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| ==RNA polymerase II elongation complex stalled at SHL(-1) of the nucleosome== | | ==RNA polymerase II elongation complex stalled at SHL(-1) of the nucleosome== |
| <StructureSection load='6a5t' size='340' side='right' caption='[[6a5t]], [[Resolution|resolution]] 6.70Å' scene=''> | | <SX load='6a5t' size='340' side='right' viewer='molstar' caption='[[6a5t]], [[Resolution|resolution]] 6.70Å' scene=''> |
| == Structural highlights == | | == Structural highlights == |
| <table><tr><td colspan='2'>[[6a5t]] is a 23 chain structure with sequence from [http://en.wikipedia.org/wiki/Kompg Kompg]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6A5T OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6A5T FirstGlance]. <br> | | <table><tr><td colspan='2'>[[6a5t]] is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/Komagataella_phaffii_GS115 Komagataella phaffii GS115]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6A5T OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6A5T FirstGlance]. <br> |
| </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><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]] 6.7Å</td></tr> |
| <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">H3F3A, H3.3A, H3F3, PP781, H3F3B, H3.3B ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=644223 KOMPG]), HIST1H4A, H4/A, H4FA, HIST1H4B, H4/I, H4FI, HIST1H4C, H4/G, H4FG, HIST1H4D, H4/B, H4FB, HIST1H4E, H4/J, H4FJ, HIST1H4F, H4/C, H4FC, HIST1H4H, H4/H, H4FH, HIST1H4I, H4/M, H4FM, HIST1H4J, H4/E, H4FE, HIST1H4K, H4/D, H4FD, HIST1H4L, H4/K, H4FK, HIST2H4A, H4/N, H4F2, H4FN, HIST2H4, HIST2H4B, H4/O, H4FO, HIST4H4 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=644223 KOMPG]), HIST1H2AB, H2AFM, HIST1H2AE, H2AFA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=644223 KOMPG]), HIST1H2BJ, H2BFR ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=644223 KOMPG])</td></tr> | | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><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/DNA-directed_RNA_polymerase DNA-directed RNA polymerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.6 2.7.7.6] </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=6a5t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6a5t OCA], [https://pdbe.org/6a5t PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6a5t RCSB], [https://www.ebi.ac.uk/pdbsum/6a5t PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6a5t 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=6a5t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6a5t OCA], [http://pdbe.org/6a5t PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6a5t RCSB], [http://www.ebi.ac.uk/pdbsum/6a5t PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6a5t ProSAT]</span></td></tr> | |
| </table> | | </table> |
| == Function == | | == Function == |
| [[http://www.uniprot.org/uniprot/C4QZQ7_KOMPG C4QZQ7_KOMPG]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates.[RuleBase:RU363031] [[http://www.uniprot.org/uniprot/C4R4Y0_KOMPG C4R4Y0_KOMPG]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates.[RuleBase:RU004279] [[http://www.uniprot.org/uniprot/F2QPE6_KOMPC F2QPE6_KOMPC]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates.[PIRNR:PIRNR005586] [[http://www.uniprot.org/uniprot/H2B1J_HUMAN H2B1J_HUMAN]] Core component of nucleosome. Nucleosomes wrap and compact DNA into chromatin, limiting DNA accessibility to the cellular machineries which require DNA as a template. Histones thereby play a central role in transcription regulation, DNA repair, DNA replication and chromosomal stability. DNA accessibility is regulated via a complex set of post-translational modifications of histones, also called histone code, and nucleosome remodeling.<ref>PMID:11859126</ref> <ref>PMID:12860195</ref> <ref>PMID:15019208</ref> Has broad antibacterial activity. May contribute to the formation of the functional antimicrobial barrier of the colonic epithelium, and to the bactericidal activity of amniotic fluid.<ref>PMID:11859126</ref> <ref>PMID:12860195</ref> <ref>PMID:15019208</ref> | | [https://www.uniprot.org/uniprot/C4R4Y0_KOMPG C4R4Y0_KOMPG] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates.[RuleBase:RU004279] |
| <div style="background-color:#fffaf0;">
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| == Publication Abstract from PubMed ==
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| Genomic DNA forms chromatin, in which the nucleosome is the repeating unit. The mechanism by which RNA polymerase II (RNAPII) transcribes the nucleosomal DNA remains unclear. Here we report the cryo-electron microscopy structures of RNAPII-nucleosome complexes, in which RNAPII pauses at the superhelical locations, SHL(-6), SHL(-5), SHL(-2), and SHL(-1), of the nucleosome. RNAPII pauses at the major histone-DNA contact sites, and the nucleosome interactions with the RNAPII subunits stabilize the pause. These structures reveal snapshots of nucleosomal transcription, where RNAPII gradually tears DNA from the histone surface, while preserving the histone octamer. Interestingly, the nucleosomes in the SHL(-1) complexes are bound to a "foreign" DNA segment, which might explain the histone transfer mechanism. These results provide the foundations for understanding chromatin transcription and epigenetic regulation.
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| Structural basis of the nucleosome transition during RNA polymerase II passage.,Kujirai T, Ehara H, Fujino Y, Shirouzu M, Sekine SI, Kurumizaka H Science. 2018 Oct 4. pii: science.aau9904. doi: 10.1126/science.aau9904. PMID:30287617<ref>PMID:30287617</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 6a5t" style="background-color:#fffaf0;"></div>
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| ==See Also== | | ==See Also== |
| *[[RNA polymerase|RNA polymerase]] | | *[[Histone 3D structures|Histone 3D structures]] |
| == References ==
| | *[[RNA polymerase 3D structures|RNA polymerase 3D structures]] |
| <references/>
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| __TOC__ | | __TOC__ |
| </StructureSection> | | </SX> |
| [[Category: DNA-directed RNA polymerase]] | | [[Category: Komagataella phaffii GS115]] |
| [[Category: Kompg]] | | [[Category: Large Structures]] |
| [[Category: Ehara, H]] | | [[Category: Ehara H]] |
| [[Category: Fujino, Y]] | | [[Category: Fujino Y]] |
| [[Category: Kujirai, T]] | | [[Category: Kujirai T]] |
| [[Category: Kurumizaka, H]] | | [[Category: Kurumizaka H]] |
| [[Category: Sekine, S]] | | [[Category: Sekine S]] |
| [[Category: Shirouzu, M]] | | [[Category: Shirouzu M]] |
| [[Category: Chromatin]]
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| [[Category: Nucleosome]]
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| [[Category: Rna polymerase]]
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| [[Category: Transcription]]
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| [[Category: Transcription-rna-dna complex]]
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