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| <SX load='5y88' size='340' side='right' viewer='molstar' caption='[[5y88]], [[Resolution|resolution]] 3.70Å' scene=''> | | <SX load='5y88' size='340' side='right' viewer='molstar' caption='[[5y88]], [[Resolution|resolution]] 3.70Å' scene=''> |
| == Structural highlights == | | == Structural highlights == |
| <table><tr><td colspan='2'>[[5y88]] is a 44 chain structure with sequence from [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_s288c Saccharomyces cerevisiae s288c]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5Y88 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5Y88 FirstGlance]. <br> | | <table><tr><td colspan='2'>[[5y88]] is a 10 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=5Y88 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5Y88 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=I6P:INOSITOL+1,2,3,4,5,6-HEXAKISPHOSPHATE'>I6P</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr> | | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy, [[Resolution|Resolution]] 3.7Å</td></tr> |
| <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=N:ANY+5-MONOPHOSPHATE+NUCLEOTIDE'>N</scene></td></tr> | | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</scene>, <scene name='pdbligand=IHP:INOSITOL+HEXAKISPHOSPHATE'>IHP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=N:ANY+5-MONOPHOSPHATE+NUCLEOTIDE'>N</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr> |
| <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5wsg|5wsg]], [[5gm6|5gm6]], [[5gmk|5gmk]]</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=5y88 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5y88 OCA], [https://pdbe.org/5y88 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5y88 RCSB], [https://www.ebi.ac.uk/pdbsum/5y88 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5y88 ProSAT]</span></td></tr> |
| <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/RNA_helicase RNA helicase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.6.4.13 3.6.4.13] </span></td></tr>
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| <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5y88 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5y88 OCA], [http://pdbe.org/5y88 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5y88 RCSB], [http://www.ebi.ac.uk/pdbsum/5y88 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5y88 ProSAT]</span></td></tr> | |
| </table> | | </table> |
| == Function == | | == Function == |
| [[http://www.uniprot.org/uniprot/PRP19_YEAST PRP19_YEAST]] Involved in pre-mRNA splicing. Acts a central component of the NTC complex (or PRP19-associated complex) that associates to the spliceosome to mediate conformational rearrangement or to stabilize the structure of the spliceosome after U4 snRNA dissociation, which leads to spliceosome maturation. Involved in DNA repair. [[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/SYF2_YEAST SYF2_YEAST]] Involved in pre-mRNA splicing and cell cycle control. As a component of the NTC complex (or PRP19-associated complex), associates to the spliceosome to mediate conformational rearrangement or to stabilize the structure of the spliceosome after U4 snRNA dissociation, which leads to spliceosome maturation. The cell cycle arrest of SYF2 defective cells may be due to the inefficient splicing of TUB1.<ref>PMID:11102353</ref> <ref>PMID:11105756</ref> <ref>PMID:12384582</ref> [[http://www.uniprot.org/uniprot/SP382_YEAST SP382_YEAST]] Involved in pre-mRNA splicing and spliceosome disassembly. Promotes release of excised lariat intron from the spliceosome by acting as a receptor for PRP43. This targeting of PRP43 leads to disassembly of the spliceosome with the separation of the U2, U5, U6 snRNPs and the NTC complex.<ref>PMID:16357217</ref> <ref>PMID:16880513</ref> [[http://www.uniprot.org/uniprot/SN309_YEAST SN309_YEAST]] Involved in pre-mRNA splicing by stabilizing the NTC (or PRP19-associated complex). As a component of the NTC complex, associates to the spliceosome to mediate conformational rearrangement or to stabilize the structure of the spliceosome after U4 snRNA dissociation, which leads to spliceosome maturation.<ref>PMID:10318896</ref> <ref>PMID:9528791</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/PRP45_YEAST PRP45_YEAST]] Involved in pre-mRNA splicing. Associated with the spliceosome throughout the splicing reactions, until after the second catalytic step.<ref>PMID:12359070</ref> <ref>PMID:12554883</ref> [[http://www.uniprot.org/uniprot/NTR2_YEAST NTR2_YEAST]] Involved in pre-mRNA splicing and spliceosome disassembly. Promotes release of excised lariat intron from the spliceosome by acting as a receptor for PRP43. This targeting of PRP43 leads to disassembly of the spliceosome with the separation of the U2, U5, U6 snRNPs and the NTC complex.<ref>PMID:16357217</ref> <ref>PMID:16880513</ref> [[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/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/PRP43_YEAST PRP43_YEAST]] Pre-mRNA processing factor involved in disassembly of spliceosomes after the release of mature mRNA.<ref>PMID:9342317</ref> <ref>PMID:16880513</ref> [[http://www.uniprot.org/uniprot/SLT11_YEAST SLT11_YEAST]] Involved in pre-mRNA splicing. Facilitates the cooperative formation of U2/U6 helix II in association with stem II in the spliceosome. Binds to RNA.<ref>PMID:11158289</ref> <ref>PMID:9528778</ref> [[http://www.uniprot.org/uniprot/CWC15_YEAST CWC15_YEAST]] Involved in pre-mRNA splicing. [[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/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/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/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/SN114_YEAST SN114_YEAST]] Component of the U5 snRNP complex required for pre-mRNA splicing. Binds GTP. [[http://www.uniprot.org/uniprot/CLF1_YEAST CLF1_YEAST]] Involved in pre-mRNA splicing and cell cycle progression. Required for the spliceosome assembly by promoting the functional integration of the U4/U6.U5 tri-snRNP particle into the U1-, U2-dependent pre-spliceosome. Also recruits PRP19 to the spliceosome, as a component of the NTC complex (or PRP19-associated complex). The association of the NTC complex to the spliceosome mediates conformational rearrangement or stabilizes the structure of the spliceosome after U4 snRNA dissociation, which leads to spliceosome maturation. Required for initiation of the DNA replication by binding the RNA replication origins, probably through its interaction with the origin recognition complex (ORC).<ref>PMID:10445879</ref> <ref>PMID:11102353</ref> <ref>PMID:11105756</ref> <ref>PMID:11973290</ref> <ref>PMID:12509417</ref> [[http://www.uniprot.org/uniprot/BUD31_YEAST BUD31_YEAST]] Involved in pre-mRNA splicing. Important for bud site selection. [[http://www.uniprot.org/uniprot/CWC2_YEAST CWC2_YEAST]] Involved in the first step of pre-mRNA splicing. Required for cell growth and cell cycle control. Plays a role in the levels of the U1, U4, U5 and U6 snRNAs and the maintenance of the U4/U6 snRNA complex. May provide the link between the "nineteen complex" NTC spliceosome protein complex and the spliceosome through the U6 snRNA. Associates predominantly with U6 snRNAs in assembled active spliceosomes. Binds directly to the internal stem-loop (ISL) domain of the U6 snRNA and to the pre-mRNA intron near the 5' splice site during the activation and catalytic phases of the spliceosome cycle. Binds also to U1, U4, U5 and U6 snRNAs and to pre-mRNAs, in vitro. Is not required for the Prp2-mediated remodeling of the activated spliceosome.<ref>PMID:19435883</ref> <ref>PMID:22246180</ref> [[http://www.uniprot.org/uniprot/PRP46_YEAST PRP46_YEAST]] Involved in pre-mRNA splicing. May also be required for cell cycle progression at G2/M (By similarity).<ref>PMID:12554883</ref> [[http://www.uniprot.org/uniprot/CWC23_YEAST CWC23_YEAST]] Involved in pre-mRNA splicing. May be involved in endoplasmic reticulum-associated protein degradation (ERAD) and required for growth at low and high temperatures.<ref>PMID:10029993</ref> <ref>PMID:12847107</ref> <ref>PMID:15170475</ref> [[http://www.uniprot.org/uniprot/SYF1_YEAST SYF1_YEAST]] Involved in pre-mRNA splicing and cell cycle control. As a component of the NTC complex (or PRP19-associated complex), associates to the spliceosome to mediate conformational rearrangement or to stabilize the structure of the spliceosome after U4 snRNA dissociation, which leads to spliceosome maturation.<ref>PMID:11102353</ref> <ref>PMID:11105756</ref> [[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/CEF1_YEAST CEF1_YEAST]] Involved in pre-mRNA splicing and cell cycle control. Required for the binding of the NTC complex (or PRP19-associated complex) components to the spliceosome to mediate conformational rearrangement or to stabilize the structure of the spliceosome after U4 snRNA dissociation, which leads to spliceosome maturation. Its absence leads to an arrest of the cell cycle, possibly due to the inefficient splicing of TUB1.<ref>PMID:10092627</ref> <ref>PMID:10570151</ref> <ref>PMID:11784857</ref> <ref>PMID:9632794</ref> [[http://www.uniprot.org/uniprot/PRP17_YEAST PRP17_YEAST]] May function in the second step of pre-mRNA splicing. Regulatory protein involved in replication and mitotic spindle formation and/or maintenance. Required for initiation and completion of S-phase and for initiation and completion of DNA replication. Might be required for the maintenance of microtubules. Essential only at elevated temperatures. [[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> | | [https://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> |
| <div style="background-color:#fffaf0;">
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| == Publication Abstract from PubMed ==
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| The disassembly of the intron lariat spliceosome (ILS) marks the end of a splicing cycle. Here we report a cryoelectron microscopy structure of the ILS complex from Saccharomyces cerevisiae at an average resolution of 3.5 A. The intron lariat remains bound in the spliceosome whereas the ligated exon is already dissociated. The step II splicing factors Prp17 and Prp18, along with Cwc21 and Cwc22 that stabilize the 5' exon binding to loop I of U5 small nuclear RNA (snRNA), have been released from the active site assembly. The DEAH family ATPase/helicase Prp43 binds Syf1 at the periphery of the spliceosome, with its RNA-binding site close to the 3' end of U6 snRNA. The C-terminal domain of Ntr1/Spp382 associates with the GTPase Snu114, and Ntr2 is anchored to Prp8 while interacting with the superhelical domain of Ntr1. These structural features suggest a plausible mechanism for the disassembly of the ILS complex.
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| Structure of an Intron Lariat Spliceosome from Saccharomyces cerevisiae.,Wan R, Yan C, Bai R, Lei J, Shi Y Cell. 2017 Sep 21;171(1):120-132.e12. doi: 10.1016/j.cell.2017.08.029. Epub 2017 , Sep 14. PMID:28919079<ref>PMID:28919079</ref>
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| From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
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| </div>
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| <div class="pdbe-citations 5y88" style="background-color:#fffaf0;"></div>
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| ==See Also== | | ==See Also== |
| | *[[Nucleoprotein 3D structures|Nucleoprotein 3D structures]] |
| *[[Pre-mRNA splicing factors 3D structures|Pre-mRNA splicing factors 3D structures]] | | *[[Pre-mRNA splicing factors 3D structures|Pre-mRNA splicing factors 3D structures]] |
| | *[[Sm-like protein 3D structures|Sm-like protein 3D structures]] |
| == References == | | == References == |
| <references/> | | <references/> |
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| </SX> | | </SX> |
| [[Category: Large Structures]] | | [[Category: Large Structures]] |
| [[Category: RNA helicase]]
| | [[Category: Saccharomyces cerevisiae S288C]] |
| [[Category: Saccharomyces cerevisiae s288c]] | | [[Category: Bai R]] |
| [[Category: Bai, R]] | | [[Category: Lei J]] |
| [[Category: Lei, J]] | | [[Category: Shi Y]] |
| [[Category: Shi, Y]] | | [[Category: Wan R]] |
| [[Category: Wan, R]] | | [[Category: Yan C]] |
| [[Category: Yan, C]] | |
| [[Category: Disassembly]]
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| [[Category: Ils complex]]
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| [[Category: Ntr complex]]
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| [[Category: Prp43]]
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| [[Category: Splicing]]
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