7coe - Revision history

OCA at 05:55, 17 September 2025

2025-09-17T05:55:02Z

← Older revision		Revision as of 05:55, 17 September 2025
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	== Function ==		== Function ==
	[https://www.uniprot.org/uniprot/SPIKE_MERS1 SPIKE_MERS1] Attaches the virion to the cell membrane by interacting with host receptor, initiating the infection (By similarity). Interacts with host DPP4 to mediate virla entry.[HAMAP-Rule:MF_04099]<ref>PMID:23486063</ref> Mediates fusion of the virion and cellular membranes by acting as a class I viral fusion protein. Under the current model, the protein has at least three conformational states: pre-fusion native state, pre-hairpin intermediate state, and post-fusion hairpin state. During viral and target cell membrane fusion, the coiled coil regions (heptad repeats) assume a trimer-of-hairpins structure, positioning the fusion peptide in close proximity to the C-terminal region of the ectodomain. The formation of this structure appears to drive apposition and subsequent fusion of viral and target cell membranes.[HAMAP-Rule:MF_04099] Acts as a viral fusion peptide which is unmasked following S2 cleavage occurring upon virus endocytosis.[HAMAP-Rule:MF_04099]		[https://www.uniprot.org/uniprot/SPIKE_MERS1 SPIKE_MERS1] Attaches the virion to the cell membrane by interacting with host receptor, initiating the infection (By similarity). Interacts with host DPP4 to mediate virla entry.[HAMAP-Rule:MF_04099]<ref>PMID:23486063</ref> Mediates fusion of the virion and cellular membranes by acting as a class I viral fusion protein. Under the current model, the protein has at least three conformational states: pre-fusion native state, pre-hairpin intermediate state, and post-fusion hairpin state. During viral and target cell membrane fusion, the coiled coil regions (heptad repeats) assume a trimer-of-hairpins structure, positioning the fusion peptide in close proximity to the C-terminal region of the ectodomain. The formation of this structure appears to drive apposition and subsequent fusion of viral and target cell membranes.[HAMAP-Rule:MF_04099] Acts as a viral fusion peptide which is unmasked following S2 cleavage occurring upon virus endocytosis.[HAMAP-Rule:MF_04099]
	~~<div style="background-color:#fffaf0;">~~
	~~== Publication Abstract from PubMed ==~~
	Middle East respiratory syndrome coronavirus (MERS-CoV) is a zoonotic virus, responsible for outbreaks of a severe respiratory illness in humans with a fatality rate of 30%. Currently, there are no vaccines or United States food and drug administration (FDA)-approved therapeutics for humans. The spike protein displayed on the surface of MERS-CoV functions in the attachment and fusion of virions to host cellular membranes and is the target of the host antibody response. Here, we provide a molecular method for neutralizing MERS-CoV through potent antibody-mediated targeting of the receptor-binding subdomain (RBD) of the spike protein. The structural characterization of the neutralizing antibody (KNIH90-F1) complexed with RBD using X-ray crystallography revealed three critical epitopes (D509, R511, and E513) in the RBD region of the spike protein. Further investigation of MERS-CoV mutants that escaped neutralization by the antibody supported the identification of these epitopes in the RBD region. The neutralizing activity of this antibody is solely provided by these specific molecular structures. This work should contribute to the development of vaccines or therapeutic antibodies for MERS-CoV.

	The structure of a novel antibody against the spike protein inhibits Middle East respiratory syndrome coronavirus infections.,Jang TH, Park WJ, Lee H, Woo HM, Lee SY, Kim KC, Kim SS, Hong E, Song J, Lee JY Sci Rep. 2022 Jan 24;12(1):1260. doi: 10.1038/s41598-022-05318-4. PMID:35075213<ref>PMID:35075213</ref>

	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~
	~~</div>~~
	~~<div class="pdbe-citations 7coe" style="background-color:#fffaf0;"></div>~~

	==See Also==		==See Also==

OCA at 16:12, 29 November 2023

2023-11-29T16:12:15Z

← Older revision		Revision as of 16:12, 29 November 2023
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[7coe]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [https://en.wikipedia.org/wiki/Middle_East_respiratory_syndrome-related_coronavirus Middle East respiratory syndrome-related coronavirus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7COE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7COE FirstGlance]. <br>		<table><tr><td colspan='2'>[[7coe]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [https://en.wikipedia.org/wiki/Middle_East_respiratory_syndrome-related_coronavirus Middle East respiratory syndrome-related coronavirus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7COE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7COE FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</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]] 2.05Å</td></tr>
			<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</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=7coe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7coe OCA], [https://pdbe.org/7coe PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7coe RCSB], [https://www.ebi.ac.uk/pdbsum/7coe PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7coe 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=7coe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7coe OCA], [https://pdbe.org/7coe PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7coe RCSB], [https://www.ebi.ac.uk/pdbsum/7coe PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7coe ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[https://www.uniprot.org/uniprot/SPIKE_MERS1 SPIKE_MERS1]] Attaches the virion to the cell membrane by interacting with host receptor, initiating the infection (By similarity). Interacts with host DPP4 to mediate virla entry.[HAMAP-Rule:MF_04099]<ref>PMID:23486063</ref> Mediates fusion of the virion and cellular membranes by acting as a class I viral fusion protein. Under the current model, the protein has at least three conformational states: pre-fusion native state, pre-hairpin intermediate state, and post-fusion hairpin state. During viral and target cell membrane fusion, the coiled coil regions (heptad repeats) assume a trimer-of-hairpins structure, positioning the fusion peptide in close proximity to the C-terminal region of the ectodomain. The formation of this structure appears to drive apposition and subsequent fusion of viral and target cell membranes.[HAMAP-Rule:MF_04099] Acts as a viral fusion peptide which is unmasked following S2 cleavage occurring upon virus endocytosis.[HAMAP-Rule:MF_04099]		[https://www.uniprot.org/uniprot/SPIKE_MERS1 SPIKE_MERS1] Attaches the virion to the cell membrane by interacting with host receptor, initiating the infection (By similarity). Interacts with host DPP4 to mediate virla entry.[HAMAP-Rule:MF_04099]<ref>PMID:23486063</ref> Mediates fusion of the virion and cellular membranes by acting as a class I viral fusion protein. Under the current model, the protein has at least three conformational states: pre-fusion native state, pre-hairpin intermediate state, and post-fusion hairpin state. During viral and target cell membrane fusion, the coiled coil regions (heptad repeats) assume a trimer-of-hairpins structure, positioning the fusion peptide in close proximity to the C-terminal region of the ectodomain. The formation of this structure appears to drive apposition and subsequent fusion of viral and target cell membranes.[HAMAP-Rule:MF_04099] Acts as a viral fusion peptide which is unmasked following S2 cleavage occurring upon virus endocytosis.[HAMAP-Rule:MF_04099]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	</div>		</div>
	<div class="pdbe-citations 7coe" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 7coe" style="background-color:#fffaf0;"></div>

			==See Also==
			*[[Antibody 3D structures\|Antibody 3D structures]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 19:43, 7 September 2022

2022-09-07T19:43:27Z

← Older revision		Revision as of 19:43, 7 September 2022
Line 1:		Line 1:

	====		==Crystal structure of Receptor binding domain of MERS-CoV and KNIH90-F1 Fab complex==
	<StructureSection load='7coe' size='340' side='right'caption='[[7coe]]' scene=''>		<StructureSection load='7coe' size='340' side='right'caption='[[7coe]], [[Resolution\|resolution]] 2.05Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id= OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol= FirstGlance]. <br>		<table><tr><td colspan='2'>[[7coe]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [https://en.wikipedia.org/wiki/Middle_East_respiratory_syndrome-related_coronavirus Middle East respiratory syndrome-related coronavirus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7COE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7COE FirstGlance]. <br>
	</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=7coe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7coe OCA], [https://pdbe.org/7coe PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7coe RCSB], [https://www.ebi.ac.uk/pdbsum/7coe PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7coe ProSAT]</span></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</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=7coe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7coe OCA], [https://pdbe.org/7coe PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7coe RCSB], [https://www.ebi.ac.uk/pdbsum/7coe PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7coe ProSAT]</span></td></tr>
	</table>		</table>
			== Function ==
			[[https://www.uniprot.org/uniprot/SPIKE_MERS1 SPIKE_MERS1]] Attaches the virion to the cell membrane by interacting with host receptor, initiating the infection (By similarity). Interacts with host DPP4 to mediate virla entry.[HAMAP-Rule:MF_04099]<ref>PMID:23486063</ref> Mediates fusion of the virion and cellular membranes by acting as a class I viral fusion protein. Under the current model, the protein has at least three conformational states: pre-fusion native state, pre-hairpin intermediate state, and post-fusion hairpin state. During viral and target cell membrane fusion, the coiled coil regions (heptad repeats) assume a trimer-of-hairpins structure, positioning the fusion peptide in close proximity to the C-terminal region of the ectodomain. The formation of this structure appears to drive apposition and subsequent fusion of viral and target cell membranes.[HAMAP-Rule:MF_04099] Acts as a viral fusion peptide which is unmasked following S2 cleavage occurring upon virus endocytosis.[HAMAP-Rule:MF_04099]
			<div style="background-color:#fffaf0;">
			== Publication Abstract from PubMed ==
			Middle East respiratory syndrome coronavirus (MERS-CoV) is a zoonotic virus, responsible for outbreaks of a severe respiratory illness in humans with a fatality rate of 30%. Currently, there are no vaccines or United States food and drug administration (FDA)-approved therapeutics for humans. The spike protein displayed on the surface of MERS-CoV functions in the attachment and fusion of virions to host cellular membranes and is the target of the host antibody response. Here, we provide a molecular method for neutralizing MERS-CoV through potent antibody-mediated targeting of the receptor-binding subdomain (RBD) of the spike protein. The structural characterization of the neutralizing antibody (KNIH90-F1) complexed with RBD using X-ray crystallography revealed three critical epitopes (D509, R511, and E513) in the RBD region of the spike protein. Further investigation of MERS-CoV mutants that escaped neutralization by the antibody supported the identification of these epitopes in the RBD region. The neutralizing activity of this antibody is solely provided by these specific molecular structures. This work should contribute to the development of vaccines or therapeutic antibodies for MERS-CoV.

			The structure of a novel antibody against the spike protein inhibits Middle East respiratory syndrome coronavirus infections.,Jang TH, Park WJ, Lee H, Woo HM, Lee SY, Kim KC, Kim SS, Hong E, Song J, Lee JY Sci Rep. 2022 Jan 24;12(1):1260. doi: 10.1038/s41598-022-05318-4. PMID:35075213<ref>PMID:35075213</ref>

			From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>
			<div class="pdbe-citations 7coe" style="background-color:#fffaf0;"></div>
			== References ==
			<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
			[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Z-~~disk~~]]		[[Category: Middle East respiratory syndrome-related coronavirus]]
			[[Category: Hong E]]
			[[Category: Jang TH]]
			[[Category: Lee HS]]
			[[Category: Lee JY]]
			[[Category: Song JY]]

OCA at 10:17, 4 August 2021

2021-08-04T10:17:22Z

← Older revision		Revision as of 10:17, 4 August 2021
Line 1:		Line 1:
	~~'''Unreleased structure'''~~

	~~The entry~~ 7coe ~~is ON HOLD until Aug 04 2022~~		====
			<StructureSection load='7coe' size='340' side='right'caption='[[7coe]]' scene=''>
	~~Authors~~: ~~Lee, J~~.Y.~~, Song, J~~.Y.~~, Lee, H~~.S., ~~Hong, E~~.~~, Jang, T~~.H.		== Structural highlights ==
			<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id= OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol= FirstGlance]. <br>
	~~Description: Crystal structure of Receptor binding domain of MERS~~-~~CoV and KNIH90-F1 Fab complex~~		</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=7coe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7coe OCA], [https://pdbe.org/7coe PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7coe RCSB], [https://www.ebi.ac.uk/pdbsum/7coe PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7coe ProSAT]</span></td></tr>
	[~~[Category~~: ~~Unreleased Structures~~]]		</table>
	[~~[Category~~: ~~Song, J~~.Y]]		__TOC__
	[~~[Category~~: ~~Lee, J~~.Y]]		</StructureSection>
	[~~[Category~~: ~~Lee, H~~.S]]		[[Category: Large Structures]]
	[[Category: ~~Hong, E~~]]		[[Category: Z-disk]]
	[[Category: ~~Jang, T.H~~]]

OCA at 04:41, 19 August 2020

2020-08-19T04:41:56Z

← Older revision		Revision as of 04:41, 19 August 2020
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

	The entry 7coe is ON HOLD		The entry 7coe is ON HOLD until Aug 04 2022

	Authors: Lee, J.Y., Song, J.Y., Lee, H.S., Hong, E., Jang, T.H.		Authors: Lee, J.Y., Song, J.Y., Lee, H.S., Hong, E., Jang, T.H.

	Description: Crystal structure of Receptor binding domain and Fab complex		Description: Crystal structure of Receptor binding domain of MERS-CoV and KNIH90-F1 Fab complex
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
	[[Category: Song, J.Y]]		[[Category: Song, J.Y]]
			[[Category: Lee, J.Y]]
			[[Category: Lee, H.S]]
	[[Category: Hong, E]]		[[Category: Hong, E]]
	[[Category: Jang, T.H]]		[[Category: Jang, T.H]]
	~~[[Category: Lee, J.Y]]~~
	~~[[Category: Lee, H.S]]~~

OCA: Protected "7coe" [edit=sysop:move=sysop]

2020-08-12T08:23:04Z

Protected "7coe" [edit=sysop:move=sysop]

← Older revision	Revision as of 08:23, 12 August 2020
(No difference)

OCA: New page: '''Unreleased structure''' The entry 7coe is ON HOLD Authors: Lee, J.Y., Song, J.Y., Lee, H.S., Hong, E., Jang, T.H. Description: Crystal structure of Receptor binding domain and Fab c...

2020-08-12T08:23:03Z

New page: '''Unreleased structure''' The entry 7coe is ON HOLD Authors: Lee, J.Y., Song, J.Y., Lee, H.S., Hong, E., Jang, T.H. Description: Crystal structure of Receptor binding domain and Fab c...

New page

'''Unreleased structure'''

The entry 7coe is ON HOLD

Authors: Lee, J.Y., Song, J.Y., Lee, H.S., Hong, E., Jang, T.H.

Description: Crystal structure of Receptor binding domain and Fab complex
[[Category: Unreleased Structures]]
[[Category: Song, J.Y]]
[[Category: Hong, E]]
[[Category: Jang, T.H]]
[[Category: Lee, J.Y]]
[[Category: Lee, H.S]]