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{{STRUCTURE_4m7d|  PDB=4m7d  |  SCENE=  }}
===crystal structure of scpliceosomal U6 snRNP core complex===


==Function==
==Crystal structure of Lsm2-8 complex bound to the RNA fragment CGUUU==
[[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/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/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/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/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/LSM6_YEAST LSM6_YEAST]] 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.<ref>PMID:10747033</ref> <ref>PMID:10761922</ref> <ref>PMID:15485930</ref> <ref>PMID:17513695</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> 
<StructureSection load='4m7d' size='340' side='right'caption='[[4m7d]], [[Resolution|resolution]] 2.59&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[4m7d]] is a 16 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae_S288C Saccharomyces cerevisiae S288C]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4M7D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4M7D FirstGlance]. <br>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.595&#8491;</td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=4m7d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4m7d OCA], [https://pdbe.org/4m7d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4m7d RCSB], [https://www.ebi.ac.uk/pdbsum/4m7d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4m7d ProSAT]</span></td></tr>
</table>
== Function ==
[https://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>  
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Splicing of precursor messenger RNA (pre-mRNA) in eukaryotic cells is carried out by the spliceosome, which consists of five small nuclear ribonucleoproteins (snRNPs) and a number of accessory factors and enzymes. Each snRNP contains a ring-shaped subcomplex of seven proteins and a specific RNA molecule. The U6 snRNP contains a unique heptameric Lsm protein complex, which specifically recognizes the U6 small nuclear RNA at its 3' end. Here we report the crystal structures of the heptameric Lsm complex, both by itself and in complex with a 3' fragment of U6 snRNA, at 2.8 A resolution. Each of the seven Lsm proteins interacts with two neighbouring Lsm components to form a doughnut-shaped assembly, with the order Lsm3-2-8-4-7-5-6. The four uridine nucleotides at the 3' end of U6 snRNA are modularly recognized by Lsm3, Lsm2, Lsm8 and Lsm4, with the uracil base specificity conferred by a highly conserved asparagine residue. The uracil base at the extreme 3' end is sandwiched by His 36 and Arg 69 from Lsm3, through pi-pi and cation-pi interactions, respectively. The distinctive end-recognition of U6 snRNA by the Lsm complex contrasts with RNA binding by the Sm complex in the other snRNPs. The structural features and associated biochemical analyses deepen mechanistic understanding of the U6 snRNP function in pre-mRNA splicing.


==About this Structure==
Crystal structures of the Lsm complex bound to the 3' end sequence of U6 small nuclear RNA.,Zhou L, Hang J, Zhou Y, Wan R, Lu G, Yin P, Yan C, Shi Y Nature. 2013 Nov 17. doi: 10.1038/nature12803. PMID:24240276<ref>PMID:24240276</ref>
[[4m7d]] is a 16 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4M7D OCA].


==Reference==
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
<references group="xtra"/><references/>
</div>
[[Category: Hang, J.]]
<div class="pdbe-citations 4m7d" style="background-color:#fffaf0;"></div>
[[Category: Lu, G.]]
 
[[Category: Shi, Y.]]
==See Also==
[[Category: Wan, R.]]
*[[Nucleoprotein 3D structures|Nucleoprotein 3D structures]]
[[Category: Yan, C.]]
*[[Sm-like protein|Sm-like protein]]
[[Category: Zhou, L.]]
== References ==
[[Category: Zhou, Y.]]
<references/>
[[Category: Rna binding protein]]
__TOC__
[[Category: Rna splicing]]
</StructureSection>
[[Category: Sm like fold]]
[[Category: Large Structures]]
[[Category: Structural protein-rna complex]]
[[Category: Saccharomyces cerevisiae S288C]]
[[Category: Hang J]]
[[Category: Lu G]]
[[Category: Shi Y]]
[[Category: Wan R]]
[[Category: Yan C]]
[[Category: Zhou L]]
[[Category: Zhou Y]]

Latest revision as of 19:33, 20 September 2023

Crystal structure of Lsm2-8 complex bound to the RNA fragment CGUUUCrystal structure of Lsm2-8 complex bound to the RNA fragment CGUUU

Structural highlights

4m7d is a 16 chain structure with sequence from Saccharomyces cerevisiae S288C. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.595Å
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

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.[1] [2] [3]

Publication Abstract from PubMed

Splicing of precursor messenger RNA (pre-mRNA) in eukaryotic cells is carried out by the spliceosome, which consists of five small nuclear ribonucleoproteins (snRNPs) and a number of accessory factors and enzymes. Each snRNP contains a ring-shaped subcomplex of seven proteins and a specific RNA molecule. The U6 snRNP contains a unique heptameric Lsm protein complex, which specifically recognizes the U6 small nuclear RNA at its 3' end. Here we report the crystal structures of the heptameric Lsm complex, both by itself and in complex with a 3' fragment of U6 snRNA, at 2.8 A resolution. Each of the seven Lsm proteins interacts with two neighbouring Lsm components to form a doughnut-shaped assembly, with the order Lsm3-2-8-4-7-5-6. The four uridine nucleotides at the 3' end of U6 snRNA are modularly recognized by Lsm3, Lsm2, Lsm8 and Lsm4, with the uracil base specificity conferred by a highly conserved asparagine residue. The uracil base at the extreme 3' end is sandwiched by His 36 and Arg 69 from Lsm3, through pi-pi and cation-pi interactions, respectively. The distinctive end-recognition of U6 snRNA by the Lsm complex contrasts with RNA binding by the Sm complex in the other snRNPs. The structural features and associated biochemical analyses deepen mechanistic understanding of the U6 snRNP function in pre-mRNA splicing.

Crystal structures of the Lsm complex bound to the 3' end sequence of U6 small nuclear RNA.,Zhou L, Hang J, Zhou Y, Wan R, Lu G, Yin P, Yan C, Shi Y Nature. 2013 Nov 17. doi: 10.1038/nature12803. PMID:24240276[4]

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

See Also

References

  1. ↑ 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
  2. ↑ 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
  3. ↑ 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
  4. ↑ Zhou L, Hang J, Zhou Y, Wan R, Lu G, Yin P, Yan C, Shi Y. Crystal structures of the Lsm complex bound to the 3' end sequence of U6 small nuclear RNA. Nature. 2013 Nov 17. doi: 10.1038/nature12803. PMID:24240276 doi:http://dx.doi.org/10.1038/nature12803

4m7d, resolution 2.59Å

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