6bef - Revision history

OCA at 14:39, 4 October 2023

2023-10-04T14:39:15Z

←Older revision		Revision as of 14:39, 4 October 2023
Line 3:		Line 3:
	<StructureSection load='6bef' size='340' side='right'caption='[[6bef]], [[Resolution\|resolution]] 3.21Å' scene=''>		<StructureSection load='6bef' size='340' side='right'caption='[[6bef]], [[Resolution\|resolution]] 3.21Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6bef]] is a 3 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Vaccw Vaccw~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6BEF OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6BEF FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6bef]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Vaccinia_virus_WR Vaccinia virus WR]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6BEF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6BEF FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=3YI:(2S,12Z,14E,16S,17S,18R,19R,20R,21S,22R,23S,24E)-8-formyl-5,6,9,17,19-pentahydroxy-23-methoxy-2,4,12,16,18,20,22-~~heptamethyl~~-1,11-dioxo-1,2-dihydro-2,7-(epoxypentadeca[1,11,13]trienoimino)naphtho[2,1-b]furan-21-yl+acetate'>3YI</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=FMT:FORMIC+ACID'>FMT</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]] 3.21Å</td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[6beb\|6beb]], [[6bec\|6bec]], [[6bed\|6bed]], [[6bee\|6bee]], [[6beg\|6beg]], [[6beh\|6beh]], [[6bei\|6bei]]</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=3YI:(2S,12Z,14E,16S,17S,18R,19R,20R,21S,22R,23S,24E)-8-formyl-5,6,9,17,19-pentahydroxy-23-methoxy-2,4,12,16,18,20,22-heptam+ethyl-1,11-dioxo-1,2-dihydro-2,7-(epoxypentadeca[1,11,13]trienoimino)naphtho[2,1-b]furan-21-yl+acetate'>3YI</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene></td></tr>
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">VACWR118, D13L ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10254 VACCW])~~</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=6bef FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6bef OCA], [https://pdbe.org/6bef PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6bef RCSB], [https://www.ebi.ac.uk/pdbsum/6bef PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6bef 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=6bef FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6bef OCA], [~~http~~://pdbe.org/6bef PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6bef RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6bef PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6bef ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/D13_VACCW D13_VACCW]] Scaffold protein which forms a transitory spherical honeycomb lattice providing curvature and rigidity to the convex membrane of crescent and immature virions (IV). This association occurs concomitantly with viral membrane formation. Targeted by the drug rifampicin, which prevents the formation of this lattice, and hence virus morphogenesis. In the presence of rifampicin, irregularly shaped membranes that lack the honeycomb layer accumulate around areas of electron-dense viroplasm. This layer is lost from virions during maturation from IV to mature virion (MV), through the proteolysis of A17 N-terminus.	+	[https://www.uniprot.org/uniprot/D13_VACCW D13_VACCW] Scaffold protein which forms a transitory spherical honeycomb lattice providing curvature and rigidity to the convex membrane of crescent and immature virions (IV). This association occurs concomitantly with viral membrane formation. Targeted by the drug rifampicin, which prevents the formation of this lattice, and hence virus morphogenesis. In the presence of rifampicin, irregularly shaped membranes that lack the honeycomb layer accumulate around areas of electron-dense viroplasm. This layer is lost from virions during maturation from IV to mature virion (MV), through the proteolysis of A17 N-terminus.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 25:		Line 24:
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Vaccw~~]]	+	[[Category: Vaccinia virus WR]]
-	[[Category: Accurso, C]]	+	[[Category: Accurso C]]
-	[[Category: Coulibaly, F]]	+	[[Category: Coulibaly F]]
-	[[Category: Garriga, D]]	+	[[Category: Garriga D]]
-	~~[[Category: Assembly]]~~	+
-	~~[[Category: Immature virion]]~~	+
-	~~[[Category: Poxvirus]]~~	+
-	~~[[Category: Rifampicin resistance protein]]~~	+
-	~~[[Category: Scaffolding protein]]~~	+
-	~~[[Category: Viral protein~~]]	+

OCA at 08:34, 8 January 2020

2020-01-08T08:34:12Z

←Older revision		Revision as of 08:34, 8 January 2020
Line 1:		Line 1:

	==Crystal structure of VACV D13 in complex with 3-formyl rifamycin SV==		==Crystal structure of VACV D13 in complex with 3-formyl rifamycin SV==
-	<StructureSection load='6bef' size='340' side='right' caption='[[6bef]], [[Resolution\|resolution]] 3.21Å' scene=''>	+	<StructureSection load='6bef' size='340' side='right'caption='[[6bef]], [[Resolution\|resolution]] 3.21Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[6bef]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Vaccw Vaccw]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6BEF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6BEF FirstGlance]. <br>		<table><tr><td colspan='2'>[[6bef]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Vaccw Vaccw]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6BEF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6BEF FirstGlance]. <br>
Line 24:		Line 24:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Vaccw]]		[[Category: Vaccw]]
	[[Category: Accurso, C]]		[[Category: Accurso, C]]

OCA at 16:36, 15 August 2018

2018-08-15T16:36:36Z

←Older revision		Revision as of 16:36, 15 August 2018
Line 11:		Line 11:
	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/D13_VACCW D13_VACCW]] Scaffold protein which forms a transitory spherical honeycomb lattice providing curvature and rigidity to the convex membrane of crescent and immature virions (IV). This association occurs concomitantly with viral membrane formation. Targeted by the drug rifampicin, which prevents the formation of this lattice, and hence virus morphogenesis. In the presence of rifampicin, irregularly shaped membranes that lack the honeycomb layer accumulate around areas of electron-dense viroplasm. This layer is lost from virions during maturation from IV to mature virion (MV), through the proteolysis of A17 N-terminus.		[[http://www.uniprot.org/uniprot/D13_VACCW D13_VACCW]] Scaffold protein which forms a transitory spherical honeycomb lattice providing curvature and rigidity to the convex membrane of crescent and immature virions (IV). This association occurs concomitantly with viral membrane formation. Targeted by the drug rifampicin, which prevents the formation of this lattice, and hence virus morphogenesis. In the presence of rifampicin, irregularly shaped membranes that lack the honeycomb layer accumulate around areas of electron-dense viroplasm. This layer is lost from virions during maturation from IV to mature virion (MV), through the proteolysis of A17 N-terminus.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Poxviruses are large DNA viruses that cause disease in animals and humans. They differ from classical enveloped viruses, because their membrane is acquired from cytoplasmic membrane precursors assembled onto a viral protein scaffold formed by the D13 protein rather than budding through cellular compartments. It was found three decades ago that the antibiotic rifampicin blocks this process and prevents scaffold formation. To elucidate the mechanism of action of rifampicin, we have determined the crystal structures of six D13-rifamycin complexes. These structures reveal that rifamycin compounds bind to a phenylalanine-rich region, or F-ring, at the membrane-proximal opening of the central channel of the D13 trimer. We show by NMR, surface plasmon resonance (SPR), and site-directed mutagenesis that A17, a membrane-associated viral protein, mediates the recruitment of the D13 scaffold by also binding to the F-ring. This interaction is the target of rifampicin, which prevents A17 binding, explaining the inhibition of viral morphogenesis. The F-ring of D13 is both conserved in sequence in mammalian poxviruses and essential for interaction with A17, defining a target for the development of assembly inhibitors. The model of the A17-D13 interaction describes a two-component system for remodeling nascent membranes that may be conserved in other large and giant DNA viruses.
		+
		+	Structural basis for the inhibition of poxvirus assembly by the antibiotic rifampicin.,Garriga D, Headey S, Accurso C, Gunzburg M, Scanlon M, Coulibaly F Proc Natl Acad Sci U S A. 2018 Aug 1. pii: 1810398115. doi:, 10.1073/pnas.1810398115. PMID:30068608<ref>PMID:30068608</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6bef" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 19:05, 1 August 2018

2018-08-01T19:05:59Z

←Older revision		Revision as of 19:05, 1 August 2018
Line 3:		Line 3:
	<StructureSection load='6bef' size='340' side='right' caption='[[6bef]], [[Resolution\|resolution]] 3.21Å' scene=''>		<StructureSection load='6bef' size='340' side='right' caption='[[6bef]], [[Resolution\|resolution]] 3.21Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6bef]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6BEF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6BEF FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6bef]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Vaccw Vaccw]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6BEF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6BEF FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=3YI:(2S,12Z,14E,16S,17S,18R,19R,20R,21S,22R,23S,24E)-8-formyl-5,6,9,17,19-pentahydroxy-23-methoxy-2,4,12,16,18,20,22-heptamethyl-1,11-dioxo-1,2-dihydro-2,7-(epoxypentadeca[1,11,13]trienoimino)naphtho[2,1-b]furan-21-yl+acetate'>3YI</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=3YI:(2S,12Z,14E,16S,17S,18R,19R,20R,21S,22R,23S,24E)-8-formyl-5,6,9,17,19-pentahydroxy-23-methoxy-2,4,12,16,18,20,22-heptamethyl-1,11-dioxo-1,2-dihydro-2,7-(epoxypentadeca[1,11,13]trienoimino)naphtho[2,1-b]furan-21-yl+acetate'>3YI</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[6beb\|6beb]], [[6bec\|6bec]], [[6bed\|6bed]], [[6bee\|6bee]], [[6beg\|6beg]], [[6beh\|6beh]], [[6bei\|6bei]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[6beb\|6beb]], [[6bec\|6bec]], [[6bed\|6bed]], [[6bee\|6bee]], [[6beg\|6beg]], [[6beh\|6beh]], [[6bei\|6bei]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">VACWR118, D13L ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10254 VACCW])</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=6bef FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6bef OCA], [http://pdbe.org/6bef PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6bef RCSB], [http://www.ebi.ac.uk/pdbsum/6bef PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6bef 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=6bef FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6bef OCA], [http://pdbe.org/6bef PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6bef RCSB], [http://www.ebi.ac.uk/pdbsum/6bef PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6bef ProSAT]</span></td></tr>
	</table>		</table>
Line 12:		Line 13:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Vaccw]]
	[[Category: Accurso, C]]		[[Category: Accurso, C]]
	[[Category: Coulibaly, F]]		[[Category: Coulibaly, F]]

OCA at 07:34, 18 July 2018

2018-07-18T07:34:18Z

←Older revision		Revision as of 07:34, 18 July 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6bef is ~~ON HOLD until Paper Publication~~	+	==Crystal structure of VACV D13 in complex with 3-formyl rifamycin SV==
-		+	<StructureSection load='6bef' size='340' side='right' caption='[[6bef]], [[Resolution\|resolution]] 3.21Å' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[6bef]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6BEF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6BEF FirstGlance]. <br>
-	~~Description~~:	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=3YI:(2S,12Z,14E,16S,17S,18R,19R,20R,21S,22R,23S,24E)-8-formyl-5,6,9,17,19-pentahydroxy-23-methoxy-2,4,12,16,18,20,22-heptamethyl-1,11-dioxo-1,2-dihydro-2,7-(epoxypentadeca[1,11,13]trienoimino)naphtho[2,1-b]furan-21-yl+acetate'>3YI</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[6beb\|6beb]], [[6bec\|6bec]], [[6bed\|6bed]], [[6bee\|6bee]], [[6beg\|6beg]], [[6beh\|6beh]], [[6bei\|6bei]]</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=6bef FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6bef OCA], [http://pdbe.org/6bef PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6bef RCSB], [http://www.ebi.ac.uk/pdbsum/6bef PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6bef ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/D13_VACCW D13_VACCW]] Scaffold protein which forms a transitory spherical honeycomb lattice providing curvature and rigidity to the convex membrane of crescent and immature virions (IV). This association occurs concomitantly with viral membrane formation. Targeted by the drug rifampicin, which prevents the formation of this lattice, and hence virus morphogenesis. In the presence of rifampicin, irregularly shaped membranes that lack the honeycomb layer accumulate around areas of electron-dense viroplasm. This layer is lost from virions during maturation from IV to mature virion (MV), through the proteolysis of A17 N-terminus.
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Accurso, C]]
		+	[[Category: Coulibaly, F]]
		+	[[Category: Garriga, D]]
		+	[[Category: Assembly]]
		+	[[Category: Immature virion]]
		+	[[Category: Poxvirus]]
		+	[[Category: Rifampicin resistance protein]]
		+	[[Category: Scaffolding protein]]
		+	[[Category: Viral protein]]

OCA at 12:23, 11 April 2018

2018-04-11T12:23:07Z

←Older revision		Revision as of 12:23, 11 April 2018
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors:		Authors:

OCA at 04:56, 28 February 2018

2018-02-28T04:56:48Z

←Older revision		Revision as of 04:56, 28 February 2018
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6bef is ON HOLD ~~until Paper Publication~~	+	The entry 6bef is ON HOLD

	Authors:		Authors:

OCA at 05:50, 13 December 2017

2017-12-13T05:50:31Z

←Older revision		Revision as of 05:50, 13 December 2017
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors:		Authors:

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

2017-11-01T04:59:37Z

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

←Older revision

Revision as of 04:59, 1 November 2017

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

2017-11-01T04:59:35Z

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

New page

'''Unreleased structure'''

The entry 6bef is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]