5uf6 - Revision history

OCA at 14:26, 6 March 2024

OCA — Wed, 06 Mar 2024 14:26:50 GMT

←Older revision		Revision as of 14:26, 6 March 2024
Line 3:		Line 3:
	<SX load='5uf6' size='340' side='right' viewer='molstar' caption='[[5uf6]], [[Resolution\|resolution]] 2.80Å' scene=''>		<SX load='5uf6' size='340' side='right' viewer='molstar' caption='[[5uf6]], [[Resolution\|resolution]] 2.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5uf6]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Adeno-associated_virus Adeno-associated virus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5UF6 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5UF6 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5uf6]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Adeno-associated_virus Adeno-associated virus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5UF6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5UF6 FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=NTO:TRISULFOAMINO+HEPARIN+PENTASACCHARIDE'>NTO</scene>~~</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]] 2.8Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~CAPSID ([http~~://~~www.ncbi.nlm.nih.gov~~/~~Taxonomy/Browser~~/~~wwwtax.cgi?mode~~=~~Info&srchmode~~=~~5&id~~=~~272636 Adeno~~-~~associated virus]~~)</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BDP:BETA-D-GLUCOPYRANURONIC+ACID'>BDP</scene>, <scene name='pdbligand=IDS:2-O-SULFO-ALPHA-L-IDOPYRANURONIC+ACID'>IDS</scene>, <scene name='pdbligand=PRD_900028:fondaparinux'>PRD_900028</scene>, <scene name='pdbligand=SGN:N,O6-DISULFO-GLUCOSAMINE'>SGN</scene>, <scene name='pdbligand=SUS:2-DEOXY-3,6-DI-O-SULFO-2-(SULFOAMINO)-ALPHA-D-GLUCOPYRANOSE'>SUS</scene>, <scene name='pdbligand=ZDO:methyl+2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranoside'>ZDO</scene></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=5uf6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5uf6 OCA], [~~http~~://pdbe.org/5uf6 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5uf6 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5uf6 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5uf6 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=5uf6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5uf6 OCA], [https://pdbe.org/5uf6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5uf6 RCSB], [https://www.ebi.ac.uk/pdbsum/5uf6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5uf6 ProSAT]</span></td></tr>
	</table>		</table>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Atomic structures of adeno-associated virus (AAV)-DJ, alone and in complex with fondaparinux, have been determined by cryoelectron microscopy at 3 A resolution. The gene therapy vector, AAV-DJ, is a hybrid of natural serotypes that was previously derived by directed evolution, selecting for hepatocyte entry and resistance to neutralization by human serum. The structure of AAV-DJ differs from that of parental serotypes in two regions where neutralizing antibodies bind, so immune escape appears to have been the primary driver of AAV-DJ's directed evolution. Fondaparinux is an analog of cell surface heparan sulfate to which several AAVs bind during entry. Fondaparinux interacts with viral arginines at a known heparin binding site, without the large conformational changes whose presence was controversial in low-resolution imaging of AAV2-heparin complexes. The glycan density suggests multi-modal binding that could accommodate sequence variation and multivalent binding along a glycan polymer, consistent with a role in attachment, prior to more specific interactions with a receptor protein mediating entry.

-	The 2.8 A Electron Microscopy Structure of Adeno-Associated Virus-DJ Bound by a Heparinoid Pentasaccharide.,Xie Q, Spear JM, Noble AJ, Sousa DR, Meyer NL, Davulcu O, Zhang F, Linhardt RJ, Stagg SM, Chapman MS Mol Ther Methods Clin Dev. 2017 Mar 8;5:1-12. doi: 10.1016/j.omtm.2017.02.004., eCollection 2017 Jun 16. PMID:28480299<ref>PMID:28480299</ref>	+	==See Also==
-		+	*[[Virus coat proteins 3D structures\|Virus coat proteins 3D structures]]
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class~~=~~"pdbe-citations 5uf6" style~~=~~"background-color:#fffaf0;"></div>~~	+
-	~~== References~~ ==	+
-	~~<references/>~~	+
	__TOC__		__TOC__
	</SX>		</SX>
	[[Category: Adeno-associated virus]]		[[Category: Adeno-associated virus]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Chapman, M]]	+	[[Category: Chapman M]]
-	[[Category: Davulcu, O]]	+	[[Category: Davulcu O]]
-	[[Category: Linhardt~~, R J~~]]	+	[[Category: Linhardt RJ]]
-	[[Category: Meyer~~, N L~~]]	+	[[Category: Meyer NL]]
-	[[Category: Noble~~, A J~~]]	+	[[Category: Noble AJ]]
-	[[Category: Sousa~~, D R~~]]	+	[[Category: Sousa DR]]
-	[[Category: Spear~~, J M~~]]	+	[[Category: Spear JM]]
-	[[Category: Stagg~~, S M~~]]	+	[[Category: Stagg SM]]
-	[[Category: Xie, Q]]	+	[[Category: Xie Q]]
-	[[Category: Zhang, F]]	+	[[Category: Zhang F]]
-	~~[[Category: Attachment]]~~	+
-	~~[[Category: Glycan]]~~	+
-	~~[[Category: Receptor]]~~	+
-	~~[[Category: Virus like particle~~]]	+

OCA at 21:53, 10 April 2020

OCA — Fri, 10 Apr 2020 21:53:44 GMT

←Older revision		Revision as of 21:53, 10 April 2020
Line 3:		Line 3:
	<SX load='5uf6' size='340' side='right' viewer='molstar' caption='[[5uf6]], [[Resolution\|resolution]] 2.80Å' scene=''>		<SX load='5uf6' size='340' side='right' viewer='molstar' caption='[[5uf6]], [[Resolution\|resolution]] 2.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5uf6]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Adeno-associated_virus Adeno-associated virus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5UF6 OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5UF6 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5uf6]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Adeno-associated_virus Adeno-associated virus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5UF6 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5UF6 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NTO:TRISULFOAMINO+HEPARIN+PENTASACCHARIDE'>NTO</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NTO:TRISULFOAMINO+HEPARIN+PENTASACCHARIDE'>NTO</scene></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">CAPSID ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=272636 Adeno-associated virus])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">CAPSID ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=272636 Adeno-associated virus])</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=5uf6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5uf6 OCA], [http://pdbe.org/5uf6 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5uf6 RCSB], [http://www.ebi.ac.uk/pdbsum/5uf6 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5uf6 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=5uf6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5uf6 OCA], [http://pdbe.org/5uf6 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5uf6 RCSB], [http://www.ebi.ac.uk/pdbsum/5uf6 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5uf6 ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 19:42, 6 March 2020

OCA — Fri, 06 Mar 2020 19:42:46 GMT

←Older revision		Revision as of 19:42, 6 March 2020
Line 1:		Line 1:

	==The 2.8 A Electron Microscopy Structure of Adeno-Associated Virus-DJ Bound by a Heparanoid Pentasaccharide==		==The 2.8 A Electron Microscopy Structure of Adeno-Associated Virus-DJ Bound by a Heparanoid Pentasaccharide==
-	<~~StructureSection~~ load='5uf6' size='340' side='right'caption='[[5uf6]], [[Resolution\|resolution]] 2.80Å' scene=''>	+	<SX load='5uf6' size='340' side='right' viewer='molstar' caption='[[5uf6]], [[Resolution\|resolution]] 2.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5uf6]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Adeno-associated_virus Adeno-associated virus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5UF6 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5UF6 FirstGlance]. <br>		<table><tr><td colspan='2'>[[5uf6]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Adeno-associated_virus Adeno-associated virus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5UF6 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5UF6 FirstGlance]. <br>
Line 20:		Line 20:
	<references/>		<references/>
	__TOC__		__TOC__
-	</~~StructureSection~~>	+	</SX>
	[[Category: Adeno-associated virus]]		[[Category: Adeno-associated virus]]
	[[Category: Large Structures]]		[[Category: Large Structures]]

OCA at 09:15, 1 January 2020

OCA — Wed, 01 Jan 2020 09:15:31 GMT

←Older revision		Revision as of 09:15, 1 January 2020
Line 1:		Line 1:

	==The 2.8 A Electron Microscopy Structure of Adeno-Associated Virus-DJ Bound by a Heparanoid Pentasaccharide==		==The 2.8 A Electron Microscopy Structure of Adeno-Associated Virus-DJ Bound by a Heparanoid Pentasaccharide==
-	<StructureSection load='5uf6' size='340' side='right' caption='[[5uf6]], [[Resolution\|resolution]] 2.80Å' scene=''>	+	<StructureSection load='5uf6' size='340' side='right'caption='[[5uf6]], [[Resolution\|resolution]] 2.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5uf6]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5UF6 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5UF6 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5uf6]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Adeno-associated_virus Adeno-associated virus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5UF6 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5UF6 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NTO:TRISULFOAMINO+HEPARIN+PENTASACCHARIDE'>NTO</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NTO:TRISULFOAMINO+HEPARIN+PENTASACCHARIDE'>NTO</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">CAPSID ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=272636 Adeno-associated virus])</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=5uf6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5uf6 OCA], [http://pdbe.org/5uf6 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5uf6 RCSB], [http://www.ebi.ac.uk/pdbsum/5uf6 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5uf6 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=5uf6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5uf6 OCA], [http://pdbe.org/5uf6 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5uf6 RCSB], [http://www.ebi.ac.uk/pdbsum/5uf6 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5uf6 ProSAT]</span></td></tr>
	</table>		</table>
Line 20:		Line 21:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Adeno-associated virus]]
		+	[[Category: Large Structures]]
	[[Category: Chapman, M]]		[[Category: Chapman, M]]
	[[Category: Davulcu, O]]		[[Category: Davulcu, O]]

OCA at 13:40, 24 May 2017

OCA — Wed, 24 May 2017 13:40:57 GMT

←Older revision		Revision as of 13:40, 24 May 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	The ~~entry~~ 5uf6 is ~~ON HOLD~~	+	==The 2.8 A Electron Microscopy Structure of Adeno-Associated Virus-DJ Bound by a Heparanoid Pentasaccharide==
		+	<StructureSection load='5uf6' size='340' side='right' caption='[[5uf6]], [[Resolution\|resolution]] 2.80Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5uf6]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5UF6 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5UF6 FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NTO:TRISULFOAMINO+HEPARIN+PENTASACCHARIDE'>NTO</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=5uf6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5uf6 OCA], [http://pdbe.org/5uf6 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5uf6 RCSB], [http://www.ebi.ac.uk/pdbsum/5uf6 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5uf6 ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Atomic structures of adeno-associated virus (AAV)-DJ, alone and in complex with fondaparinux, have been determined by cryoelectron microscopy at 3 A resolution. The gene therapy vector, AAV-DJ, is a hybrid of natural serotypes that was previously derived by directed evolution, selecting for hepatocyte entry and resistance to neutralization by human serum. The structure of AAV-DJ differs from that of parental serotypes in two regions where neutralizing antibodies bind, so immune escape appears to have been the primary driver of AAV-DJ's directed evolution. Fondaparinux is an analog of cell surface heparan sulfate to which several AAVs bind during entry. Fondaparinux interacts with viral arginines at a known heparin binding site, without the large conformational changes whose presence was controversial in low-resolution imaging of AAV2-heparin complexes. The glycan density suggests multi-modal binding that could accommodate sequence variation and multivalent binding along a glycan polymer, consistent with a role in attachment, prior to more specific interactions with a receptor protein mediating entry.

-	~~Authors~~:	+	The 2.8 A Electron Microscopy Structure of Adeno-Associated Virus-DJ Bound by a Heparinoid Pentasaccharide.,Xie Q, Spear JM, Noble AJ, Sousa DR, Meyer NL, Davulcu O, Zhang F, Linhardt RJ, Stagg SM, Chapman MS Mol Ther Methods Clin Dev. 2017 Mar 8;5:1-12. doi: 10.1016/j.omtm.2017.02.004., eCollection 2017 Jun 16. PMID:28480299<ref>PMID:28480299</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 5uf6" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Chapman, M]]
		+	[[Category: Davulcu, O]]
		+	[[Category: Linhardt, R J]]
		+	[[Category: Meyer, N L]]
		+	[[Category: Noble, A J]]
		+	[[Category: Sousa, D R]]
		+	[[Category: Spear, J M]]
		+	[[Category: Stagg, S M]]
		+	[[Category: Xie, Q]]
		+	[[Category: Zhang, F]]
		+	[[Category: Attachment]]
		+	[[Category: Glycan]]
		+	[[Category: Receptor]]
		+	[[Category: Virus like particle]]

OCA at 14:25, 9 March 2017

OCA — Thu, 09 Mar 2017 14:25:04 GMT

←Older revision		Revision as of 14:25, 9 March 2017
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5uf6 is ON HOLD ~~until sometime in the future~~	+	The entry 5uf6 is ON HOLD

	Authors:		Authors:

OCA: Protected "5uf6" [edit=sysop:move=sysop]

OCA — Wed, 18 Jan 2017 14:50:14 GMT

Protected "5uf6" [edit=sysop:move=sysop]

←Older revision

Revision as of 14:50, 18 January 2017

OCA: New page: '''Unreleased structure''' The entry 5uf6 is ON HOLD until sometime in the future Authors: Description: Category: Unreleased Structures

OCA — Wed, 18 Jan 2017 14:50:13 GMT

New page: '''Unreleased structure''' The entry 5uf6 is ON HOLD until sometime in the future Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 5uf6 is ON HOLD until sometime in the future

Authors:

Description:
[[Category: Unreleased Structures]]