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6kut

From Proteopedia

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Current revision (10:44, 27 March 2024) (edit) (undo)
 
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<SX load='6kut' size='340' side='right' viewer='molstar' caption='[[6kut]], [[Resolution|resolution]] 4.10&Aring;' scene=''>
<SX load='6kut' size='340' side='right' viewer='molstar' caption='[[6kut]], [[Resolution|resolution]] 4.10&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[6kut]] is a 5 chain structure with sequence from [https://en.wikipedia.org/wiki/Influenza_c_virus_(c/swine/oklahoma/1334/2011) Influenza c virus (c/swine/oklahoma/1334/2011)]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=6abe 6abe]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6KUT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6KUT FirstGlance]. <br>
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<table><tr><td colspan='2'>[[6kut]] is a 5 chain structure with sequence from [https://en.wikipedia.org/wiki/Influenza_D_virus_(D/swine/Oklahoma/1334/2011) Influenza D virus (D/swine/Oklahoma/1334/2011)] 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=6abe 6abe]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6KUT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6KUT FirstGlance]. <br>
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</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">P3 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1173138 Influenza C virus (C/swine/Oklahoma/1334/2011)]), PB1 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1173138 Influenza C virus (C/swine/Oklahoma/1334/2011)]), PB2 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1173138 Influenza C virus (C/swine/Oklahoma/1334/2011)])</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]] 4.1&#8491;</td></tr>
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<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/RNA-directed_RNA_polymerase RNA-directed RNA polymerase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.48 2.7.7.48] </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=6kut FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6kut OCA], [https://pdbe.org/6kut PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6kut RCSB], [https://www.ebi.ac.uk/pdbsum/6kut PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6kut 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=6kut FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6kut OCA], [https://pdbe.org/6kut PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6kut RCSB], [https://www.ebi.ac.uk/pdbsum/6kut PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6kut ProSAT]</span></td></tr>
</table>
</table>
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<div style="background-color:#fffaf0;">
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== Function ==
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== Publication Abstract from PubMed ==
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[https://www.uniprot.org/uniprot/K9LHJ4_9ORTO K9LHJ4_9ORTO]
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The influenza virus polymerase uses capped RNA primers to initiate transcription, and a combination of terminal and internal de novo initiations for the two-step replication process by binding the conserved viral genomic RNA (vRNA) or complementary RNA (cRNA) promoter. Here, we determined the apo and promoter-bound influenza D polymerase structures using cryo-electron microscopy and found the polymerase has an evolutionarily conserved stable core structure with inherently flexible peripheral domains. Strikingly, two conformations (mode A and B) of the vRNA promoter were observed where the 3'-vRNA end can bind at two different sites, whereas the cRNA promoter only binds in the mode B conformation. Functional studies confirmed the critical role of the mode B conformation for vRNA synthesis via the intermediate cRNA but not for cRNA production, which is mainly regulated by the mode A conformation. Both conformations participate in the regulation of the transcription process. This work advances our understanding of the regulatory mechanisms for the synthesis of different RNA species by influenza virus polymerase and opens new opportunities for antiviral drug design.
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Structural insight into RNA synthesis by influenza D polymerase.,Peng Q, Liu Y, Peng R, Wang M, Yang W, Song H, Chen Y, Liu S, Han M, Zhang X, Wang P, Yan J, Zhang B, Qi J, Deng T, Gao GF, Shi Y Nat Microbiol. 2019 Jun 17. pii: 10.1038/s41564-019-0487-5. doi:, 10.1038/s41564-019-0487-5. PMID:31209309<ref>PMID:31209309</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 6kut" style="background-color:#fffaf0;"></div>
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==See Also==
==See Also==
*[[RNA polymerase 3D structures|RNA polymerase 3D structures]]
*[[RNA polymerase 3D structures|RNA polymerase 3D structures]]
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== References ==
 
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<references/>
 
__TOC__
__TOC__
</SX>
</SX>
[[Category: Large Structures]]
[[Category: Large Structures]]
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[[Category: RNA-directed RNA polymerase]]
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[[Category: Synthetic construct]]
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[[Category: Gao, G F]]
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[[Category: Gao GF]]
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[[Category: Peng, Q]]
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[[Category: Peng Q]]
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[[Category: Peng, R]]
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[[Category: Peng R]]
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[[Category: Qi, J]]
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[[Category: Qi J]]
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[[Category: Shi, Y]]
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[[Category: Shi Y]]
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[[Category: Cryo-em]]
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[[Category: Influenza d virus]]
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[[Category: Polymerase]]
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[[Category: Viral protein-rna complex]]
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Current revision

Structure of influenza D virus polymerase bound to vRNA promoter in Mode B conformation (Class B2)

6kut, resolution 4.10Å

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OCA

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