8apl - Revision history

OCA at 06:45, 24 July 2024

2024-07-24T06:45:41Z

← Older revision		Revision as of 06:45, 24 July 2024
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	==~~Symmetric hexamer of vaccinia~~ virus DNA helicase D5 residues 323-785==		==Vaccinia virus DNA helicase D5 residues 323-785 hexamer with bound DNA processed in C6==
	<StructureSection load='8apl' size='340' side='right'caption='[[8apl]], [[Resolution\|resolution]] 4.10Å' scene=''>		<StructureSection load='8apl' size='340' side='right'caption='[[8apl]], [[Resolution\|resolution]] 4.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
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	</table>		</table>
	== Function ==		== Function ==
	[https://www.uniprot.org/uniprot/~~D5_VACCC D5_VACCC~~] ~~Primase which may have roles in initiation~~ of DNA ~~replication or lagging-strand synthesis~~.		[https://www.uniprot.org/uniprot/PG117_VACCC PG117_VACCC] Multifunctional protein required for genome uncoating and replication. Major viral uncoating protein that is required for the release of the viral genome from incoming viral cores containing the viral DNA genome. Possesses an ATPase activity that is required for hexamerization and uncoating.[UniProtKB:P04305]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
	Poxviruses are large DNA viruses with a linear double-stranded DNA genome circularized at the extremities. The helicase-primase D5, composed of six identical 90 kDa subunits, is required for DNA replication. D5 consists of a primase fragment flexibly attached to the hexameric C-terminal polypeptide (res. 323-785) with confirmed nucleotide hydrolase and DNA-binding activity but an elusive helicase activity. We determined its structure by single-particle cryo-electron microscopy. It displays an AAA+ helicase core flanked by N- and C-terminal domains. Model building was greatly helped by the predicted structure of D5 using AlphaFold2. The 3.9 A structure of the N-terminal domain forms a well-defined tight ring while the resolution decreases towards the C-terminus, still allowing the fit of the predicted structure. The N-terminal domain is partially present in papillomavirus E1 and polyomavirus LTA helicases, as well as in a bacteriophage NrS-1 helicase domain, which is also closely related to the AAA+ helicase domain of D5. Using the Pfam domain database, a D5_N domain followed by DUF5906 and Pox_D5 domains could be assigned to the cryo-EM structure, providing the first 3D structures for D5_N and Pox_D5 domains. The same domain organization has been identified in a family of putative helicases from large DNA viruses, bacteriophages, and selfish DNA elements.		Poxviruses are large DNA viruses with a linear double-stranded DNA genome circularized at the extremities. The helicase-primase D5, composed of six identical 90 kDa subunits, is required for DNA replication. D5 consists of a primase fragment flexibly attached to the hexameric C-terminal polypeptide (res. 323-785) with confirmed nucleotide hydrolase and DNA-binding activity but an elusive helicase activity. We determined its structure by single-particle cryo-electron microscopy. It displays an AAA+ helicase core flanked by N- and C-terminal domains. Model building was greatly helped by the predicted structure of D5 using AlphaFold2. The 3.9 A structure of the N-terminal domain forms a well-defined tight ring while the resolution decreases towards the C-terminus, still allowing the fit of the predicted structure. The N-terminal domain is partially present in papillomavirus E1 and polyomavirus LTA helicases, as well as in a bacteriophage NrS-1 helicase domain, which is also closely related to the AAA+ helicase domain of D5. Using the Pfam domain database, a D5_N domain followed by DUF5906 and Pox_D5 domains could be assigned to the cryo-EM structure, providing the first 3D structures for D5_N and Pox_D5 domains. The same domain organization has been identified in a family of putative helicases from large DNA viruses, bacteriophages, and selfish DNA elements.

	The Vaccinia Virus DNA Helicase Structure from Combined Single-Particle Cryo-Electron Microscopy and AlphaFold2 Prediction.,Hutin S, Ling WL, Tarbouriech N, Schoehn G, Grimm C, Fischer U, Burmeister WP Viruses. 2022 Oct 7;14(10)~~. pii~~: ~~v14102206~~. doi: 10.3390/v14102206. PMID:36298761<ref>PMID:36298761</ref>		The Vaccinia Virus DNA Helicase Structure from Combined Single-Particle Cryo-Electron Microscopy and AlphaFold2 Prediction.,Hutin S, Ling WL, Tarbouriech N, Schoehn G, Grimm C, Fischer U, Burmeister WP Viruses. 2022 Oct 7;14(10):2206. doi: 10.3390/v14102206. PMID:36298761<ref>PMID:36298761</ref>

	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>

OCA at 06:55, 9 August 2023

2023-08-09T06:55:48Z

← Older revision		Revision as of 06:55, 9 August 2023
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[8apl]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Vaccinia_virus_Copenhagen Vaccinia virus Copenhagen]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8APL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8APL FirstGlance]. <br>		<table><tr><td colspan='2'>[[8apl]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Vaccinia_virus_Copenhagen Vaccinia virus Copenhagen]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8APL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8APL FirstGlance]. <br>
	</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=8apl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8apl OCA], [https://pdbe.org/8apl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8apl RCSB], [https://www.ebi.ac.uk/pdbsum/8apl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8apl ProSAT]</span></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='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=8apl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8apl OCA], [https://pdbe.org/8apl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8apl RCSB], [https://www.ebi.ac.uk/pdbsum/8apl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8apl ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==

OCA at 07:31, 9 November 2022

2022-11-09T07:31:46Z

← Older revision		Revision as of 07:31, 9 November 2022
Line 1:		Line 1:
	~~'''Unreleased structure'''~~

	The ~~entry 8apl~~ is ~~ON HOLD~~		==Symmetric hexamer of vaccinia virus DNA helicase D5 residues 323-785==
			<StructureSection load='8apl' size='340' side='right'caption='[[8apl]], [[Resolution\|resolution]] 4.10Å' scene=''>
			== Structural highlights ==
			<table><tr><td colspan='2'>[[8apl]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Vaccinia_virus_Copenhagen Vaccinia virus Copenhagen]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8APL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8APL FirstGlance]. <br>
			</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=8apl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8apl OCA], [https://pdbe.org/8apl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8apl RCSB], [https://www.ebi.ac.uk/pdbsum/8apl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8apl ProSAT]</span></td></tr>
			</table>
			== Function ==
			[https://www.uniprot.org/uniprot/D5_VACCC D5_VACCC] Primase which may have roles in initiation of DNA replication or lagging-strand synthesis.
			<div style="background-color:#fffaf0;">
			== Publication Abstract from PubMed ==
			Poxviruses are large DNA viruses with a linear double-stranded DNA genome circularized at the extremities. The helicase-primase D5, composed of six identical 90 kDa subunits, is required for DNA replication. D5 consists of a primase fragment flexibly attached to the hexameric C-terminal polypeptide (res. 323-785) with confirmed nucleotide hydrolase and DNA-binding activity but an elusive helicase activity. We determined its structure by single-particle cryo-electron microscopy. It displays an AAA+ helicase core flanked by N- and C-terminal domains. Model building was greatly helped by the predicted structure of D5 using AlphaFold2. The 3.9 A structure of the N-terminal domain forms a well-defined tight ring while the resolution decreases towards the C-terminus, still allowing the fit of the predicted structure. The N-terminal domain is partially present in papillomavirus E1 and polyomavirus LTA helicases, as well as in a bacteriophage NrS-1 helicase domain, which is also closely related to the AAA+ helicase domain of D5. Using the Pfam domain database, a D5_N domain followed by DUF5906 and Pox_D5 domains could be assigned to the cryo-EM structure, providing the first 3D structures for D5_N and Pox_D5 domains. The same domain organization has been identified in a family of putative helicases from large DNA viruses, bacteriophages, and selfish DNA elements.

	~~Authors: Burmeister, W.P~~., Hutin, S., Ling, ~~W.L.~~, Grimm, C., ~~Schoehn~~, G.		The Vaccinia Virus DNA Helicase Structure from Combined Single-Particle Cryo-Electron Microscopy and AlphaFold2 Prediction.,Hutin S, Ling WL, Tarbouriech N, Schoehn G, Grimm C, Fischer U, Burmeister WP Viruses. 2022 Oct 7;14(10). pii: v14102206. doi: 10.3390/v14102206. PMID:36298761<ref>PMID:36298761</ref>

	~~Description: Symmetric hexamer~~ of ~~vaccinia virus DNA helicase D5 residues 323~~-~~785~~		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	[[Category: ~~Unreleased~~ Structures]]		</div>
	[[Category: ~~Schoehn, G~~]]		<div class="pdbe-citations 8apl" style="background-color:#fffaf0;"></div>
	[[Category: Grimm, C]]		== References ==
	[[Category: ~~Ling, W.L~~]]		<references/>
	[[Category: ~~Burmeister, W.P~~]]		__TOC__
	[[Category: ~~Hutin, S~~]]		</StructureSection>
			[[Category: Large Structures]]
			[[Category: Vaccinia virus Copenhagen]]
			[[Category: Burmeister WP]]
			[[Category: Grimm C]]
			[[Category: Hutin S]]
			[[Category: Ling WL]]
			[[Category: Schoehn G]]

OCA: Protected "8apl" [edit=sysop:move=sysop]

2022-08-18T03:54:18Z

Protected "8apl" [edit=sysop:move=sysop]

← Older revision	Revision as of 03:54, 18 August 2022
(No difference)

OCA: New page: '''Unreleased structure''' The entry 8apl is ON HOLD Authors: Burmeister, W.P., Hutin, S., Ling, W.L., Grimm, C., Schoehn, G. Description: Symmetric hexamer of vaccinia virus DNA helic...

2022-08-18T03:54:16Z

New page: '''Unreleased structure''' The entry 8apl is ON HOLD Authors: Burmeister, W.P., Hutin, S., Ling, W.L., Grimm, C., Schoehn, G. Description: Symmetric hexamer of vaccinia virus DNA helic...

New page

'''Unreleased structure'''

The entry 8apl is ON HOLD

Authors: Burmeister, W.P., Hutin, S., Ling, W.L., Grimm, C., Schoehn, G.

Description: Symmetric hexamer of vaccinia virus DNA helicase D5 residues 323-785
[[Category: Unreleased Structures]]
[[Category: Schoehn, G]]
[[Category: Grimm, C]]
[[Category: Ling, W.L]]
[[Category: Burmeister, W.P]]
[[Category: Hutin, S]]