6ff4

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Current revision (12:38, 6 November 2024) (edit) (undo)
 
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<SX load='6ff4' size='340' side='right' viewer='molstar' caption='[[6ff4]], [[Resolution|resolution]] 3.40&Aring;' scene=''>
<SX load='6ff4' size='340' side='right' viewer='molstar' caption='[[6ff4]], [[Resolution|resolution]] 3.40&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[6ff4]] is a 28 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=6FF4 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6FF4 FirstGlance]. <br>
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<table><tr><td colspan='2'>[[6ff4]] is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6FF4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6FF4 FirstGlance]. <br>
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</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=ZN:ZINC+ION'>ZN</scene></td></tr>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy, [[Resolution|Resolution]] 3.4&#8491;</td></tr>
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<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>
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<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=ZN:ZINC+ION'>ZN</scene></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6ff4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ff4 OCA], [http://pdbe.org/6ff4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6ff4 RCSB], [http://www.ebi.ac.uk/pdbsum/6ff4 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6ff4 ProSAT]</span></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=6ff4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ff4 OCA], [https://pdbe.org/6ff4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6ff4 RCSB], [https://www.ebi.ac.uk/pdbsum/6ff4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6ff4 ProSAT]</span></td></tr>
</table>
</table>
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== Disease ==
 
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[[http://www.uniprot.org/uniprot/R113A_HUMAN R113A_HUMAN]] The disease is caused by mutations affecting the gene represented in this entry. [[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. [[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>
 
== Function ==
== Function ==
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[[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/SF3B2_HUMAN SF3B2_HUMAN]] Subunit of the splicing factor SF3B required for 'A' complex assembly formed by the stable binding of U2 snRNP to the branchpoint sequence (BPS) in pre-mRNA. Sequence independent binding of SF3A/SF3B complex upstream of the branch site is essential, it may anchor U2 snRNP to the pre-mRNA. May also be involved in the assembly of the 'E' complex. Belongs also to the minor U12-dependent spliceosome, which is involved in the splicing of rare class of nuclear pre-mRNA intron. [[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/CWC27_HUMAN CWC27_HUMAN]] PPIases accelerate the folding of proteins. [[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/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/PHF5A_HUMAN PHF5A_HUMAN]] Acts as a transcriptional regulator by binding to the GJA1/Cx43 promoter and enhancing its up-regulation by ESR1/ER-alpha. Also involved in pre-mRNA splicing.<ref>PMID:12234937</ref> [[http://www.uniprot.org/uniprot/SF3B3_HUMAN SF3B3_HUMAN]] Subunit of the splicing factor SF3B required for 'A' complex assembly formed by the stable binding of U2 snRNP to the branchpoint sequence (BPS) in pre-mRNA. Sequence independent binding of SF3A/SF3B complex upstream of the branch site is essential, it may anchor U2 snRNP to the pre-mRNA. May also be involved in the assembly of the 'E' complex. Belongs also to the minor U12-dependent spliceosome, which is involved in the splicing of rare class of nuclear pre-mRNA intron. [[http://www.uniprot.org/uniprot/SF3A2_HUMAN SF3A2_HUMAN]] Subunit of the splicing factor SF3A required for 'A' complex assembly formed by the stable binding of U2 snRNP to the branchpoint sequence (BPS) in pre-mRNA. Sequence independent binding of SF3A/SF3B complex upstream of the branch site is essential, it may anchor U2 snRNP to the pre-mRNA. May also be involved in the assembly of the 'E' complex. [[http://www.uniprot.org/uniprot/SF3B6_HUMAN SF3B6_HUMAN]] Involved in pre-mRNA splicing as a component of the splicing factor SF3B complex (PubMed:27720643). SF3B complex is required for 'A' complex assembly formed by the stable binding of U2 snRNP to the branchpoint sequence (BPS) in pre-mRNA (PubMed:12234937). Directly contacts the pre-mRNA branch site adenosine for the first catalytic step of splicing (PubMed:16432215). Enters the spliceosome and associates with the pre-mRNA branch site as part of the 17S U2 or, in the case of the minor spliceosome, as part of the 18S U11/U12 snRNP complex, and thus may facilitate the interaction of these snRNP with the branch sites of U2 and U12 respectively (PubMed:16432215).<ref>PMID:12234937</ref> <ref>PMID:16432215</ref> <ref>PMID:27720643</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/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> [[http://www.uniprot.org/uniprot/SRRM1_HUMAN SRRM1_HUMAN]] Part of pre- and post-splicing multiprotein mRNP complexes. Involved in numerous pre-mRNA processing events. Promotes constitutive and exonic splicing enhancer (ESE)-dependent splicing activation by bridging together sequence-specific (SR family proteins, SFRS4, SFRS5 and TRA2B/SFRS10) and basal snRNP (SNRP70 and SNRPA1) factors of the spliceosome. Stimulates mRNA 3'-end cleavage independently of the formation of an exon junction complex. Binds both pre-mRNA and spliced mRNA 20-25 nt upstream of exon-exon junctions. Binds RNA and DNA with low sequence specificity and has similar preference for either double- or single-stranded nucleic acid substrates.<ref>PMID:9531537</ref> <ref>PMID:10339552</ref> <ref>PMID:10668804</ref> <ref>PMID:11739730</ref> <ref>PMID:12944400</ref> <ref>PMID:12600940</ref> [[http://www.uniprot.org/uniprot/CRNL1_HUMAN CRNL1_HUMAN]] Involved in pre-mRNA splicing process. [[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/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/SF3B1_HUMAN SF3B1_HUMAN]] Subunit of the splicing factor SF3B required for 'A' complex assembly formed by the stable binding of U2 snRNP to the branchpoint sequence (BPS) in pre-mRNA. Sequence independent binding of SF3A/SF3B complex upstream of the branch site is essential, it may anchor U2 snRNP to the pre-mRNA. May also be involved in the assembly of the 'E' complex. Belongs also to the minor U12-dependent spliceosome, which is involved in the splicing of rare class of nuclear pre-mRNA intron. [[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/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>
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[https://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>
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<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
== Publication Abstract from PubMed ==
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[[Category: Homo sapiens]]
[[Category: Homo sapiens]]
[[Category: Large Structures]]
[[Category: Large Structures]]
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[[Category: Peptidylprolyl isomerase]]
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[[Category: Agafonov D]]
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[[Category: Agafonov, D]]
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[[Category: Graf B]]
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[[Category: Graf, B]]
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[[Category: Hartmuth K]]
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[[Category: Hartmuth, K]]
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[[Category: Haselbach D]]
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[[Category: Haselbach, D]]
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[[Category: Kastner B]]
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[[Category: Kastner, B]]
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[[Category: Komarov I]]
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[[Category: Komarov, I]]
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[[Category: Luehrmann R]]
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[[Category: Luehrmann, R]]
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[[Category: Stark H]]
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[[Category: Stark, H]]
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[[Category: Bact]]
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[[Category: Dynamic]]
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[[Category: Hela]]
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[[Category: Human]]
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[[Category: Spliceosome]]
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[[Category: Splicing]]
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Current revision

human Bact spliceosome core structure

6ff4, resolution 3.40Å

Proteopedia Page Contributors and Editors (what is this?)

OCA

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