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| | ==Overall structure of the yeast spliceosome immediately after branching.== | | ==Overall structure of the yeast spliceosome immediately after branching.== |
| - | <StructureSection load='5lj5' size='340' side='right'caption='[[5lj5]], [[Resolution|resolution]] 3.80Å' scene=''> | + | <SX load='5lj5' size='340' side='right' viewer='molstar' caption='[[5lj5]], [[Resolution|resolution]] 3.80Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[5lj5]] is a 45 chain structure with sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5LJ5 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5LJ5 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[5lj5]] is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5LJ5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5LJ5 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=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]] 3.8Å</td></tr> |
| - | <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=UNK:UNKNOWN'>UNK</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=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></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>
| + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=5lj5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5lj5 OCA], [https://pdbe.org/5lj5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5lj5 RCSB], [https://www.ebi.ac.uk/pdbsum/5lj5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5lj5 ProSAT]</span></td></tr> |
| - | <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=5lj5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5lj5 OCA], [http://pdbe.org/5lj5 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5lj5 RCSB], [http://www.ebi.ac.uk/pdbsum/5lj5 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5lj5 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/PRP16_YEAST PRP16_YEAST]] Influences the fidelity of branchpoint recognition in yeast splicing. This is RNA-dependent ATPase which is essential for viability. It may mediate one of the many ATP-requiring steps of spliceosome assembly and that accuracy of branchpoint recognition may be coupled to ATP binding and/or hydrolysis.<ref>PMID:1825134</ref> [[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/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/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/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/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/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/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/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/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/CWC21_YEAST CWC21_YEAST]] Involved in pre-mRNA splicing. May function at or prior to the first catalytic step of splicing at the catalytic center of the spliceosome, together with ISY1. May do so by stabilizing the catalytic center or the position of the RNA substrate.<ref>PMID:19789211</ref> <ref>PMID:19854871</ref> [[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/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/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/ISY1_YEAST ISY1_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. Also involved in DNA repair.<ref>PMID:10094305</ref> <ref>PMID:11018040</ref> <ref>PMID:12384582</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/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/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/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/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/CWC25_YEAST CWC25_YEAST]] Involved in pre-mRNA splicing.<ref>PMID:14690591</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/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> | + | [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;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | ==See Also== | | ==See Also== |
| | + | *[[Helicase 3D structures|Helicase 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|Sm-like protein]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| - | </StructureSection> | + | </SX> |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: RNA helicase]] | |
| | [[Category: Saccharomyces cerevisiae]] | | [[Category: Saccharomyces cerevisiae]] |
| - | [[Category: Fica, S M]] | + | [[Category: Fica SM]] |
| - | [[Category: Galej, W P]] | + | [[Category: Galej WP]] |
| - | [[Category: Nagai, K]] | + | [[Category: Nagai K]] |
| - | [[Category: Newman, A J]] | + | [[Category: Newman AJ]] |
| - | [[Category: Oubridge, C]] | + | [[Category: Oubridge C]] |
| - | [[Category: Wilkinson, M F]] | + | [[Category: Wilkinson MF]] |
| - | [[Category: Complex c]]
| + | |
| - | [[Category: Lariat intermediate]]
| + | |
| - | [[Category: Pre-mrna splicing]]
| + | |
| - | [[Category: Snrnp]]
| + | |
| - | [[Category: Spliceosome]]
| + | |
| - | [[Category: Splicing]]
| + | |
| - | [[Category: Trans-esterification]]
| + | |
