5y9e - Revision history

OCA at 10:22, 27 March 2024

2024-03-27T10:22:18Z

←Older revision		Revision as of 10:22, 27 March 2024
Line 3:		Line 3:
	<StructureSection load='5y9e' size='340' side='right'caption='[[5y9e]], [[Resolution\|resolution]] 2.04Å' scene=''>		<StructureSection load='5y9e' size='340' side='right'caption='[[5y9e]], [[Resolution\|resolution]] 2.04Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5y9e]] is a 5 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5Y9E OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5Y9E FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5y9e]] is a 5 chain structure with sequence from [https://en.wikipedia.org/wiki/Human_papillomavirus_58 Human papillomavirus 58]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5Y9E OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5Y9E FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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]] 2.042Å</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=5y9e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5y9e OCA], [~~http~~://pdbe.org/5y9e PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5y9e RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5y9e PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5y9e ProSAT]</span></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></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=5y9e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5y9e OCA], [https://pdbe.org/5y9e PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5y9e RCSB], [https://www.ebi.ac.uk/pdbsum/5y9e PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5y9e ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/VL1_HPV58 VL1_HPV58]] Forms an icosahedral capsid with a T=7 symmetry and a 50 nm diameter. The capsid is composed of 72 pentamers linked to each other by disulfide bonds and associated with L2 proteins. Binds to heparan sulfate proteoglycans on cell surface of basal layer keratinocytes to provide initial virion attachment. This binding mediates a conformational change in the virus capsid that facilitates efficient infection. The virion enters the host cell via endocytosis. During virus trafficking, L1 protein dissociates from the viral DNA and the genomic DNA is released to the host nucleus. The virion assembly takes place within the cell nucleus. Encapsulates the genomic DNA together with protein L2.[HAMAP-Rule:MF_04002]<ref>PMID:12610160</ref>	+	[https://www.uniprot.org/uniprot/VL1_HPV58 VL1_HPV58] Forms an icosahedral capsid with a T=7 symmetry and a 50 nm diameter. The capsid is composed of 72 pentamers linked to each other by disulfide bonds and associated with L2 proteins. Binds to heparan sulfate proteoglycans on cell surface of basal layer keratinocytes to provide initial virion attachment. This binding mediates a conformational change in the virus capsid that facilitates efficient infection. The virion enters the host cell via endocytosis. During virus trafficking, L1 protein dissociates from the viral DNA and the genomic DNA is released to the host nucleus. The virion assembly takes place within the cell nucleus. Encapsulates the genomic DNA together with protein L2.[HAMAP-Rule:MF_04002]<ref>PMID:12610160</ref>
-	~~<div style="background-color:#fffaf0;">~~	+
-	~~== Publication Abstract from PubMed ==~~	+
-	Persistent, high-risk human papillomavirus (HPV) infection is the primary cause of cervical cancer. Neutralizing antibodies elicited by L1-only virus-like particles (VLPs) can block HPV infection; however, the lack of high-resolution structures has limited our understanding of the mode of virus infection and the requirement for type specificity at the molecular level. Here, we describe two antibodies, A12A3 and 28F10, that specifically bind to and neutralize HPV58 and HPV59, respectively, through two distinct binding stoichiometries. We show that the epitopes of A12A3 are clustered in the DE loops of two adjacent HPV58 L1 monomers, whereas 28F10 recognizes the HPV59 FG loop of a single monomer. Via structure-based mutagenesis and analysis of antibody binding, we further identified the residues HPV58 D154, S168, and N170 and HPV59 M267, Q270, E273, Y276, K278, and R283, which play critical roles in virus infection. By substituting these strategic epitope residues into other HPV genotypes, we could then redirect the type-specific binding of the antibodies to these genotypes, thus highlighting the importance of these specific residues, HPV58 R161, S168, and N308 and HPV59 Q270, E273, and D281. Overall, our findings provide molecular insights into potential structural determinants of HPV required for infectivity and type specificity.IMPORTANCE High-risk human papillomaviruses (HPVs) are considered the major causative pathogens of cancers that affect epithelial mucosa, such as cervical cancer. However, because of the lack of high-resolution structural information on the sites of neutralization, we have yet to determine the precise mode of HPV infection and how different types of HPV cause infection. Our crystal structures in this study have uncovered discrete binding stoichiometries for two different antibodies. We show that one A12A3 Fab binds to the center of one HPV58 pentamer, whereas five 28F10 Fabs bind along the top fringe of one HPV59 pentamer. Furthermore, through targeted epitope analysis, we show that 6 to 7 discontinuous residues of the L1 major capsid protein of HPV are determinants, at least in part, for virus infection and type specificity. This knowledge will help us to unravel the process of HPV infection and can potentially be used to drive the development of therapeutics that target neutralization-sensitive sites.	+
-		+
-	Crystal Structures of Two Immune Complexes Identify Determinants for Viral Infectivity and Type-Specific Neutralization of Human Papillomavirus.,Li Z, Wang D, Gu Y, Song S, He M, Shi J, Liu X, Wei S, Li J, Yu H, Zheng Q, Yan X, Baker TS, Zhang J, McLellan JS, Li S, Xia N MBio. 2017 Sep 26;8(5). pii: e00787-17. doi: 10.1128/mBio.00787-17. PMID:28951471<ref>PMID:28951471</ref>	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class="pdbe-citations 5y9e" style="background-color:#fffaf0;"></div~~>	+

	==See Also==		==See Also==
-	*[[~~Major capsid protein L1~~\|~~Major capsid protein L1~~]]	+	*[[Virus coat proteins 3D structures\|Virus coat proteins 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Human papillomavirus 58]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Li~~, S W~~]]	+	[[Category: Li SW]]
-	[[Category: Li~~, Z H]]~~	+	[[Category: Li ZH]]
-	~~[[Category: Capsid protein]]~~	+
-	~~[[Category: Pentamer]]~~	+
-	~~[[Category: Structural protein~~]]	+

OCA at 09:13, 21 October 2020

2020-10-21T09:13:34Z

←Older revision		Revision as of 09:13, 21 October 2020
Line 1:		Line 1:

	==Crystal structure of HPV58 pentamer==		==Crystal structure of HPV58 pentamer==
-	<StructureSection load='5y9e' size='340' side='right' caption='[[5y9e]], [[Resolution\|resolution]] 2.04Å' scene=''>	+	<StructureSection load='5y9e' size='340' side='right'caption='[[5y9e]], [[Resolution\|resolution]] 2.04Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5y9e]] is a 5 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5Y9E OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5Y9E FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5y9e]] is a 5 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5Y9E OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5Y9E FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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=5y9e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5y9e OCA], [http://pdbe.org/5y9e PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5y9e RCSB], [http://www.ebi.ac.uk/pdbsum/5y9e PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5y9e 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=5y9e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5y9e OCA], [http://pdbe.org/5y9e PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5y9e RCSB], [http://www.ebi.ac.uk/pdbsum/5y9e PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5y9e ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 18:		Line 18:
	</div>		</div>
	<div class="pdbe-citations 5y9e" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5y9e" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Major capsid protein L1\|Major capsid protein L1]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Li, S W]]		[[Category: Li, S W]]
	[[Category: Li, Z H]]		[[Category: Li, Z H]]

OCA at 06:58, 25 October 2017

2017-10-25T06:58:18Z

←Older revision		Revision as of 06:58, 25 October 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5y9e is ~~ON HOLD~~	+	==Crystal structure of HPV58 pentamer==
		+	<StructureSection load='5y9e' size='340' side='right' caption='[[5y9e]], [[Resolution\|resolution]] 2.04Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5y9e]] is a 5 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5Y9E OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5Y9E FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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=5y9e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5y9e OCA], [http://pdbe.org/5y9e PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5y9e RCSB], [http://www.ebi.ac.uk/pdbsum/5y9e PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5y9e ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/VL1_HPV58 VL1_HPV58]] Forms an icosahedral capsid with a T=7 symmetry and a 50 nm diameter. The capsid is composed of 72 pentamers linked to each other by disulfide bonds and associated with L2 proteins. Binds to heparan sulfate proteoglycans on cell surface of basal layer keratinocytes to provide initial virion attachment. This binding mediates a conformational change in the virus capsid that facilitates efficient infection. The virion enters the host cell via endocytosis. During virus trafficking, L1 protein dissociates from the viral DNA and the genomic DNA is released to the host nucleus. The virion assembly takes place within the cell nucleus. Encapsulates the genomic DNA together with protein L2.[HAMAP-Rule:MF_04002]<ref>PMID:12610160</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Persistent, high-risk human papillomavirus (HPV) infection is the primary cause of cervical cancer. Neutralizing antibodies elicited by L1-only virus-like particles (VLPs) can block HPV infection; however, the lack of high-resolution structures has limited our understanding of the mode of virus infection and the requirement for type specificity at the molecular level. Here, we describe two antibodies, A12A3 and 28F10, that specifically bind to and neutralize HPV58 and HPV59, respectively, through two distinct binding stoichiometries. We show that the epitopes of A12A3 are clustered in the DE loops of two adjacent HPV58 L1 monomers, whereas 28F10 recognizes the HPV59 FG loop of a single monomer. Via structure-based mutagenesis and analysis of antibody binding, we further identified the residues HPV58 D154, S168, and N170 and HPV59 M267, Q270, E273, Y276, K278, and R283, which play critical roles in virus infection. By substituting these strategic epitope residues into other HPV genotypes, we could then redirect the type-specific binding of the antibodies to these genotypes, thus highlighting the importance of these specific residues, HPV58 R161, S168, and N308 and HPV59 Q270, E273, and D281. Overall, our findings provide molecular insights into potential structural determinants of HPV required for infectivity and type specificity.IMPORTANCE High-risk human papillomaviruses (HPVs) are considered the major causative pathogens of cancers that affect epithelial mucosa, such as cervical cancer. However, because of the lack of high-resolution structural information on the sites of neutralization, we have yet to determine the precise mode of HPV infection and how different types of HPV cause infection. Our crystal structures in this study have uncovered discrete binding stoichiometries for two different antibodies. We show that one A12A3 Fab binds to the center of one HPV58 pentamer, whereas five 28F10 Fabs bind along the top fringe of one HPV59 pentamer. Furthermore, through targeted epitope analysis, we show that 6 to 7 discontinuous residues of the L1 major capsid protein of HPV are determinants, at least in part, for virus infection and type specificity. This knowledge will help us to unravel the process of HPV infection and can potentially be used to drive the development of therapeutics that target neutralization-sensitive sites.

-	~~Authors:~~ Li, S~~.W.~~, Li, Z.H.	+	Crystal Structures of Two Immune Complexes Identify Determinants for Viral Infectivity and Type-Specific Neutralization of Human Papillomavirus.,Li Z, Wang D, Gu Y, Song S, He M, Shi J, Liu X, Wei S, Li J, Yu H, Zheng Q, Yan X, Baker TS, Zhang J, McLellan JS, Li S, Xia N MBio. 2017 Sep 26;8(5). pii: e00787-17. doi: 10.1128/mBio.00787-17. PMID:28951471<ref>PMID:28951471</ref>

-	~~Description: Crystal structure~~ of ~~HPV58 pentamer~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
-	[[Category: Li, Z.H]]	+	<div class="pdbe-citations 5y9e" style="background-color:#fffaf0;"></div>
-	[[Category: ~~Li, S.W~~]]	+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Li, S W]]
		+	[[Category: Li, Z H]]
		+	[[Category: Capsid protein]]
		+	[[Category: Pentamer]]
		+	[[Category: Structural protein]]

OCA: Protected "5y9e" [edit=sysop:move=sysop]

2017-09-27T16:17:44Z

Protected "5y9e" [edit=sysop:move=sysop]

←Older revision

Revision as of 16:17, 27 September 2017

OCA: New page: '''Unreleased structure''' The entry 5y9e is ON HOLD Authors: Li, S.W., Li, Z.H. Description: Crystal structure of HPV58 pentamer Category: Unreleased Structures [[Category: Li, Z....

2017-09-27T16:17:43Z

New page: '''Unreleased structure''' The entry 5y9e is ON HOLD Authors: Li, S.W., Li, Z.H. Description: Crystal structure of HPV58 pentamer Category: Unreleased Structures [[Category: Li, Z....

New page

'''Unreleased structure'''

The entry 5y9e is ON HOLD

Authors: Li, S.W., Li, Z.H.

Description: Crystal structure of HPV58 pentamer
[[Category: Unreleased Structures]]
[[Category: Li, Z.H]]
[[Category: Li, S.W]]