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| | ==RNA polymerase II elongation complex stalled at SHL(-1) of the nucleosome, with foreign DNA (+1 position)== | | ==RNA polymerase II elongation complex stalled at SHL(-1) of the nucleosome, with foreign DNA (+1 position)== |
| - | <StructureSection load='6inq' size='340' side='right'caption='[[6inq]], [[Resolution|resolution]] 6.90Å' scene=''> | + | <SX load='6inq' size='340' side='right' viewer='molstar' caption='[[6inq]], [[Resolution|resolution]] 6.90Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[6inq]] is a 24 chain structure with sequence from [http://en.wikipedia.org/wiki/ ] and [http://en.wikipedia.org/wiki/Komagataella_phaffii_(strain_gs115_/_atcc_20864) Komagataella phaffii (strain gs115 / atcc 20864)]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=6a5v 6a5v]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6INQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6INQ FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[6inq]] is a 13 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens], [https://en.wikipedia.org/wiki/Komagataella_phaffii_GS115 Komagataella phaffii GS115] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=6a5v 6a5v]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6INQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6INQ 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]] 6.9Å</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='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='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=6inq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6inq OCA], [http://pdbe.org/6inq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6inq RCSB], [http://www.ebi.ac.uk/pdbsum/6inq PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6inq ProSAT]</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=6inq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6inq OCA], [https://pdbe.org/6inq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6inq RCSB], [https://www.ebi.ac.uk/pdbsum/6inq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6inq 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/H4_HUMAN H4_HUMAN] |
| - | <div style="background-color:#fffaf0;">
| + | |
| - | == Publication Abstract from PubMed ==
| + | |
| - | 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.
| + | |
| | | | |
| - | 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>
| + | ==See Also== |
| - | | + | *[[Histone 3D structures|Histone 3D structures]] |
| - | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
| + | *[[RNA polymerase 3D structures|RNA polymerase 3D structures]] |
| - | </div>
| + | |
| - | <div class="pdbe-citations 6inq" style="background-color:#fffaf0;"></div>
| + | |
| - | == References ==
| + | |
| - | <references/>
| + | |
| | __TOC__ | | __TOC__ |
| - | </StructureSection> | + | </SX> |
| - | [[Category: DNA-directed RNA polymerase]] | + | [[Category: Homo sapiens]] |
| | + | [[Category: Komagataella phaffii GS115]] |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Ehara, H]] | + | [[Category: Synthetic construct]] |
| - | [[Category: Fujino, Y]] | + | [[Category: Ehara H]] |
| - | [[Category: Kujirai, T]] | + | [[Category: Fujino Y]] |
| - | [[Category: Kurumizaka, H]] | + | [[Category: Kujirai T]] |
| - | [[Category: Sekine, S]] | + | [[Category: Kurumizaka H]] |
| - | [[Category: Shirouzu, M]] | + | [[Category: Sekine S]] |
| - | [[Category: Chromatin]]
| + | [[Category: Shirouzu M]] |
| - | [[Category: Nucleosome]]
| + | |
| - | [[Category: Rna polymerase]]
| + | |
| - | [[Category: Transcription]]
| + | |
| - | [[Category: Transcription-rna-dna complex]]
| + | |
