7dzy - Revision history

OCA at 11:07, 2 August 2023

OCA — Wed, 02 Aug 2023 11:07:14 GMT

←Older revision		Revision as of 11:07, 2 August 2023
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-	====	+	==Spike protein from SARS-CoV2 with Fab fragment of enhancing antibody 2490==
-	<StructureSection load='7dzy' size='340' side='right'caption='[[7dzy]]' scene=''>	+	<StructureSection load='7dzy' size='340' side='right'caption='[[7dzy]], [[Resolution\|resolution]] 3.60Å' 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'>[[7dzy]] is a 9 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [https://en.wikipedia.org/wiki/Severe_acute_respiratory_syndrome_coronavirus_2 Severe acute respiratory syndrome coronavirus 2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7DZY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7DZY 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=7dzy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7dzy OCA], [https://pdbe.org/7dzy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7dzy RCSB], [https://www.ebi.ac.uk/pdbsum/7dzy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7dzy ProSAT]</span></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]] 3.6Å</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=7dzy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7dzy OCA], [https://pdbe.org/7dzy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7dzy RCSB], [https://www.ebi.ac.uk/pdbsum/7dzy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7dzy ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/SPIKE_SARS2 SPIKE_SARS2] attaches the virion to the cell membrane by interacting with host receptor, initiating the infection (By similarity). Binding to human ACE2 receptor and internalization of the virus into the endosomes of the host cell induces conformational changes in the Spike glycoprotein (PubMed:32142651, PubMed:32075877, PubMed:32155444). Uses also human TMPRSS2 for priming in human lung cells which is an essential step for viral entry (PubMed:32142651). Proteolysis by cathepsin CTSL may unmask the fusion peptide of S2 and activate membranes fusion within endosomes.[HAMAP-Rule:MF_04099]<ref>PMID:32075877</ref> <ref>PMID:32142651</ref> <ref>PMID:32155444</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 ==
		+	Antibodies against the receptor-binding domain (RBD) of the SARS-CoV-2 spike protein prevent SARS-CoV-2 infection. However, the effects of antibodies against other spike protein domains are largely unknown. Here, we screened a series of anti-spike monoclonal antibodies from coronavirus disease 2019 (COVID-19) patients and found that some of antibodies against the N-terminal domain (NTD) induced the open conformation of RBD and thus enhanced the binding capacity of the spike protein to ACE2 and infectivity of SARS-CoV-2. Mutational analysis revealed that all of the infectivity-enhancing antibodies recognized a specific site on the NTD. Structural analysis demonstrated that all infectivity-enhancing antibodies bound to NTD in a similar manner. The antibodies against this infectivity-enhancing site were detected at high levels in severe patients. Moreover, we identified antibodies against the infectivity-enhancing site in uninfected donors, albeit at a lower frequency. These findings demonstrate that not only neutralizing antibodies but also enhancing antibodies are produced during SARS-CoV-2 infection.
		+
		+	An infectivity-enhancing site on the SARS-CoV-2 spike protein targeted by antibodies.,Liu Y, Soh WT, Kishikawa JI, Hirose M, Nakayama EE, Li S, Sasai M, Suzuki T, Tada A, Arakawa A, Matsuoka S, Akamatsu K, Matsuda M, Ono C, Torii S, Kishida K, Jin H, Nakai W, Arase N, Nakagawa A, Matsumoto M, Nakazaki Y, Shindo Y, Kohyama M, Tomii K, Ohmura K, Ohshima S, Okamoto T, Yamamoto M, Nakagami H, Matsuura Y, Nakagawa A, Kato T, Okada M, Standley DM, Shioda T, Arase H Cell. 2021 Jun 24;184(13):3452-3466.e18. doi: 10.1016/j.cell.2021.05.032. Epub, 2021 May 24. PMID:34139176<ref>PMID:34139176</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7dzy" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Antibody 3D structures\|Antibody 3D structures]]
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Z-disk~~]]	+	[[Category: Severe acute respiratory syndrome coronavirus 2]]
		+	[[Category: Arase H]]
		+	[[Category: Hirose M]]
		+	[[Category: Kato T]]
		+	[[Category: Kishikawa J]]
		+	[[Category: Li S]]
		+	[[Category: Liu Y]]
		+	[[Category: Okada M]]
		+	[[Category: Soh WT]]
		+	[[Category: Standley D]]

OCA at 14:34, 2 June 2021

OCA — Wed, 02 Jun 2021 14:34:59 GMT

←Older revision		Revision as of 14:34, 2 June 2021
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-	'''Unreleased structure'''

-	~~The entry~~ 7dzy ~~is ON HOLD until Paper Publication~~	+	====
-		+	<StructureSection load='7dzy' size='340' side='right'caption='[[7dzy]]' scene=''>
-	~~Authors~~: ~~Liu, Y~~.~~, Soh, W~~.T.~~, Li, S~~.~~, Kishikawa, J~~.~~, Hirose, M~~.~~, Kato, T., Standley, D., Okada, M., Arase, 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~~: ~~Spike protein from SARS-CoV2 with Fab fragment of enhancing antibody 2490~~	+	</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=7dzy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7dzy OCA], [https://pdbe.org/7dzy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7dzy RCSB], [https://www.ebi.ac.uk/pdbsum/7dzy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7dzy ProSAT]</span></td></tr>
-	[~~[Category~~: ~~Unreleased Structures~~]]	+	</table>
-	[~~[Category~~: ~~Standley~~, ~~D]]~~	+	__TOC__
-	[~~[Category~~: ~~Li, S~~]]	+	</StructureSection>
-	[~~[Category~~: ~~Kishikawa, J~~]]	+	[[Category: Large Structures]]
-	~~[[Category: Okada~~, ~~M]]~~	+	[[Category: Z-disk]]
-	[~~[Category~~: ~~Kato, T~~]]	+
-	~~[[Category: Hirose~~, ~~M]]~~	+
-	[~~[Category~~: ~~Liu, Y]~~]	+
-	[[Category: ~~Arase, H~~]]	+
-	[[Category: ~~Soh, W.T~~]]	+

OCA at 13:15, 3 March 2021

OCA — Wed, 03 Mar 2021 13:15:22 GMT

←Older revision		Revision as of 13:15, 3 March 2021
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 7dzy is ON HOLD	+	The entry 7dzy is ON HOLD until Paper Publication

	Authors: Liu, Y., Soh, W.T., Li, S., Kishikawa, J., Hirose, M., Kato, T., Standley, D., Okada, M., Arase, H.		Authors: Liu, Y., Soh, W.T., Li, S., Kishikawa, J., Hirose, M., Kato, T., Standley, D., Okada, M., Arase, H.

-	Description: ~~Apo spike~~ protein from SARS-CoV2 with Fab fragment of enhancing antibody 2490	+	Description: Spike protein from SARS-CoV2 with Fab fragment of enhancing antibody 2490
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
	[[Category: Standley, D]]		[[Category: Standley, D]]

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

OCA — Wed, 03 Feb 2021 09:21:32 GMT

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

←Older revision

Revision as of 09:21, 3 February 2021

OCA: New page: '''Unreleased structure''' The entry 7dzy is ON HOLD Authors: Liu, Y., Soh, W.T., Li, S., Kishikawa, J., Hirose, M., Kato, T., Standley, D., Okada, M., Arase, H. Description: Apo spike...

OCA — Wed, 03 Feb 2021 09:21:31 GMT

New page: '''Unreleased structure''' The entry 7dzy is ON HOLD Authors: Liu, Y., Soh, W.T., Li, S., Kishikawa, J., Hirose, M., Kato, T., Standley, D., Okada, M., Arase, H. Description: Apo spike...

New page

'''Unreleased structure'''

The entry 7dzy is ON HOLD

Authors: Liu, Y., Soh, W.T., Li, S., Kishikawa, J., Hirose, M., Kato, T., Standley, D., Okada, M., Arase, H.

Description: Apo spike protein from SARS-CoV2 with Fab fragment of enhancing antibody 2490
[[Category: Unreleased Structures]]
[[Category: Standley, D]]
[[Category: Li, S]]
[[Category: Kishikawa, J]]
[[Category: Okada, M]]
[[Category: Kato, T]]
[[Category: Hirose, M]]
[[Category: Liu, Y]]
[[Category: Arase, H]]
[[Category: Soh, W.T]]