4ffy - Revision history

OCA at 04:54, 7 October 2022

OCA — Fri, 07 Oct 2022 04:54:46 GMT

←Older revision		Revision as of 04:54, 7 October 2022
Line 1:		Line 1:

	==Crystal structure of DENV1-E111 single chain variable fragment bound to DENV-1 DIII, strain 16007.==		==Crystal structure of DENV1-E111 single chain variable fragment bound to DENV-1 DIII, strain 16007.==
-	<StructureSection load='4ffy' size='340' side='right' caption='[[4ffy]], [[Resolution\|resolution]] 2.50Å' scene=''>	+	<StructureSection load='4ffy' size='340' side='right'caption='[[4ffy]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4ffy]] is a 3 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Dengue_virus_1 Dengue virus 1] and [~~http~~://en.wikipedia.org/wiki/~~Lk3_transgenic_mice Lk3 transgenic mice~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4FFY OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4FFY FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4ffy]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Dengue_virus_1 Dengue virus 1] and [https://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4FFY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4FFY FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>~~</td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3irc\|3irc]], [[4ffz\|4ffz]]</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=4ffy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ffy OCA], [https://pdbe.org/4ffy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4ffy RCSB], [https://www.ebi.ac.uk/pdbsum/4ffy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4ffy ProSAT]</span></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Envelope domain III ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=11053 Dengue virus 1])</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=4ffy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ffy OCA], [~~http~~://pdbe.org/4ffy PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4ffy RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4ffy PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4ffy ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/Q9J7C6_9FLAV Q9J7C6_9FLAV]] Envelope protein E binding to host cell surface receptor is followed by virus internalization through clathrin-mediated endocytosis. Envelope protein E is subsequently involved in membrane fusion between virion and host late endosomes. Synthesized as a homodimer with prM which acts as a chaperone for envelope protein E. After cleavage of prM, envelope protein E dissociate from small envelope protein M and homodimerizes (By similarity).[SAAS:SAAS026470_004_099774]	+	[https://www.uniprot.org/uniprot/Q9J7C6_9FLAV Q9J7C6_9FLAV] Envelope protein E binding to host cell surface receptor is followed by virus internalization through clathrin-mediated endocytosis. Envelope protein E is subsequently involved in membrane fusion between virion and host late endosomes. Synthesized as a homodimer with prM which acts as a chaperone for envelope protein E. After cleavage of prM, envelope protein E dissociate from small envelope protein M and homodimerizes (By similarity).[SAAS:SAAS026470_004_099774]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 25:		Line 23:
	</StructureSection>		</StructureSection>
	[[Category: Dengue virus 1]]		[[Category: Dengue virus 1]]
-	[[Category: ~~Lk3 transgenic mice~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Austin, S K~~]]	+	[[Category: Mus musculus]]
-	[[Category: ~~Structural genomic~~]]	+	[[Category: Austin SK]]
-	[[Category: Fremont~~, D H~~]]	+	[[Category: Fremont DH]]
-	[[Category: Nelson~~, C A]]~~	+	[[Category: Nelson CA]]
-	~~[[Category: Antibody epitope]]~~	+
-	~~[[Category: Csgid]]~~	+
-	~~[[Category: Dengue virus]]~~	+
-	~~[[Category: Flavivirus]]~~	+
-	~~[[Category: Immune system]]~~	+
-	~~[[Category: Immune system-viral protein complex]]~~	+
-	~~[[Category: National institute of allergy and infectious disease]]~~	+
-	~~[[Category: Niaid]]~~	+
-	~~[[Category: Viral envelope protein~~]]	+

OCA at 15:38, 4 August 2016

OCA — Thu, 04 Aug 2016 15:38:26 GMT

←Older revision		Revision as of 15:38, 4 August 2016
Line 1:		Line 1:
		+
	==Crystal structure of DENV1-E111 single chain variable fragment bound to DENV-1 DIII, strain 16007.==		==Crystal structure of DENV1-E111 single chain variable fragment bound to DENV-1 DIII, strain 16007.==
	<StructureSection load='4ffy' size='340' side='right' caption='[[4ffy]], [[Resolution\|resolution]] 2.50Å' scene=''>		<StructureSection load='4ffy' size='340' side='right' caption='[[4ffy]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4ffy]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Dengue_virus_1 Dengue virus 1] and [http://en.wikipedia.org/wiki/~~Mus_musculus Mus musculus~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4FFY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4FFY FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4ffy]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Dengue_virus_1 Dengue virus 1] and [http://en.wikipedia.org/wiki/Lk3_transgenic_mice Lk3 transgenic mice]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4FFY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4FFY FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3irc\|3irc]], [[4ffz\|4ffz]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3irc\|3irc]], [[4ffz\|4ffz]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Envelope domain III ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=11053 Dengue virus 1])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Envelope domain III ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=11053 Dengue virus 1])</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=4ffy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ffy OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4ffy RCSB], [http://www.ebi.ac.uk/pdbsum/4ffy PDBsum]</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=4ffy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ffy OCA], [http://pdbe.org/4ffy PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4ffy RCSB], [http://www.ebi.ac.uk/pdbsum/4ffy PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4ffy ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 18:		Line 19:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 4ffy" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
Line 23:		Line 25:
	</StructureSection>		</StructureSection>
	[[Category: Dengue virus 1]]		[[Category: Dengue virus 1]]
-	[[Category: ~~Mus musculus~~]]	+	[[Category: Lk3 transgenic mice]]
	[[Category: Austin, S K]]		[[Category: Austin, S K]]
	[[Category: Structural genomic]]		[[Category: Structural genomic]]

OCA at 16:29, 24 December 2014

OCA — Wed, 24 Dec 2014 16:29:59 GMT

←Older revision		Revision as of 16:29, 24 December 2014
Line 8:		Line 8:
	<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=4ffy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ffy OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4ffy RCSB], [http://www.ebi.ac.uk/pdbsum/4ffy PDBsum]</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=4ffy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ffy OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4ffy RCSB], [http://www.ebi.ac.uk/pdbsum/4ffy PDBsum]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/Q9J7C6_9FLAV Q9J7C6_9FLAV]] Envelope protein E binding to host cell surface receptor is followed by virus internalization through clathrin-mediated endocytosis. Envelope protein E is subsequently involved in membrane fusion between virion and host late endosomes. Synthesized as a homodimer with prM which acts as a chaperone for envelope protein E. After cleavage of prM, envelope protein E dissociate from small envelope protein M and homodimerizes (By similarity).[SAAS:SAAS026470_004_099774]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==

OCA at 16:23, 9 December 2014

OCA — Tue, 09 Dec 2014 16:23:21 GMT

←Older revision		Revision as of 16:23, 9 December 2014
Line 1:		Line 1:
-	[[~~Image:~~4ffy.~~png~~\|~~left~~\|~~200px~~]]	+	==Crystal structure of DENV1-E111 single chain variable fragment bound to DENV-1 DIII, strain 16007.==
		+	<StructureSection load='4ffy' size='340' side='right' caption='[[4ffy]], [[Resolution\|resolution]] 2.50Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4ffy]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Dengue_virus_1 Dengue virus 1] and [http://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4FFY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4FFY FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3irc\|3irc]], [[4ffz\|4ffz]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Envelope domain III ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=11053 Dengue virus 1])</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=4ffy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ffy OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4ffy RCSB], [http://www.ebi.ac.uk/pdbsum/4ffy PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	We previously developed a panel of neutralizing monoclonal antibodies against Dengue virus (DENV)-1, of which few exhibited inhibitory activity against all DENV-1 genotypes. This finding is consistent with reports observing variable neutralization of different DENV strains and genotypes using serum from individuals that experienced natural infection or immunization. Herein, we describe the crystal structures of DENV1-E111 bound to a novel CC' loop epitope on domain III (DIII) of the E protein from two different DENV-1 genotypes. Docking of our structure onto the available cryo-electron microscopy models of DENV virions revealed that the DENV1-E111 epitope was inaccessible, suggesting that this antibody recognizes an uncharacterized virus conformation. While the affinity of binding between DENV1-E111 and DIII varied by genotype, we observed limited correlation with inhibitory activity. Instead, our results support the conclusion that potent neutralization depends on genotype-dependent exposure of the CC' loop epitope. These findings establish new structural complexity of the DENV virion, which may be relevant for the choice of DENV strain for induction or analysis of neutralizing antibodies in the context of vaccine development.

-	~~{{STRUCTURE_4ffy\| PDB=4ffy \| SCENE= }}~~	+	Structural Basis of Differential Neutralization of DENV-1 Genotypes by an Antibody that Recognizes a Cryptic Epitope.,Austin SK, Dowd KA, Shrestha B, Nelson CA, Edeling MA, Johnson S, Pierson TC, Diamond MS, Fremont DH PLoS Pathog. 2012 Oct;8(10):e1002930. doi: 10.1371/journal.ppat.1002930. Epub, 2012 Oct 4. PMID:23055922<ref>PMID:23055922</ref>

-	~~===Crystal structure~~ of ~~DENV1-E111 single chain variable fragment bound to DENV-1 DIII, strain 16007~~.~~===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_23055922}}~~	+	== References ==
-		+	<references/>
-	==~~About this Structure~~==	+	__TOC__
-	~~[[4ffy]] is a 3 chain structure with sequence from [http:~~//en.wikipedia.org/wiki/Dengue_virus_1 Dengue virus 1] and [http://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4FFY OCA].	+	</StructureSection>
	[[Category: Dengue virus 1]]		[[Category: Dengue virus 1]]
	[[Category: Mus musculus]]		[[Category: Mus musculus]]
-	[[Category: Austin, S K.]]	+	[[Category: Austin, S K]]
-	[[Category: ~~CSGID, Center for~~ Structural ~~Genomics of Infectious Diseases.~~]]	+	[[Category: Structural genomic]]
-	[[Category: Fremont, D H.]]	+	[[Category: Fremont, D H]]
-	[[Category: Nelson, C A.]]	+	[[Category: Nelson, C A]]
	[[Category: Antibody epitope]]		[[Category: Antibody epitope]]
-	[[Category: Center for structural genomics of infectious disease]]
	[[Category: Csgid]]		[[Category: Csgid]]
	[[Category: Dengue virus]]		[[Category: Dengue virus]]
Line 24:		Line 34:
	[[Category: National institute of allergy and infectious disease]]		[[Category: National institute of allergy and infectious disease]]
	[[Category: Niaid]]		[[Category: Niaid]]
-	[[Category: Structural genomic]]
	[[Category: Viral envelope protein]]		[[Category: Viral envelope protein]]

OCA at 06:38, 31 October 2012

OCA — Wed, 31 Oct 2012 06:38:57 GMT

←Older revision		Revision as of 06:38, 31 October 2012
Line 1:		Line 1:
-	[[Image:4ffy.~~jpg~~\|left\|200px]]	+	[[Image:4ffy.png\|left\|200px]]

	{{STRUCTURE_4ffy\| PDB=4ffy \| SCENE= }}		{{STRUCTURE_4ffy\| PDB=4ffy \| SCENE= }}
Line 5:		Line 5:
	===Crystal structure of DENV1-E111 single chain variable fragment bound to DENV-1 DIII, strain 16007.===		===Crystal structure of DENV1-E111 single chain variable fragment bound to DENV-1 DIII, strain 16007.===

		+	{{ABSTRACT_PUBMED_23055922}}

	==About this Structure==		==About this Structure==

OCA at 08:01, 20 June 2012

OCA — Wed, 20 Jun 2012 08:01:41 GMT

←Older revision		Revision as of 08:01, 20 June 2012
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	[[Image:4ffy.jpg\|left\|200px]]

-	~~The entry~~ 4ffy ~~is ON HOLD~~	+	{{STRUCTURE_4ffy\| PDB=4ffy \| SCENE= }}

-	~~Authors: Austin~~, S.~~K., Fremont, D.H., Center for Structural Genomics of Infectious Diseases (CSGID)~~	+	===Crystal structure of DENV1-E111 single chain variable fragment bound to DENV-1 DIII, strain 16007.===

-	~~Description: Crystal~~ structure ~~of DENV1-E111 single chain variable fragment bound to DENV~~-1 ~~DIII~~, ~~strain 16007~~.	+
		+	==About this Structure==
		+	[[4ffy]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Dengue_virus_1 Dengue virus 1] and [http://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4FFY OCA].
		+	[[Category: Dengue virus 1]]
		+	[[Category: Mus musculus]]
		+	[[Category: Austin, S K.]]
		+	[[Category: CSGID, Center for Structural Genomics of Infectious Diseases.]]
		+	[[Category: Fremont, D H.]]
		+	[[Category: Nelson, C A.]]
		+	[[Category: Antibody epitope]]
		+	[[Category: Center for structural genomics of infectious disease]]
		+	[[Category: Csgid]]
		+	[[Category: Dengue virus]]
		+	[[Category: Flavivirus]]
		+	[[Category: Immune system]]
		+	[[Category: Immune system-viral protein complex]]
		+	[[Category: National institute of allergy and infectious disease]]
		+	[[Category: Niaid]]
		+	[[Category: Structural genomic]]
		+	[[Category: Viral envelope protein]]

OCA: Protected "4ffy" [edit=sysop:move=sysop]

OCA — Wed, 13 Jun 2012 05:51:13 GMT

Protected "4ffy" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:51, 13 June 2012

OCA: New page: '''Unreleased structure''' The entry 4ffy is ON HOLD Authors: Austin, S.K., Fremont, D.H., Center for Structural Genomics of Infectious Diseases (CSGID) Description: Crystal structure ...

OCA — Wed, 13 Jun 2012 05:51:12 GMT

New page: '''Unreleased structure''' The entry 4ffy is ON HOLD Authors: Austin, S.K., Fremont, D.H., Center for Structural Genomics of Infectious Diseases (CSGID) Description: Crystal structure ...

New page

'''Unreleased structure'''

The entry 4ffy is ON HOLD

Authors: Austin, S.K., Fremont, D.H., Center for Structural Genomics of Infectious Diseases (CSGID)

Description: Crystal structure of DENV1-E111 single chain variable fragment bound to DENV-1 DIII, strain 16007.