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| ==RNA polymerase II elongation complex bound with Spt4/5 and foreign DNA, stalled at SHL(-1) of the nucleosome== | | ==RNA polymerase II elongation complex bound with Spt4/5 and foreign DNA, stalled at SHL(-1) of the nucleosome== |
| <StructureSection load='6j4z' size='340' side='right' caption='[[6j4z]], [[Resolution|resolution]] 4.10Å' scene=''> | | <SX load='6j4z' size='340' side='right' viewer='molstar' caption='[[6j4z]], [[Resolution|resolution]] 4.10Å' scene=''> |
| == Structural highlights == | | == Structural highlights == |
| <table><tr><td colspan='2'>[[6j4z]] is a 26 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_28485 Atcc 28485], [http://en.wikipedia.org/wiki/Kompc Kompc] and [http://en.wikipedia.org/wiki/Kompg Kompg]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6J4Z OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6J4Z FirstGlance]. <br> | | <table><tr><td colspan='2'>[[6j4z]] is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/Komagataella_phaffii_CBS_7435 Komagataella phaffii CBS 7435] and [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=6J4Z OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6J4Z 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]] 4.1Å</td></tr> |
| <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">PAS_chr2-1_0350 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=644223 KOMPG]), 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=6j4z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6j4z OCA], [https://pdbe.org/6j4z PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6j4z RCSB], [https://www.ebi.ac.uk/pdbsum/6j4z PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6j4z 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=6j4z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6j4z OCA], [http://pdbe.org/6j4z PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6j4z RCSB], [http://www.ebi.ac.uk/pdbsum/6j4z PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6j4z ProSAT]</span></td></tr> | |
| </table> | | </table> |
| == Function == | | == Function == |
| [[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> [[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/C4R0E6_KOMPG C4R0E6_KOMPG]] The SPT4-SPT5 complex mediates both activation and inhibition of transcription elongation, and plays a role in pre-mRNA processing. This complex seems to be important for the stability of the RNA polymerase II elongation machinery on the chromatin template but not for the inherent ability of this machinery to translocate down the gene.[PIRNR:PIRNR025023] [[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] | | [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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| RNA polymerase II (RNAPII) transcribes chromosomal DNA that contains multiple nucleosomes. The nucleosome forms transcriptional barriers, and nucleosomal transcription requires several additional factors in vivo. We demonstrate that the transcription elongation factors Elf1 and Spt4/5 cooperatively lower the barriers and increase the RNAPII processivity in the nucleosome. The cryo-electron microscopy structures of the nucleosome-transcribing RNAPII elongation complexes (ECs) reveal that Elf1 and Spt4/5 reshape the EC downstream edge and intervene between RNAPII and the nucleosome. They facilitate RNAPII progression through superhelical location SHL(-1) by adjusting the nucleosome in favor of the forward progression. They suppress pausing at SHL(-5) by preventing the stable RNAPII-nucleosome interaction. Thus, the EC overcomes the nucleosomal barriers while providing a platform for various chromatin functions.
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| Structural insight into nucleosome transcription by RNA polymerase II with elongation factors.,Ehara H, Kujirai T, Fujino Y, Shirouzu M, Kurumizaka H, Sekine SI Science. 2019 Feb 15;363(6428):744-747. doi: 10.1126/science.aav8912. Epub 2019, Feb 7. PMID:30733384<ref>PMID:30733384</ref>
| | ==See Also== |
| | | *[[Elongation factor 3D structures|Elongation factor 3D structures]] |
| From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
| | *[[Histone 3D structures|Histone 3D structures]] |
| </div>
| | *[[RNA polymerase 3D structures|RNA polymerase 3D structures]] |
| <div class="pdbe-citations 6j4z" style="background-color:#fffaf0;"></div>
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| == References ==
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| <references/>
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| __TOC__ | | __TOC__ |
| </StructureSection> | | </SX> |
| [[Category: Atcc 28485]] | | [[Category: Komagataella phaffii CBS 7435]] |
| [[Category: DNA-directed RNA polymerase]] | | [[Category: Komagataella phaffii GS115]] |
| [[Category: Kompc]] | | [[Category: Large Structures]] |
| [[Category: Kompg]]
| | [[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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