7uzc - Revision history

OCA at 09:58, 25 October 2023

2023-10-25T09:58:30Z

←Older revision		Revision as of 09:58, 25 October 2023
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[7uzc]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Mus_musculus Mus musculus] 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=7UZC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7UZC FirstGlance]. <br>		<table><tr><td colspan='2'>[[7uzc]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Mus_musculus Mus musculus] 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=7UZC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7UZC FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</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]] 2.2Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</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=7uzc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7uzc OCA], [https://pdbe.org/7uzc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7uzc RCSB], [https://www.ebi.ac.uk/pdbsum/7uzc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7uzc 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=7uzc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7uzc OCA], [https://pdbe.org/7uzc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7uzc RCSB], [https://www.ebi.ac.uk/pdbsum/7uzc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7uzc ProSAT]</span></td></tr>
	</table>		</table>

OCA at 07:35, 11 January 2023

2023-01-11T07:35:10Z

←Older revision		Revision as of 07:35, 11 January 2023
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 7uzc is ~~ON HOLD~~ ~~until Paper~~ Publication	+	==Structure of the SARS-CoV-2 RBD in complex with the mouse antibody Fab fragment, M8a-34==
		+	<StructureSection load='7uzc' size='340' side='right'caption='[[7uzc]], [[Resolution\|resolution]] 2.20Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[7uzc]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Mus_musculus Mus musculus] 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=7UZC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7UZC FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</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=7uzc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7uzc OCA], [https://pdbe.org/7uzc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7uzc RCSB], [https://www.ebi.ac.uk/pdbsum/7uzc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7uzc ProSAT]</span></td></tr>
		+	</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 ==
		+	Increased immune evasion by SARS-CoV-2 variants of concern highlights the need for new therapeutic neutralizing antibodies. Immunization with nanoparticles co-displaying spike receptor-binding domains (RBDs) from eight sarbecoviruses (mosaic-8 RBD-nanoparticles) efficiently elicits cross-reactive polyclonal antibodies against conserved sarbecovirus RBD epitopes. Here, we identified monoclonal antibodies (mAbs) capable of cross-reactive binding and neutralization of animal sarbecoviruses and SARS-CoV-2 variants by screening single mouse B cells secreting IgGs that bind two or more sarbecovirus RBDs. Single-particle cryo-EM structures of antibody-spike complexes, including a Fab-Omicron complex, mapped neutralizing mAbs to conserved class 1/4 RBD epitopes. Structural analyses revealed neutralization mechanisms, potentials for intra-spike trimer cross-linking by IgGs, and induced changes in trimer upon Fab binding. In addition, we identified a mAb-resembling Bebtelovimab, an EUA-approved human class 3 anti-RBD mAb. These results support using mosaic RBD-nanoparticle vaccination to generate and identify therapeutic pan-sarbecovirus and pan-variant mAbs.

-	~~Authors: Fan~~, C., ~~Bjorkman~~, P.J.	+	Neutralizing monoclonal antibodies elicited by mosaic RBD nanoparticles bind conserved sarbecovirus epitopes.,Fan C, Cohen AA, Park M, Hung AF, Keeffe JR, Gnanapragasam PNP, Lee YE, Gao H, Kakutani LM, Wu Z, Kleanthous H, Malecek KE, Williams JC, Bjorkman PJ Immunity. 2022 Dec 13;55(12):2419-2435.e10. doi: 10.1016/j.immuni.2022.10.019. , Epub 2022 Oct 27. PMID:36370711<ref>PMID:36370711</ref>

-	~~Description: Structure~~ of the ~~SARS~~-~~CoV~~-~~2 RBD in complex with the mouse antibody Fab fragment, M8a-34~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased~~ Structures]]	+	</div>
-	[[Category: Bjorkman~~, P.J~~]]	+	<div class="pdbe-citations 7uzc" style="background-color:#fffaf0;"></div>
-	[[Category: Fan, C]]	+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Mus musculus]]
		+	[[Category: Severe acute respiratory syndrome coronavirus 2]]
		+	[[Category: Bjorkman PJ]]
		+	[[Category: Fan C]]

OCA at 03:51, 15 June 2022

2022-06-15T03:51:51Z

←Older revision		Revision as of 03:51, 15 June 2022
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors: Fan, C., Bjorkman, P.J.		Authors: Fan, C., Bjorkman, P.J.

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

2022-05-18T09:04:58Z

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

←Older revision

Revision as of 09:04, 18 May 2022

OCA: New page: '''Unreleased structure''' The entry 7uzc is ON HOLD Authors: Fan, C., Bjorkman, P.J. Description: Structure of the SARS-CoV-2 RBD in complex with the mouse antibody Fab fragment, M8a-...

2022-05-18T09:04:57Z

New page: '''Unreleased structure''' The entry 7uzc is ON HOLD Authors: Fan, C., Bjorkman, P.J. Description: Structure of the SARS-CoV-2 RBD in complex with the mouse antibody Fab fragment, M8a-...

New page

'''Unreleased structure'''

The entry 7uzc is ON HOLD

Authors: Fan, C., Bjorkman, P.J.

Description: Structure of the SARS-CoV-2 RBD in complex with the mouse antibody Fab fragment, M8a-34
[[Category: Unreleased Structures]]
[[Category: Bjorkman, P.J]]
[[Category: Fan, C]]