and PRP21, are necessary for binding of the U2 snRNP to the pre-mRNA in an early step of spliceosome assembly. [HSH49_YEAST] Possible SF3b-like factor. [PRP11_YEAST] mRNA splicing factors, PRP9, PRP11, and PRP21, are necessary for addition of the U2 snRNP to the pre-mRNA in an early step of spliceosome assembly.[19] [SMD1_YEAST] Involved in pre-mRNA splicing. Binds snRNA U1, U2, U4 and U5 which contain a highly conserved structural motif called the Sm binding site. Also binds telomerase RNA and is required for its accumulation.[20] [21] [PRP38_YEAST] Required for pre-mRNA splicing and maintenance of stable U6 small nuclear RNA levels. Implicated in the formation of stable and biologically active snRNP structures. As part of the U4/U6.U5 tri-snRNP particle, dispensible for spliceosome assembly, but required for conformational changes, which result in U4 snRNA release and the subsequent catalytic activation of the spliceosome.[22] [23] [PRP3_YEAST] Participates in pre-mRNA splicing. Part of the U4/U5/U6 tri-snRNP complex, one of the building blocks of the spliceosome.[24] [CUS1_YEAST] Essential splicing protein required for U2 snRNP binding to pre-mRNA during spliceosome assembly. [SN114_YEAST] Component of the U5 snRNP complex required for pre-mRNA splicing. Binds GTP. [RSMB_YEAST] Involved in pre-mRNA splicing. Binds snRNA U1, U2, U4 and U5 which contain a highly conserved structural motif called the Sm binding site. [DIB1_YEAST] Essential role in pre-mRNA splicing. Also essential for entry into mitosis (G2/M progression) as well as for chromosome segregation during mitosis. [LSM4_YEAST] Component of LSm protein complexes, which are involved in RNA processing and may function in a chaperone-like manner. Component of the cytoplasmic LSM1-LSM7 complex which is thought to be involved in mRNA degradation by activating the decapping step. Component of the nuclear LSM2-LSM8 complex, which is involved in splicing of nuclear mRNAs. LSM2-LSM8 associates with multiple spliceosome snRNP complexes containing the U6 snRNA (U4/U6 snRNP, U4/U6.U5 snRNP, and free U6 snRNP). It binds directly to the U6 snRNA and plays a role in the biogenesis and stability of the U6 snRNP and U4/U6 snRNP complexes. It probably also is involved degradation of nuclear pre-mRNA by targeting them for decapping. LSM4 binds specifically to the 3'-terminal U-tract of U6 snRNA. LSM2-LSM8 probably is involved in processing of pre-tRNAs, pre-rRNAs and U3 snoRNA. LSM4, probably in a complex that contains LSM2-LSM7 but not LSM1 or LSM8, associates with the precursor of the RNA component of RNase P (pre-P RNA) and may be involved in maturing pre-P RNA. LSM4 is required for processing of pre-tRNAs, pre-rRNAs and U3 snoRNA.[25] [26] [27] [28] [29] [SF3B1_YEAST] Contacts pre-mRNA on both sides of the branch site early in spliceosome assembly. [PRP31_YEAST] Promotes the association of the U4/U6.U5 tri-snRNP particle with pre-spliceosomes to form the mature spliceosomal complex.[30] [RSE1_YEAST] Involved in G2/M transition (By similarity). Required for pre-mRNA splicing and endoplasmic reticulum (ER) to Golgi secretion pathway. U2 snRNPs associated protein required for the pre-spliceosome assembly. The involvement in ER to Golgi secretion is probably indirect and due to the splicing of the pre-mRNA coding for SAR1, a small GTP-binding protein required for COPII vesicle formation from the ER.[31] [32] [PRP21_YEAST] mRNA splicing factors, PRP9, PRP11, and PRP21, are necessary for binding of the U2 snRNP to the pre-mRNA in an early step of spliceosome assembly. [LSM7_YEAST] Component of LSm protein complexes, which are involved in RNA processing and may function in a chaperone-like manner. Component of the cytoplasmic LSM1-LSM7 complex which is thought to be involved in mRNA degradation by activating the decapping step. Component of the nuclear LSM2-LSM8 complex, which is involved in splicing of nuclear mRNAs. LSM2-LSM8 associates with multiple snRNP complexes containing the U6 snRNA (U4/U6 snRNP, spliceosomal U4/U6.U5 snRNP, and free U6 snRNP). It binds directly to the U6 snRNA and plays a role in the biogenesis and stability of the U6 snRNP and U4/U6 snRNP complexes. It probably also is involved degradation of nuclear pre-mRNA by targeting them for decapping. LSM7 binds specifically to the 3'-terminal U-tract of U6 snRNA. LSM2-LSM8 probably is involved in processing of pre-tRNAs, pre-rRNAs and U3 snoRNA. LSM7, probably in a complex that contains LSM2-LSM7 but not LSM1 or LSM8, associates with the precursor of the RNA component of RNase P (pre-P RNA) and may be involved in maturing pre-P RNA.[33] [34] [35] [RUXG_YEAST] Involved in pre-mRNA splicing. Binds snRNA U1, U2, U4 and U5 which contain a highly conserved structural motif called the Sm binding site. [SMD3_YEAST] Involved in pre-mRNA splicing. Binds snRNA U1, U2, U4 and U5 which contain a highly conserved structural motif called the Sm binding site. Also binds telomerase RNA and is required for its accumulation.[36] [37] [BRR2_YEAST] RNA helicase that plays an essential role in pre-mRNA splicing as component of the U5 snRNP and U4/U6-U5 tri-snRNP complexes. Involved in spliceosome assembly, activation and disassembly. Mediates changes in the dynamic network of RNA-RNA interactions in the spliceosome. Catalyzes the ATP-dependent unwinding of U4/U6 RNA duplices, an essential step in the assembly of a catalytically active spliceosome.[38] [39] [40] [41] [SMD2_YEAST] Involved in pre-mRNA splicing. Binds snRNA U1, U2, U4 and U5 which contain a highly conserved structural motif called the Sm binding site. [SNU66_YEAST] Component of the U4/U6.U5 tri-snRNP particle, one of the building blocks of the spliceosome. Required for pre-mRNA splicing.[42] [PRP4_YEAST] Involved in RNA splicing. Is required for the association of U4/U6 snRNP with U5 snRNP in an early step of spliceosome assembly. [RUXF_YEAST] Involved in pre-mRNA splicing. Binds snRNA U1, U2, U4 and U5 which contain a highly conserved structural motif called the Sm binding site. [PRP8_YEAST] Required for pre-spliceosome formation, which is the first step of pre-mRNA splicing. This protein is associated with snRNP U5. Has a role in branch site-3' splice site selection. Associates with the branch site-3' splice 3'-exon region. Also has a role in cell cycle.[43] [44] [45] [46] [LSM2_YEAST] Component of LSm protein complexes, which are involved in RNA processing and may function in a chaperone-like manner. Component of the cytoplasmic LSM1-LSM7 complex which is thought to be involved in mRNA degradation by activating the decapping step. Component of the nuclear LSM2-LSM8 complex, which is involved in splicing of nuclear mRNAs. LSM2-LSM8 associates with multiple snRNP complexes containing the U6 snRNA (U4/U6 snRNP, U4/U6.U5 snRNP, and free U6 snRNP). It binds directly to the U6 snRNA and plays a role in the biogenesis and stability of the U6 snRNP and U4/U6 snRNP complexes. It probably also is involved degradation of nuclear pre-mRNA by targeting them for decapping. LSM2 binds specifically to the 3'-terminal U-tract of U6 snRNA. LSM2-LSM8 probably is involved in processing of pre-tRNAs, pre-rRNAs and U3 snoRNA. LSM2, probably in a complex that contains LSM2-LSM7 but not LSM1 or LSM8, associates with the precursor of the RNA component of RNase P (pre-P RNA) and may be involved in maturing pre-P RNA. LSM2 is required for processing of pre-tRNAs, pre-rRNAs and U3 snoRNA.[47] [48] [49] [50] [51] [RUXE_YEAST] Involved in pre-mRNA splicing. Binds and is required for the stability of snRNA U1, U2, U4 and U5 which contain a highly conserved structural motif called the Sm binding site. Involved in cap modification.[52] [LSM5_YEAST] Component of LSm protein complexes, which are involved in RNA processing and may function in a chaperone-like manner. Component of the cytoplasmic LSM1-LSM7 complex which is thought to be involved in mRNA degradation by activating the decapping step. Component of the nuclear LSM2-LSM8 complex, which is involved in splicing of nuclear mRNAs. LSM2-LSM8 associates with multiple snRNP complexes containing the U6 snRNA (U4/U6 snRNP, U4/U6.U5 snRNP, and free U6 snRNP). It binds directly to the U6 snRNA and plays a role in the biogenesis and stability of the U6 snRNP and U4/U6 snRNP complexes. It probably also is involved degradation of nuclear pre-mRNA by targeting them for decapping. LSM5 binds specifically to the 3'-terminal U-tract of U6 snRNA. LSM2-LSM8 probably is involved in processing of pre-tRNAs, pre-rRNAs and U3 snoRNA. LSM5, probably in a complex that contains LSM2-LSM7 but not LSM1 or LSM8, associates with the precursor of the RNA component of RNase P (pre-P RNA) and may be involved in maturing pre-P RNA. LSM5 is required for processing of pre-tRNAs, pre-rRNAs and U3 snoRNA.[53] [54] [55] [56] [57] [SNU23_YEAST] Participates in pre-mRNA splicing. Part of the U4/U5/U6 tri-snRNP complex, one of the building blocks of the spliceosome.

Publication Abstract from PubMed

Intron removal requires assembly of the spliceosome on precursor mRNA (pre-mRNA) and extensive remodelling to form the spliceosome's catalytic centre. Here we report the cryo-electron microscopy structure of the yeast Saccharomyces cerevisiae pre-catalytic B complex spliceosome at near-atomic resolution. The mobile U2 small nuclear ribonucleoprotein particle (snRNP) associates with U4/U6.U5 tri-snRNP through the U2/U6 helix II and an interface between U4/U6 di-snRNP and the U2 snRNP SF3b-containing domain, which also transiently contacts the helicase Brr2. The 3' region of the U2 snRNP is flexibly attached to the SF3b-containing domain and protrudes over the concave surface of tri-snRNP, where the U1 snRNP may reside before its release from the pre-mRNA 5' splice site. The U6 ACAGAGA sequence forms a hairpin that weakly tethers the 5' splice site. The B complex proteins Prp38, Snu23 and Spp381 bind the Prp8 N-terminal domain and stabilize U6 ACAGAGA stem-pre-mRNA and Brr2-U4 small nuclear RNA interactions. These results provide important insights into the events leading to active site formation.

Structure of a pre-catalytic spliceosome.,Plaschka C, Lin PC, Nagai K Nature. 2017 Jun 29;546(7660):617-621. doi: 10.1038/nature22799. Epub 2017 May, 22. PMID:28530653[58]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

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  48. ↑ Kufel J, Allmang C, Verdone L, Beggs JD, Tollervey D. Lsm proteins are required for normal processing of pre-tRNAs and their efficient association with La-homologous protein Lhp1p. Mol Cell Biol. 2002 Jul;22(14):5248-56. PMID:12077351
  49. ↑ Kufel J, Allmang C, Petfalski E, Beggs J, Tollervey D. Lsm Proteins are required for normal processing and stability of ribosomal RNAs. J Biol Chem. 2003 Jan 24;278(4):2147-56. Epub 2002 Nov 15. PMID:12438310 doi:http://dx.doi.org/10.1074/jbc.M208856200
  50. ↑ Kufel J, Allmang C, Verdone L, Beggs J, Tollervey D. A complex pathway for 3' processing of the yeast U3 snoRNA. Nucleic Acids Res. 2003 Dec 1;31(23):6788-97. PMID:14627812
  51. ↑ Kufel J, Bousquet-Antonelli C, Beggs JD, Tollervey D. Nuclear pre-mRNA decapping and 5' degradation in yeast require the Lsm2-8p complex. Mol Cell Biol. 2004 Nov;24(21):9646-57. PMID:15485930 doi:http://dx.doi.org/10.1128/MCB.24.21.9646-9657.2004
  52. ↑ Bordonne R, Tarassov I. The yeast SME1 gene encodes the homologue of the human E core protein. Gene. 1996 Oct 17;176(1-2):111-7. PMID:8918241
  53. ↑ Bouveret E, Rigaut G, Shevchenko A, Wilm M, Seraphin B. A Sm-like protein complex that participates in mRNA degradation. EMBO J. 2000 Apr 3;19(7):1661-71. PMID:10747033 doi:10.1093/emboj/19.7.1661
  54. ↑ Tharun S, He W, Mayes AE, Lennertz P, Beggs JD, Parker R. Yeast Sm-like proteins function in mRNA decapping and decay. Nature. 2000 Mar 30;404(6777):515-8. PMID:10761922 doi:10.1038/35006676
  55. ↑ Kufel J, Allmang C, Verdone L, Beggs JD, Tollervey D. Lsm proteins are required for normal processing of pre-tRNAs and their efficient association with La-homologous protein Lhp1p. Mol Cell Biol. 2002 Jul;22(14):5248-56. PMID:12077351
  56. ↑ Kufel J, Allmang C, Petfalski E, Beggs J, Tollervey D. Lsm Proteins are required for normal processing and stability of ribosomal RNAs. J Biol Chem. 2003 Jan 24;278(4):2147-56. Epub 2002 Nov 15. PMID:12438310 doi:http://dx.doi.org/10.1074/jbc.M208856200
  57. ↑ Kufel J, Bousquet-Antonelli C, Beggs JD, Tollervey D. Nuclear pre-mRNA decapping and 5' degradation in yeast require the Lsm2-8p complex. Mol Cell Biol. 2004 Nov;24(21):9646-57. PMID:15485930 doi:http://dx.doi.org/10.1128/MCB.24.21.9646-9657.2004
  58. ↑ Plaschka C, Lin PC, Nagai K. Structure of a pre-catalytic spliceosome. Nature. 2017 Jun 29;546(7660):617-621. doi: 10.1038/nature22799. Epub 2017 May, 22. PMID:28530653 doi:http://dx.doi.org/10.1038/nature22799

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