5hd9 - Revision history

OCA at 07:32, 9 August 2023

OCA — Wed, 09 Aug 2023 07:32:04 GMT

←Older revision		Revision as of 07:32, 9 August 2023
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	<StructureSection load='5hd9' size='340' side='right'caption='[[5hd9]], [[Resolution\|resolution]] 1.94Å' scene=''>		<StructureSection load='5hd9' size='340' side='right'caption='[[5hd9]], [[Resolution\|resolution]] 1.94Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5hd9]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Bpph2 Bpph2~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5HD9 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5HD9 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5hd9]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_virus_phi29 Bacillus virus phi29]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5HD9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5HD9 FirstGlance]. <br>
-	</td></tr><tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"~~><scene name~~=~~'pdbligand=MSE:SELENOMETHIONINE'>MSE</scene~~></td></tr>	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 1.941Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~16, gp16 ([http~~:/~~/www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10756 BPPH2])~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</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=5hd9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5hd9 OCA], [~~http~~://pdbe.org/5hd9 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5hd9 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5hd9 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5hd9 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=5hd9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5hd9 OCA], [https://pdbe.org/5hd9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5hd9 RCSB], [https://www.ebi.ac.uk/pdbsum/5hd9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5hd9 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/~~VG16_BPPH2 VG16_BPPH2~~]~~] Required~~ for the genome encapsidation reaction.	+	[https://www.uniprot.org/uniprot/PKG16_BPPH2 PKG16_BPPH2] ATPase required for the genome encapsidation reaction. Part of the active packaging motor via the binding to the packaging RNA (pRNA), itself fixed to the head-tail connector at the unique portal vertex of the prohead. Binds and supercoils the DNA-gp3 to produce an initiation complex for DNA packaging. Provides the energy to actively pump the viral DNA into the prohead. Approximately one molecule of ATP is used in the packaging of 2 bp of viral DNA. After packaging, the ATPase and the pRNA are released from the prohead.<ref>PMID:11130079</ref> <ref>PMID:18674782</ref> <ref>PMID:2960820</ref> <ref>PMID:3879485</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Bpph2~~]]	+	[[Category: Bacillus virus phi29]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Mao, H]]	+	[[Category: Mao H]]
-	[[Category: Morais~~, M C~~]]	+	[[Category: Morais MC]]
-	[[Category: Reyes-Aldrete, E]]	+	[[Category: Reyes-Aldrete E]]
-	~~[[Category: Asce fold]]~~	+
-	~~[[Category: Viral protein~~]]	+

OCA at 11:40, 25 December 2019

OCA — Wed, 25 Dec 2019 11:40:49 GMT

←Older revision		Revision as of 11:40, 25 December 2019
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	==Crystal Structure of the N-terminal domain of the DNA packaging ATPase from bacteriophage phi29==		==Crystal Structure of the N-terminal domain of the DNA packaging ATPase from bacteriophage phi29==
-	<StructureSection load='5hd9' size='340' side='right' caption='[[5hd9]], [[Resolution\|resolution]] 1.94Å' scene=''>	+	<StructureSection load='5hd9' size='340' side='right'caption='[[5hd9]], [[Resolution\|resolution]] 1.94Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5hd9]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Bpph2 Bpph2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5HD9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5HD9 FirstGlance]. <br>		<table><tr><td colspan='2'>[[5hd9]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Bpph2 Bpph2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5HD9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5HD9 FirstGlance]. <br>
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	</StructureSection>		</StructureSection>
	[[Category: Bpph2]]		[[Category: Bpph2]]
		+	[[Category: Large Structures]]
	[[Category: Mao, H]]		[[Category: Mao, H]]
	[[Category: Morais, M C]]		[[Category: Morais, M C]]

OCA at 09:58, 22 November 2017

OCA — Wed, 22 Nov 2017 09:58:19 GMT

←Older revision		Revision as of 09:58, 22 November 2017
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	<StructureSection load='5hd9' size='340' side='right' caption='[[5hd9]], [[Resolution\|resolution]] 1.94Å' scene=''>		<StructureSection load='5hd9' size='340' side='right' caption='[[5hd9]], [[Resolution\|resolution]] 1.94Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5hd9]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5HD9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5HD9 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5hd9]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Bpph2 Bpph2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5HD9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5HD9 FirstGlance]. <br>
	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>		</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">16, gp16 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10756 BPPH2])</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=5hd9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5hd9 OCA], [http://pdbe.org/5hd9 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5hd9 RCSB], [http://www.ebi.ac.uk/pdbsum/5hd9 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5hd9 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=5hd9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5hd9 OCA], [http://pdbe.org/5hd9 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5hd9 RCSB], [http://www.ebi.ac.uk/pdbsum/5hd9 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5hd9 ProSAT]</span></td></tr>
	</table>		</table>
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Bpph2]]
	[[Category: Mao, H]]		[[Category: Mao, H]]
	[[Category: Morais, M C]]		[[Category: Morais, M C]]

OCA at 06:56, 6 October 2017

OCA — Fri, 06 Oct 2017 06:56:08 GMT

←Older revision		Revision as of 06:56, 6 October 2017
Line 5:		Line 5:
	<table><tr><td colspan='2'>[[5hd9]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5HD9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5HD9 FirstGlance]. <br>		<table><tr><td colspan='2'>[[5hd9]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5HD9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5HD9 FirstGlance]. <br>
	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>		</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</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=5hd9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5hd9 OCA], [http://pdbe.org/5hd9 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5hd9 RCSB], [http://www.ebi.ac.uk/pdbsum/5hd9 PDBsum]</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=5hd9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5hd9 OCA], [http://pdbe.org/5hd9 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5hd9 RCSB], [http://www.ebi.ac.uk/pdbsum/5hd9 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5hd9 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==

OCA at 03:37, 10 March 2016

OCA — Thu, 10 Mar 2016 03:37:01 GMT

←Older revision		Revision as of 03:37, 10 March 2016
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5hd9 is ~~ON HOLD until Jan 05 2018~~	+	==Crystal Structure of the N-terminal domain of the DNA packaging ATPase from bacteriophage phi29==
		+	<StructureSection load='5hd9' size='340' side='right' caption='[[5hd9]], [[Resolution\|resolution]] 1.94Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5hd9]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5HD9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5HD9 FirstGlance]. <br>
		+	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</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=5hd9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5hd9 OCA], [http://pdbe.org/5hd9 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5hd9 RCSB], [http://www.ebi.ac.uk/pdbsum/5hd9 PDBsum]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/VG16_BPPH2 VG16_BPPH2]] Required for the genome encapsidation reaction.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Ring NTPases are a class of ubiquitous molecular motors involved in basic biological partitioning processes. dsDNA viruses encode ring ATPases that translocate their genomes to near-crystalline densities within pre-assembled viral capsids. Here, X-ray crystallography, cryoEM, and biochemical analyses of the dsDNA packaging motor in bacteriophage phi29 show how individual subunits are arranged in a pentameric ATPase ring and suggest how their activities are coordinated to translocate dsDNA. The resulting pseudo-atomic structure of the motor and accompanying functional analyses show how ATP is bound in the ATPase active site; identify two DNA contacts, including a potential DNA translocating loop; demonstrate that a trans-acting arginine finger is involved in coordinating hydrolysis around the ring; and suggest a functional coupling between the arginine finger and the DNA translocating loop. The ability to visualize the motor in action illuminates how the different motor components interact with each other and with their DNA substrate.

-	~~Authors: Morais, M.C~~., Mao, H., Reyes-Aldrete, E.	+	Structural and Molecular Basis for Coordination in a Viral DNA Packaging Motor.,Mao H, Saha M, Reyes-Aldrete E, Sherman MB, Woodson M, Atz R, Grimes S, Jardine PJ, Morais MC Cell Rep. 2016 Mar 1;14(8):2017-29. doi: 10.1016/j.celrep.2016.01.058. Epub 2016 , Feb 18. PMID:26904950<ref>PMID:26904950</ref>

-	~~Description: Crystal Structure~~ of the ~~N-terminal domain~~ of ~~the DNA packaging ATPase from bacteriophage phi29~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[Category: Unreleased Structures]]~~	+	</div>
-	~~[[Category~~: ~~Morais, M.C]]~~	+	<div class="pdbe-citations 5hd9" style="background-color:#fffaf0;"></div>
-	~~[[Category: Reyes-Aldrete, E]]~~	+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Mao, H]]		[[Category: Mao, H]]
		+	[[Category: Morais, M C]]
		+	[[Category: Reyes-Aldrete, E]]
		+	[[Category: Asce fold]]
		+	[[Category: Viral protein]]

OCA at 15:49, 26 February 2016

OCA — Fri, 26 Feb 2016 15:49:08 GMT

←Older revision		Revision as of 15:49, 26 February 2016
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5hd9 is ON HOLD	+	The entry 5hd9 is ON HOLD until Jan 05 2018

	Authors: Morais, M.C., Mao, H., Reyes-Aldrete, E.		Authors: Morais, M.C., Mao, H., Reyes-Aldrete, E.

OCA: Protected "5hd9" [edit=sysop:move=sysop]

OCA — Wed, 13 Jan 2016 18:52:09 GMT

Protected "5hd9" [edit=sysop:move=sysop]

←Older revision

Revision as of 18:52, 13 January 2016

OCA: New page: '''Unreleased structure''' The entry 5hd9 is ON HOLD Authors: Morais, M.C., Mao, H., Reyes-Aldrete, E. Description: Crystal Structure of the N-terminal domain of the DNA packaging ATPa...

OCA — Wed, 13 Jan 2016 18:52:08 GMT

New page: '''Unreleased structure''' The entry 5hd9 is ON HOLD Authors: Morais, M.C., Mao, H., Reyes-Aldrete, E. Description: Crystal Structure of the N-terminal domain of the DNA packaging ATPa...

New page

'''Unreleased structure'''

The entry 5hd9 is ON HOLD

Authors: Morais, M.C., Mao, H., Reyes-Aldrete, E.

Description: Crystal Structure of the N-terminal domain of the DNA packaging ATPase from bacteriophage phi29
[[Category: Unreleased Structures]]
[[Category: Morais, M.C]]
[[Category: Reyes-Aldrete, E]]
[[Category: Mao, H]]