6v1w - Revision history

OCA at 11:05, 14 June 2023

2023-06-14T11:05:19Z

←Older revision		Revision as of 11:05, 14 June 2023
Line 1:		Line 1:

	==NMR Structure of C-terminal Domain of phi29 ATPase==		==NMR Structure of C-terminal Domain of phi29 ATPase==
-	<StructureSection load='6v1w' size='340' side='right'caption='[[6v1w~~]], [[NMR_Ensembles_of_Models \| 15 NMR models~~]]' scene=''>	+	<StructureSection load='6v1w' size='340' side='right'caption='[[6v1w]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6v1w]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Bpph2 Bpph2~~]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6V1W OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6V1W FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6v1w]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_virus_phi29 Bacillus virus phi29]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6V1W OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6V1W FirstGlance]. <br>
-	</td></tr>~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">16 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10756 BPPH2])</td></tr>~~	+	</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=6v1w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6v1w OCA], [https://pdbe.org/6v1w PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6v1w RCSB], [https://www.ebi.ac.uk/pdbsum/6v1w PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6v1w ProSAT]</span></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=6v1w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6v1w OCA], [~~http~~://pdbe.org/6v1w PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6v1w RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6v1w PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6v1w ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://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>	+	[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 ==
Line 22:		Line 21:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Bpph2~~]]	+	[[Category: Bacillus virus phi29]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Mahler, B]]	+	[[Category: Mahler B]]
-	[[Category: Mao, H]]	+	[[Category: Mao H]]
-	[[Category: Morais~~, M C]]~~	+	[[Category: Morais MC]]
-	~~[[Category: Rnase h fold]]~~	+
-	~~[[Category: Terminase]]~~	+
-	~~[[Category: Viral packaging motor]]~~	+
-	~~[[Category: Viral protein~~]]	+

OCA at 07:35, 4 November 2020

2020-11-04T07:35:39Z

←Older revision		Revision as of 07:35, 4 November 2020
Line 1:		Line 1:

	==NMR Structure of C-terminal Domain of phi29 ATPase==		==NMR Structure of C-terminal Domain of phi29 ATPase==
-	<StructureSection load='6v1w' size='340' side='right'caption='[[6v1w]]' scene=''>	+	<StructureSection load='6v1w' size='340' side='right'caption='[[6v1w]], [[NMR_Ensembles_of_Models \| 15 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>Full ~~crystallographic~~ information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6V1W OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6V1W FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6v1w]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Bpph2 Bpph2]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6V1W OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6V1W FirstGlance]. <br>
-	</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6v1w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6v1w OCA], [http://pdbe.org/6v1w PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6v1w RCSB], [http://www.ebi.ac.uk/pdbsum/6v1w PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6v1w ProSAT]</span></td></tr>	+	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">16 ([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://proteopedia.org/fgij/fg.htm?mol=6v1w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6v1w OCA], [http://pdbe.org/6v1w PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6v1w RCSB], [http://www.ebi.ac.uk/pdbsum/6v1w PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6v1w ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://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;">
		+	== Publication Abstract from PubMed ==
		+	Double-stranded DNA viruses use ATP-powered molecular motors to package their genomic DNA. To ensure efficient genome encapsidation, these motors regulate functional transitions between initiation, translocation, and termination modes. Here, we report structural and biophysical analyses of the C-terminal domain of the bacteriophage phi29 ATPase (CTD) that suggest a structural basis for these functional transitions. Sedimentation experiments show that the inter-domain linker in the full-length protein promotes oligomerization and thus may play a role in assembly of the functional motor. The NMR solution structure of the CTD indicates it is a vestigial nuclease domain that likely evolved from conserved nuclease domains in phage terminases. Despite the loss of nuclease activity, fluorescence binding assays confirm the CTD retains its DNA binding capabilities and fitting the CTD into cryoEM density of the phi29 motor shows that the CTD directly binds DNA. However, the interacting residues differ from those identified by NMR titration in solution, suggesting that packaging motors undergo conformational changes to transition between initiation, translocation, and termination. Taken together, these results provide insight into the evolution of functional transitions in viral dsDNA packaging motors.
		+
		+	NMR structure of a vestigial nuclease provides insight into the evolution of functional transitions in viral dsDNA packaging motors.,Mahler BP, Bujalowski PJ, Mao H, Dill EA, Jardine PJ, Choi KH, Morais MC Nucleic Acids Res. 2020 Oct 21. pii: 5934415. doi: 10.1093/nar/gkaa874. PMID:33089330<ref>PMID:33089330</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6v1w" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Bpph2]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Mahler B]]	+	[[Category: Mahler, B]]
-	[[Category: Mao H]]	+	[[Category: Mao, H]]
-	[[Category: Morais MC]]	+	[[Category: Morais, M C]]
		+	[[Category: Rnase h fold]]
		+	[[Category: Terminase]]
		+	[[Category: Viral packaging motor]]
		+	[[Category: Viral protein]]

OCA at 07:09, 30 September 2020

2020-09-30T07:09:02Z

←Older revision		Revision as of 07:09, 30 September 2020
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6v1w is ~~ON HOLD until Paper Publication~~	+	==NMR Structure of C-terminal Domain of phi29 ATPase==
-		+	<StructureSection load='6v1w' size='340' side='right'caption='[[6v1w]]' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6V1W OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6V1W FirstGlance]. <br>
-	~~Description~~:	+	</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6v1w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6v1w OCA], [http://pdbe.org/6v1w PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6v1w RCSB], [http://www.ebi.ac.uk/pdbsum/6v1w PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6v1w ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Mahler B]]
		+	[[Category: Mao H]]
		+	[[Category: Morais MC]]

OCA at 06:34, 4 December 2019

2019-12-04T06:34:44Z

←Older revision		Revision as of 06:34, 4 December 2019
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6v1w is ON HOLD	+	The entry 6v1w is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "6v1w" [edit=sysop:move=sysop]

2019-11-27T05:30:02Z

Protected "6v1w" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:30, 27 November 2019

OCA: New page: '''Unreleased structure''' The entry 6v1w is ON HOLD Authors: Description: Category: Unreleased Structures

2019-11-27T05:30:00Z

New page: '''Unreleased structure''' The entry 6v1w is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 6v1w is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]