7cnb - Revision history

OCA at 10:51, 27 March 2024

2024-03-27T10:51:45Z

←Older revision		Revision as of 10:51, 27 March 2024
Line 3:		Line 3:
	<StructureSection load='7cnb' size='340' side='right'caption='[[7cnb]], [[Resolution\|resolution]] 2.32Å' scene=''>		<StructureSection load='7cnb' size='340' side='right'caption='[[7cnb]], [[Resolution\|resolution]] 2.32Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[7cnb]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Bpph2 Bpph2~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7CNB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7CNB FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7cnb]] 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=7CNB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7CNB FirstGlance]. <br>
-	</td></tr><tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~16 (~~[~~https://www~~.~~ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info~~&~~srchmode=5&id=10756 BPPH2])~~</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]] 2.32Å</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=7cnb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7cnb OCA], [https://pdbe.org/7cnb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7cnb RCSB], [https://www.ebi.ac.uk/pdbsum/7cnb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7cnb 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=7cnb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7cnb OCA], [https://pdbe.org/7cnb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7cnb RCSB], [https://www.ebi.ac.uk/pdbsum/7cnb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7cnb ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[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>	+	[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;">~~	+
-	~~== Publication Abstract from PubMed ==~~	+
-	Biological motors, ubiquitous in living systems, convert chemical energy into different kinds of mechanical motions critical to cellular functions. Gene product 16 (gp16) in bacteriophage varphi29 is among the most powerful biomotors known, which adopts a multisubunit ring-shaped structure and hydrolyzes ATP to package double-stranded DNA (dsDNA) into a preformed procapsid. Here we report the crystal structure of the C-terminal domain of gp16 (gp16-CTD). Structure-based alignment and molecular dynamics simulations revealed an essential binding surface of gp16-CTD for prohead RNA, a unique component of the motor complex. Furthermore, our simulations highlighted a dynamic interplay between the N-terminal domain and the CTD of gp16, which may play a role in driving movement of DNA into the procapsid. Lastly, we assembled an atomic structural model of the complete varphi29 dsDNA packaging motor complex by integrating structural and experimental data from multiple sources. Collectively, our findings provided a refined inchworm-revolution model for dsDNA translocation in bacteriophage varphi29 and suggested how the individual domains of gp16 work together to power such translocation.	+
-		+
-	Structural Insights into gp16 ATPase in the Bacteriophage varphi29 DNA Packaging Motor.,Saeed AFUH, Chan C, Guan H, Gong B, Guo P, Cheng X, Ouyang S Biochemistry. 2021 Mar 23;60(11):886-897. doi: 10.1021/acs.biochem.0c00935. Epub , 2021 Mar 9. PMID:33689296<ref>PMID:33689296</ref>	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class="pdbe-citations 7cnb" style="background-color:#fffaf0;"></div~~>	+
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Bpph2~~]]	+	[[Category: Bacillus virus phi29]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Ouyang~~, S Y~~]]	+	[[Category: Ouyang SY]]
-	[[Category: Saeed~~, A F.U H]]~~	+	[[Category: Saeed AFUH]]
-	~~[[Category: Crystal structure of gp16 c-terminal domain from bacillus virus phi29]]~~	+
-	~~[[Category: Motor protein~~]]	+

OCA at 07:11, 7 April 2021

2021-04-07T07:11:46Z

←Older revision		Revision as of 07:11, 7 April 2021
Line 3:		Line 3:
	<StructureSection load='7cnb' size='340' side='right'caption='[[7cnb]], [[Resolution\|resolution]] 2.32Å' scene=''>		<StructureSection load='7cnb' size='340' side='right'caption='[[7cnb]], [[Resolution\|resolution]] 2.32Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[7cnb]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7CNB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7CNB FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7cnb]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Bpph2 Bpph2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7CNB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7CNB 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=7cnb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7cnb OCA], [https://pdbe.org/7cnb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7cnb RCSB], [https://www.ebi.ac.uk/pdbsum/7cnb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7cnb ProSAT]</span></td></tr>	+	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">16 ([https://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'>[https://proteopedia.org/fgij/fg.htm?mol=7cnb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7cnb OCA], [https://pdbe.org/7cnb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7cnb RCSB], [https://www.ebi.ac.uk/pdbsum/7cnb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7cnb ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 21:		Line 22:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Bpph2]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Ouyang, S Y]]		[[Category: Ouyang, S Y]]

OCA at 10:47, 31 March 2021

2021-03-31T10:47:56Z

←Older revision		Revision as of 10:47, 31 March 2021
Line 1:		Line 1:

	==Crystal structure of Gp16 C-terminal domain from Bacillus virus phi29==		==Crystal structure of Gp16 C-terminal domain from Bacillus virus phi29==
-	<StructureSection load='7cnb' size='340' side='right'caption='[[7cnb]]' scene=''>	+	<StructureSection load='7cnb' size='340' side='right'caption='[[7cnb]], [[Resolution\|resolution]] 2.32Å' 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=7CNB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7CNB FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7cnb]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7CNB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7CNB 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=7cnb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7cnb OCA], [https://pdbe.org/7cnb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7cnb RCSB], [https://www.ebi.ac.uk/pdbsum/7cnb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7cnb ProSAT]</span></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=7cnb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7cnb OCA], [https://pdbe.org/7cnb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7cnb RCSB], [https://www.ebi.ac.uk/pdbsum/7cnb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7cnb ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[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;">
		+	== Publication Abstract from PubMed ==
		+	Biological motors, ubiquitous in living systems, convert chemical energy into different kinds of mechanical motions critical to cellular functions. Gene product 16 (gp16) in bacteriophage varphi29 is among the most powerful biomotors known, which adopts a multisubunit ring-shaped structure and hydrolyzes ATP to package double-stranded DNA (dsDNA) into a preformed procapsid. Here we report the crystal structure of the C-terminal domain of gp16 (gp16-CTD). Structure-based alignment and molecular dynamics simulations revealed an essential binding surface of gp16-CTD for prohead RNA, a unique component of the motor complex. Furthermore, our simulations highlighted a dynamic interplay between the N-terminal domain and the CTD of gp16, which may play a role in driving movement of DNA into the procapsid. Lastly, we assembled an atomic structural model of the complete varphi29 dsDNA packaging motor complex by integrating structural and experimental data from multiple sources. Collectively, our findings provided a refined inchworm-revolution model for dsDNA translocation in bacteriophage varphi29 and suggested how the individual domains of gp16 work together to power such translocation.
		+
		+	Structural Insights into gp16 ATPase in the Bacteriophage varphi29 DNA Packaging Motor.,Saeed AFUH, Chan C, Guan H, Gong B, Guo P, Cheng X, Ouyang S Biochemistry. 2021 Mar 23;60(11):886-897. doi: 10.1021/acs.biochem.0c00935. Epub , 2021 Mar 9. PMID:33689296<ref>PMID:33689296</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7cnb" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Ouyang SY]]	+	[[Category: Ouyang, S Y]]
-	[[Category: Saeed ~~AFUH~~]]	+	[[Category: Saeed, A F.U H]]
		+	[[Category: Crystal structure of gp16 c-terminal domain from bacillus virus phi29]]
		+	[[Category: Motor protein]]

OCA at 06:40, 24 March 2021

2021-03-24T06:40:19Z

←Older revision		Revision as of 06:40, 24 March 2021
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 7cnb ~~is ON HOLD until Jul 30 2022~~	+	==Crystal structure of Gp16 C-terminal domain from Bacillus virus phi29==
-		+	<StructureSection load='7cnb' size='340' side='right'caption='[[7cnb]]' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7CNB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7CNB FirstGlance]. <br>
-	~~Description~~:	+	</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=7cnb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7cnb OCA], [https://pdbe.org/7cnb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7cnb RCSB], [https://www.ebi.ac.uk/pdbsum/7cnb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7cnb ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Ouyang SY]]
		+	[[Category: Saeed AFUH]]

OCA at 07:29, 9 September 2020

2020-09-09T07:29:27Z

←Older revision		Revision as of 07:29, 9 September 2020
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 7cnb is ON HOLD	+	The entry 7cnb is ON HOLD until Jul 30 2022

	Authors:		Authors:

OCA: Protected "7cnb" [edit=sysop:move=sysop]

2020-08-05T04:12:23Z

Protected "7cnb" [edit=sysop:move=sysop]

←Older revision

Revision as of 04:12, 5 August 2020

OCA: New page: '''Unreleased structure''' The entry 7cnb is ON HOLD Authors: Description: Category: Unreleased Structures

2020-08-05T04:12:21Z

New page: '''Unreleased structure''' The entry 7cnb is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 7cnb is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]