5mqf
From Proteopedia
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| - | '''Unreleased structure''' | ||
| - | The entry | + | ==Cryo-EM structure of a human spliceosome activated for step 2 of splicing (C* complex)== |
| + | <StructureSection load='5mqf' size='340' side='right' caption='[[5mqf]], [[Resolution|resolution]] 5.90Å' scene=''> | ||
| + | == Structural highlights == | ||
| + | <table><tr><td colspan='2'>[[5mqf]] is a 46 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5MQF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5MQF FirstGlance]. <br> | ||
| + | </td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr> | ||
| + | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Peptidylprolyl_isomerase Peptidylprolyl isomerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.2.1.8 5.2.1.8] </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=5mqf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5mqf OCA], [http://pdbe.org/5mqf PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5mqf RCSB], [http://www.ebi.ac.uk/pdbsum/5mqf PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5mqf ProSAT]</span></td></tr> | ||
| + | </table> | ||
| + | == Disease == | ||
| + | [[http://www.uniprot.org/uniprot/U5S1_HUMAN U5S1_HUMAN]] Mandibulofacial dysostosis-microcephaly syndrome. The disease is caused by mutations affecting the gene represented in this entry. [[http://www.uniprot.org/uniprot/PRP8_HUMAN PRP8_HUMAN]] Defects in PRPF8 are the cause of retinitis pigmentosa type 13 (RP13) [MIM:[http://omim.org/entry/600059 600059]]. RP leads to degeneration of retinal photoreceptor cells. Patients typically have night vision blindness and loss of midperipheral visual field. As their condition progresses, they lose their far peripheral visual field and eventually central vision as well. RP13 inheritance is autosomal dominant.<ref>PMID:17317632</ref> <ref>PMID:11468273</ref> [:]<ref>PMID:11910553</ref> <ref>PMID:12714658</ref> [[http://www.uniprot.org/uniprot/CDC5L_HUMAN CDC5L_HUMAN]] Note=A chromosomal aberration involving CDC5L is found in multicystic renal dysplasia. Translocation t(6;19)(p21;q13.1) with USF2. | ||
| + | == Function == | ||
| + | [[http://www.uniprot.org/uniprot/RU2B_HUMAN RU2B_HUMAN]] Involved in pre-mRNA splicing. This protein is associated with snRNP U2. It binds stem loop IV of U2 snRNA only in presence of the U2A' protein. [[http://www.uniprot.org/uniprot/PRP19_HUMAN PRP19_HUMAN]] Plays a role in DNA double-strand break (DSB) repair. Binds double-stranded DNA in a sequence-nonspecific manner. Acts as a structural component of the nuclear framework. May also serve as a support for spliceosome binding and activity. Essential for spliceosome assembly in a oligomerization-dependent manner and might also be important for spliceosome stability. May have E3 ubiquitin ligase activity. The PSO4 complex is required in the DNA interstrand cross-links (ICLs) repair process. Component of the PRP19-CDC5L complex that forms an integral part of the spliceosome and is required for activating pre-mRNA splicing.<ref>PMID:11082287</ref> <ref>PMID:12960389</ref> <ref>PMID:16332694</ref> <ref>PMID:15660529</ref> <ref>PMID:16223718</ref> <ref>PMID:16388800</ref> [[http://www.uniprot.org/uniprot/SMD3_HUMAN SMD3_HUMAN]] Appears to function in the U7 snRNP complex that is involved in histone 3'-end processing. Binds to the downstream cleavage product (DCP) of histone pre-mRNA in a U7 snRNP dependent manner.<ref>PMID:11574479</ref> [[http://www.uniprot.org/uniprot/U5S1_HUMAN U5S1_HUMAN]] Component of the U5 snRNP and the U4/U6-U5 tri-snRNP complex required for pre-mRNA splicing. Binds GTP. [[http://www.uniprot.org/uniprot/CWC22_HUMAN CWC22_HUMAN]] Required for pre-mRNA splicing and for exon-junction complex (EJC) assembly. Hinders EIF4A3 from non-specifically binding RNA and escorts it to the splicing machinery to promote EJC assembly on mature mRNAs. Through its role in EJC assembly, required for nonsense-mediated mRNA decay.<ref>PMID:22959432</ref> <ref>PMID:22961380</ref> <ref>PMID:23236153</ref> [[http://www.uniprot.org/uniprot/PRP8_HUMAN PRP8_HUMAN]] Central component of the spliceosome, which may play a role in aligning the pre-mRNA 5'- and 3'-exons for ligation. Interacts with U5 snRNA, and with pre-mRNA 5'-splice sites in B spliceosomes and 3'-splice sites in C spliceosomes. [[http://www.uniprot.org/uniprot/AQR_HUMAN AQR_HUMAN]] Intron-binding spliceosomal protein required to link pre-mRNA splicing and snoRNP (small nucleolar ribonucleoprotein) biogenesis. Plays a key role in position-dependent assembly of intron-encoded box C/D small snoRNP, splicing being required for snoRNP assembly. May act by helping the folding of the snoRNA sequence. Binds to intron of pre-mRNAs in a sequence-independent manner, contacting the region between snoRNA and the branchpoint of introns (40 nucleotides upstream of the branchpoint) during the late stages of splicing.<ref>PMID:16949364</ref> [[http://www.uniprot.org/uniprot/IF4A3_HUMAN IF4A3_HUMAN]] ATP-dependent RNA helicase. Component of a splicing-dependent multiprotein exon junction complex (EJC) deposited at splice junction on mRNAs. The EJC is a dynamic structure consisting of a few core proteins and several more peripheral nuclear and cytoplasmic associated factors that join the complex only transiently either during EJC assembly or during subsequent mRNA metabolism. Core components of the EJC, that remains bound to spliced mRNAs throughout all stages of mRNA metabolism, functions to mark the position of the exon-exon junction in the mature mRNA and thereby influences downstream processes of gene expression including mRNA splicing, nuclear mRNA export, subcellular mRNA localization, translation efficiency and nonsense-mediated mRNA decay (NMD). Constitutes at least part of the platform anchoring other EJC proteins to spliced mRNAs. Its RNA-dependent ATPase and RNA-helicase activities are induced by CASC3, but abolished in presence of the MAGOH/RBM8A heterodimer, thereby trapping the ATP-bound EJC core onto spliced mRNA in a stable conformation. The inhibition of ATPase activity by the MAGOH/RBM8A heterodimer increases the RNA-binding affinity of the EJC. Involved in translational enhancement of spliced mRNAs after formation of the 80S ribosome complex. Binds spliced mRNA in sequence-independent manner, 20-24 nucleotides upstream of mRNA exon-exon junctions. Shows higher affinity for single-stranded RNA in an ATP-bound core EJC complex than after the ATP is hydrolyzed.<ref>PMID:15034551</ref> <ref>PMID:16209946</ref> <ref>PMID:16170325</ref> <ref>PMID:17375189</ref> <ref>PMID:19409878</ref> [[http://www.uniprot.org/uniprot/SRRM2_HUMAN SRRM2_HUMAN]] Involved in pre-mRNA splicing. May function at or prior to the first catalytic step of splicing at the catalytic center of the spliceosome. May do so by stabilizing the catalytic center or the position of the RNA substrate (By similarity). Binds to RNA.<ref>PMID:10668804</ref> [[http://www.uniprot.org/uniprot/RSMB_HUMAN RSMB_HUMAN]] Appears to function in the U7 snRNP complex that is involved in histone 3'-end processing. Associated with snRNP U1, U2, U4/U6 and U5. May have a functional role in the pre-mRNA splicing or in snRNP structure. Binds to the downstream cleavage product (DCP) of histone pre-mRNA in a U7 snRNP dependent manner (By similarity). [[http://www.uniprot.org/uniprot/RUXG_HUMAN RUXG_HUMAN]] Appears to function in the U7 snRNP complex that is involved in histone 3'-end processing. Associated with snRNP U1, U2, U4/U6 and U5. [[http://www.uniprot.org/uniprot/SMD1_HUMAN SMD1_HUMAN]] May act as a charged protein scaffold to promote snRNP assembly or strengthen snRNP-snRNP interactions through nonspecific electrostatic contacts with RNA. [[http://www.uniprot.org/uniprot/RU2A_HUMAN RU2A_HUMAN]] This protein is associated with sn-RNP U2. It helps the A' protein to bind stem loop IV of U2 snRNA. [[http://www.uniprot.org/uniprot/RUXE_HUMAN RUXE_HUMAN]] Appears to function in the U7 snRNP complex that is involved in histone 3'-end processing. Associated with snRNP U1, U2, U4/U6 and U5. [[http://www.uniprot.org/uniprot/SYF1_HUMAN SYF1_HUMAN]] Involved in transcription-coupled repair (TCR), transcription and pre-mRNA splicing.<ref>PMID:10944529</ref> <ref>PMID:17981804</ref> [[http://www.uniprot.org/uniprot/DHX8_HUMAN DHX8_HUMAN]] Facilitates nuclear export of spliced mRNA by releasing the RNA from the spliceosome.<ref>PMID:8608946</ref> [[http://www.uniprot.org/uniprot/SYF2_HUMAN SYF2_HUMAN]] May be involved in pre-mRNA splicing. [[http://www.uniprot.org/uniprot/SMD2_HUMAN SMD2_HUMAN]] Required for pre-mRNA splicing. Required for snRNP biogenesis (By similarity). [[http://www.uniprot.org/uniprot/RBM22_HUMAN RBM22_HUMAN]] Involved in the first step of pre-mRNA splicing. 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. Involved in both translocations of the nuclear SLU7 to the cytoplasm and the cytosolic calcium-binding protein PDCD6 to the nucleus upon cellular stress responses.<ref>PMID:17045351</ref> <ref>PMID:21122810</ref> <ref>PMID:22246180</ref> [[http://www.uniprot.org/uniprot/RUXF_HUMAN RUXF_HUMAN]] Appears to function in the U7 snRNP complex that is involved in histone 3'-end processing. Associated with snRNP U1, U2, U4/U6 and U5. [[http://www.uniprot.org/uniprot/PPIE_HUMAN PPIE_HUMAN]] PPIases accelerate the folding of proteins. It catalyzes the cis-trans isomerization of proline imidic peptide bonds in oligopeptides. Combines RNA-binding and PPIase activities. May be involved in muscle- and brain-specific processes. May be involved in pre-mRNA splicing. [[http://www.uniprot.org/uniprot/SNR40_HUMAN SNR40_HUMAN]] Component of the U5 small nuclear ribonucleoprotein (snRNP) complex. The U5 snRNP is part of the spliceosome, a multiprotein complex that catalyzes the removal of introns from pre-messenger RNAs.<ref>PMID:9774689</ref> [[http://www.uniprot.org/uniprot/SNW1_HUMAN SNW1_HUMAN]] Involved in transcriptional regulation. Modulates TGF-beta-mediated transcription via association with SMAD proteins, MYOD1-mediated transcription via association with PABPN1, RB1-mediated transcriptional repression, and retinoid-X receptor (RXR)- and vitamin D receptor (VDR)-dependent gene transcription in a cell line-specific manner probably involving coactivators NCOA1 and GRIP1. Is involved in NOTCH1-mediated transcriptional activation. Binds to multimerized forms of Notch intracellular domain (NICD) and is proposed to recruit transcriptional coactivators such as MAML1 to form an intermediate preactivation complex which associates with DNA-bound CBF-1/RBPJ to form a transcriptional activation complex by releasing SNW1 and redundant NOTCH1 NICD. Proposed to be involved in transcriptional activation by EBV EBNA2 of CBF-1/RBPJ-repressed promoters. Is recruited by HIV-1 Tat to Tat:P-TEFb:TAR RNA complexes and is involved in Tat transcription by recruitment of MYC, MEN1 and TRRAP to the HIV promoter. Functions as a splicing factor in pre-mRNA splicing. Is required in the specific splicing of CDKN1A pre-mRNA; the function probably involves the recruitment of U2AF2 to the mRNA. Is proposed to recruit PPIL1 to the spliceosome. May be involved in cyclin-D1/CCND1 mRNA stability through the SNARP complex which associates with both the 3'end of the CCND1 gene and its mRNA.<ref>PMID:10644367</ref> <ref>PMID:11278756</ref> <ref>PMID:11371506</ref> <ref>PMID:11514567</ref> <ref>PMID:12840015</ref> <ref>PMID:14985122</ref> <ref>PMID:15194481</ref> <ref>PMID:15905409</ref> <ref>PMID:18794151</ref> <ref>PMID:19818711</ref> <ref>PMID:21245387</ref> <ref>PMID:21460037</ref> <ref>PMID:9632709</ref> [[http://www.uniprot.org/uniprot/CDC5L_HUMAN CDC5L_HUMAN]] DNA-binding protein involved in cell cycle control. May act as a transcription activator. Component of the PRP19-CDC5L complex that forms an integral part of the spliceosome and is required for activating pre-mRNA splicing.<ref>PMID:9038199</ref> <ref>PMID:9632794</ref> <ref>PMID:9468527</ref> <ref>PMID:10570151</ref> <ref>PMID:11101529</ref> <ref>PMID:11082045</ref> <ref>PMID:11544257</ref> <ref>PMID:12927788</ref> <ref>PMID:18583928</ref> [[http://www.uniprot.org/uniprot/CRNL1_HUMAN CRNL1_HUMAN]] Involved in pre-mRNA splicing process. [[http://www.uniprot.org/uniprot/CWC15_HUMAN CWC15_HUMAN]] Component of the PRP19-CDC5L complex that forms an integral part of the spliceosome and is required for activating pre-mRNA splicing.<ref>PMID:20176811</ref> [[http://www.uniprot.org/uniprot/SPF27_HUMAN SPF27_HUMAN]] Component of the PRP19-CDC5L complex that forms an integral part of the spliceosome and is required for activating pre-mRNA splicing. May have a scaffolding role in the spliceosome assembly as it contacts all other components of the core complex. The PRP19-CDC5L complex may also play a role in the response to DNA damage (DDR).<ref>PMID:24332808</ref> [[http://www.uniprot.org/uniprot/PLRG1_HUMAN PLRG1_HUMAN]] Component of the PRP19-CDC5L complex that forms an integral part of the spliceosome and is required for activating pre-mRNA splicing. [[http://www.uniprot.org/uniprot/PPIL1_HUMAN PPIL1_HUMAN]] PPIases accelerate the folding of proteins. It catalyzes the cis-trans isomerization of proline imidic peptide bonds in oligopeptides. May be involved in pre-mRNA splicing.<ref>PMID:16595688</ref> [[http://www.uniprot.org/uniprot/PRP17_HUMAN PRP17_HUMAN]] Associates with the spliceosome late in the splicing pathway and may function in the second step of pre-mRNA splicing.<ref>PMID:9830021</ref> | ||
| + | <div style="background-color:#fffaf0;"> | ||
| + | == Publication Abstract from PubMed == | ||
| + | Spliceosome rearrangements facilitated by RNA helicase PRP16 before catalytic step two of splicing are poorly understood. Here we report a 3D cryo-electron microscopy structure of the human spliceosomal C complex stalled directly after PRP16 action (C*). The architecture of the catalytic U2-U6 ribonucleoprotein (RNP) core of the human C* spliceosome is very similar to that of the yeast pre-Prp16 C complex. However, in C* the branched intron region is separated from the catalytic centre by approximately 20 A, and its position close to the U6 small nuclear RNA ACAGA box is stabilized by interactions with the PRP8 RNase H-like and PRP17 WD40 domains. RNA helicase PRP22 is located about 100 A from the catalytic centre, suggesting that it destabilizes the spliced mRNA after step two from a distance. Comparison of the structure of the yeast C and human C* complexes reveals numerous RNP rearrangements that are likely to be facilitated by PRP16, including a large-scale movement of the U2 small nuclear RNP. | ||
| - | + | Cryo-EM structure of a human spliceosome activated for step 2 of splicing.,Bertram K, Agafonov DE, Liu WT, Dybkov O, Will CL, Hartmuth K, Urlaub H, Kastner B, Stark H, Luhrmann R Nature. 2017 Feb 16;542(7641):318-323. doi: 10.1038/nature21079. Epub 2017 Jan, 11. PMID:28076346<ref>PMID:28076346</ref> | |
| - | + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |
| - | [[Category: | + | </div> |
| + | <div class="pdbe-citations 5mqf" style="background-color:#fffaf0;"></div> | ||
| + | == References == | ||
| + | <references/> | ||
| + | __TOC__ | ||
| + | </StructureSection> | ||
| + | [[Category: Homo sapiens]] | ||
| + | [[Category: Peptidylprolyl isomerase]] | ||
| + | [[Category: Bertram, K]] | ||
| + | [[Category: Hartmuth, K]] | ||
| + | [[Category: Kastner, B]] | ||
| + | [[Category: Macromolecular complex]] | ||
| + | [[Category: Pre-mrna splicing]] | ||
| + | [[Category: Spliceosome]] | ||
| + | [[Category: Splicing]] | ||
Revision as of 16:23, 22 March 2017
Cryo-EM structure of a human spliceosome activated for step 2 of splicing (C* complex)
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