6omc - Revision history

OCA at 09:24, 20 March 2024

OCA — Wed, 20 Mar 2024 09:24:49 GMT

←Older revision		Revision as of 09:24, 20 March 2024
Line 3:		Line 3:
	<SX load='6omc' size='340' side='right' viewer='molstar' caption='[[6omc]], [[Resolution\|resolution]] 3.80Å' scene=''>		<SX load='6omc' size='340' side='right' viewer='molstar' caption='[[6omc]], [[Resolution\|resolution]] 3.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6omc]] is a 13 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Escherichia_phage_t5~~ Escherichia ~~phage t5~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6OMC OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6OMC FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6omc]] is a 13 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_virus_T5 Escherichia virus T5]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6OMC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6OMC 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=6omc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6omc OCA], [~~http~~://pdbe.org/6omc PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6omc RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6omc PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6omc 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]] 3.8Å</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=6omc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6omc OCA], [https://pdbe.org/6omc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6omc RCSB], [https://www.ebi.ac.uk/pdbsum/6omc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6omc ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/CAPSD_BPT5 CAPSD_BPT5]] Major capsid protein that self-associates to form 120 hexamers and 11 pentamers, building the T=13 icosahedral capsid which about 860 Angstroms in diameter. Responsible for its self-assembly into a procapsid. The phage does not need to encode a separate scaffolfing protein because its capsid protein contains the delta domain that carries that function. The capsid gains its final stability through the reorganization of the subunits that takes place upon expansion. DNA encapsidation through the portal triggers capsid expansion and the binding of the decoration protein to the capsid exterior.<ref>PMID:20573812</ref> <ref>PMID:23500494</ref> <ref>PMID:26616586</ref>	+	[https://www.uniprot.org/uniprot/CAPSD_BPT5 CAPSD_BPT5] Major capsid protein that self-associates to form 120 hexamers and 11 pentamers, building the T=13 icosahedral capsid which about 860 Angstroms in diameter. Responsible for its self-assembly into a procapsid. The phage does not need to encode a separate scaffolfing protein because its capsid protein contains the delta domain that carries that function. The capsid gains its final stability through the reorganization of the subunits that takes place upon expansion. DNA encapsidation through the portal triggers capsid expansion and the binding of the decoration protein to the capsid exterior.<ref>PMID:20573812</ref> <ref>PMID:23500494</ref> <ref>PMID:26616586</ref>
-	~~<div style="background-color:#fffaf0;">~~	+
-	~~== Publication Abstract from PubMed ==~~	+
-	The large (90-nm) icosahedral capsid of bacteriophage T5 is composed of 775 copies of the major capsid protein (mcp) together with portal, protease, and decoration proteins. Its assembly is a regulated process that involves several intermediates, including a thick-walled round precursor prohead that expands as the viral DNA is packaged to yield a thin-walled and angular mature capsid. We investigated capsid maturation by comparing cryoelectron microscopy (cryo-EM) structures of the prohead, the empty expanded capsid both with and without decoration protein, and the virion capsid at a resolution of 3.8 A for the latter. We detail the molecular structure of the mcp, its complex pattern of interactions, and their evolution during maturation. The bacteriophage T5 mcp is a variant of the canonical HK97-fold with a high level of plasticity that allows for the precise assembly of a giant macromolecule and the adaptability needed to interact with other proteins and the packaged DNA.	+
-		+
-	Capsid expansion of bacteriophage T5 revealed by high resolution cryoelectron microscopy.,Huet A, Duda RL, Boulanger P, Conway JF Proc Natl Acad Sci U S A. 2019 Oct 15;116(42):21037-21046. doi:, 10.1073/pnas.1909645116. Epub 2019 Oct 2. PMID:31578255<ref>PMID:31578255</ref>	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class="pdbe-citations 6omc" style="background-color:#fffaf0;"></div~~>	+
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</SX>		</SX>
-	[[Category: Escherichia ~~phage t5~~]]	+	[[Category: Escherichia virus T5]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Boulanger, P]]	+	[[Category: Boulanger P]]
-	[[Category: Conway~~, J F~~]]	+	[[Category: Conway JF]]
-	[[Category: Duda~~, R L~~]]	+	[[Category: Duda RL]]
-	[[Category: Huet, A]]	+	[[Category: Huet A]]
-	~~[[Category: Capsid]]~~	+
-	~~[[Category: Dsdna-phage]]~~	+
-	~~[[Category: Hk97-fold]]~~	+
-	~~[[Category: Icosahedral]]~~	+
-	~~[[Category: Virus~~]]	+

OCA at 04:06, 11 April 2020

OCA — Sat, 11 Apr 2020 04:06:18 GMT

←Older revision		Revision as of 04:06, 11 April 2020
Line 3:		Line 3:
	<SX load='6omc' size='340' side='right' viewer='molstar' caption='[[6omc]], [[Resolution\|resolution]] 3.80Å' scene=''>		<SX load='6omc' size='340' side='right' viewer='molstar' caption='[[6omc]], [[Resolution\|resolution]] 3.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6omc]] is a 13 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_phage_t5 Escherichia phage t5]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6OMC OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6OMC FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6omc]] is a 13 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_phage_t5 Escherichia phage t5]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6OMC OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6OMC FirstGlance]. <br>
-	</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=6omc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6omc OCA], [http://pdbe.org/6omc PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6omc RCSB], [http://www.ebi.ac.uk/pdbsum/6omc PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6omc ProSAT]</span></td></tr>	+	</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=6omc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6omc OCA], [http://pdbe.org/6omc PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6omc RCSB], [http://www.ebi.ac.uk/pdbsum/6omc PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6omc ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==

OCA at 04:38, 5 March 2020

OCA — Thu, 05 Mar 2020 04:38:54 GMT

←Older revision		Revision as of 04:38, 5 March 2020
Line 1:		Line 1:

	==capsid of T5 virion==		==capsid of T5 virion==
-	<~~StructureSection~~ load='6omc' size='340' side='right'caption='[[6omc]], [[Resolution\|resolution]] 3.80Å' scene=''>	+	<SX load='6omc' size='340' side='right' viewer='molstar' caption='[[6omc]], [[Resolution\|resolution]] 3.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[6omc]] is a 13 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_phage_t5 Escherichia phage t5]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6OMC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6OMC FirstGlance]. <br>		<table><tr><td colspan='2'>[[6omc]] is a 13 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_phage_t5 Escherichia phage t5]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6OMC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6OMC FirstGlance]. <br>
Line 20:		Line 20:
	<references/>		<references/>
	__TOC__		__TOC__
-	</~~StructureSection~~>	+	</SX>
	[[Category: Escherichia phage t5]]		[[Category: Escherichia phage t5]]
	[[Category: Large Structures]]		[[Category: Large Structures]]

OCA at 11:45, 13 November 2019

OCA — Wed, 13 Nov 2019 11:45:45 GMT

←Older revision		Revision as of 11:45, 13 November 2019
Line 8:		Line 8:
	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/CAPSD_BPT5 CAPSD_BPT5]] Major capsid protein that self-associates to form 120 hexamers and 11 pentamers, building the T=13 icosahedral capsid which about 860 Angstroms in diameter. Responsible for its self-assembly into a procapsid. The phage does not need to encode a separate scaffolfing protein because its capsid protein contains the delta domain that carries that function. The capsid gains its final stability through the reorganization of the subunits that takes place upon expansion. DNA encapsidation through the portal triggers capsid expansion and the binding of the decoration protein to the capsid exterior.<ref>PMID:20573812</ref> <ref>PMID:23500494</ref> <ref>PMID:26616586</ref>		[[http://www.uniprot.org/uniprot/CAPSD_BPT5 CAPSD_BPT5]] Major capsid protein that self-associates to form 120 hexamers and 11 pentamers, building the T=13 icosahedral capsid which about 860 Angstroms in diameter. Responsible for its self-assembly into a procapsid. The phage does not need to encode a separate scaffolfing protein because its capsid protein contains the delta domain that carries that function. The capsid gains its final stability through the reorganization of the subunits that takes place upon expansion. DNA encapsidation through the portal triggers capsid expansion and the binding of the decoration protein to the capsid exterior.<ref>PMID:20573812</ref> <ref>PMID:23500494</ref> <ref>PMID:26616586</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The large (90-nm) icosahedral capsid of bacteriophage T5 is composed of 775 copies of the major capsid protein (mcp) together with portal, protease, and decoration proteins. Its assembly is a regulated process that involves several intermediates, including a thick-walled round precursor prohead that expands as the viral DNA is packaged to yield a thin-walled and angular mature capsid. We investigated capsid maturation by comparing cryoelectron microscopy (cryo-EM) structures of the prohead, the empty expanded capsid both with and without decoration protein, and the virion capsid at a resolution of 3.8 A for the latter. We detail the molecular structure of the mcp, its complex pattern of interactions, and their evolution during maturation. The bacteriophage T5 mcp is a variant of the canonical HK97-fold with a high level of plasticity that allows for the precise assembly of a giant macromolecule and the adaptability needed to interact with other proteins and the packaged DNA.
		+
		+	Capsid expansion of bacteriophage T5 revealed by high resolution cryoelectron microscopy.,Huet A, Duda RL, Boulanger P, Conway JF Proc Natl Acad Sci U S A. 2019 Oct 15;116(42):21037-21046. doi:, 10.1073/pnas.1909645116. Epub 2019 Oct 2. PMID:31578255<ref>PMID:31578255</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6omc" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 10:29, 2 October 2019

OCA — Wed, 02 Oct 2019 10:29:15 GMT

←Older revision		Revision as of 10:29, 2 October 2019
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6omc ~~is ON HOLD until Paper Publication~~	+	==capsid of T5 virion==
-		+	<StructureSection load='6omc' size='340' side='right'caption='[[6omc]], [[Resolution\|resolution]] 3.80Å' scene=''>
-	~~Authors~~: ~~Huet~~, A., ~~Duda~~, R.L., ~~Boulanger, P~~., ~~Conway, J~~.F.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[6omc]] is a 13 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_phage_t5 Escherichia phage t5]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6OMC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6OMC FirstGlance]. <br>
-	~~Description~~: capsid of ~~T5 virion~~	+	</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=6omc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6omc OCA], [http://pdbe.org/6omc PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6omc RCSB], [http://www.ebi.ac.uk/pdbsum/6omc PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6omc ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/CAPSD_BPT5 CAPSD_BPT5]] Major capsid protein that self-associates to form 120 hexamers and 11 pentamers, building the T=13 icosahedral capsid which about 860 Angstroms in diameter. Responsible for its self-assembly into a procapsid. The phage does not need to encode a separate scaffolfing protein because its capsid protein contains the delta domain that carries that function. The capsid gains its final stability through the reorganization of the subunits that takes place upon expansion. DNA encapsidation through the portal triggers capsid expansion and the binding of the decoration protein to the capsid exterior.<ref>PMID:20573812</ref> <ref>PMID:23500494</ref> <ref>PMID:26616586</ref>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Escherichia phage t5]]
		+	[[Category: Large Structures]]
	[[Category: Boulanger, P]]		[[Category: Boulanger, P]]
-	[[Category: Duda, R.L]]	+	[[Category: Conway, J F]]
		+	[[Category: Duda, R L]]
	[[Category: Huet, A]]		[[Category: Huet, A]]
-	[[Category: ~~Conway, J.F~~]]	+	[[Category: Capsid]]
		+	[[Category: Dsdna-phage]]
		+	[[Category: Hk97-fold]]
		+	[[Category: Icosahedral]]
		+	[[Category: Virus]]

OCA at 21:05, 5 June 2019

OCA — Wed, 05 Jun 2019 21:05:01 GMT

←Older revision		Revision as of 21:05, 5 June 2019
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors: Huet, A., Duda, R.L., Boulanger, P., Conway, J.F.		Authors: Huet, A., Duda, R.L., Boulanger, P., Conway, J.F.

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

OCA — Wed, 24 Apr 2019 05:05:45 GMT

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

←Older revision

Revision as of 05:05, 24 April 2019

OCA: New page: '''Unreleased structure''' The entry 6omc is ON HOLD Authors: Huet, A., Duda, R.L., Boulanger, P., Conway, J.F. Description: capsid of T5 virion Category: Unreleased Structures [[C...

OCA — Wed, 24 Apr 2019 05:05:44 GMT

New page: '''Unreleased structure''' The entry 6omc is ON HOLD Authors: Huet, A., Duda, R.L., Boulanger, P., Conway, J.F. Description: capsid of T5 virion Category: Unreleased Structures [[C...

New page

'''Unreleased structure'''

The entry 6omc is ON HOLD

Authors: Huet, A., Duda, R.L., Boulanger, P., Conway, J.F.

Description: capsid of T5 virion
[[Category: Unreleased Structures]]
[[Category: Boulanger, P]]
[[Category: Duda, R.L]]
[[Category: Huet, A]]
[[Category: Conway, J.F]]