This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.

4xak

From Proteopedia

(Difference between revisions)

Jump to: navigation, search

Revision as of 16:17, 16 November 2017

Crystal structure of potent neutralizing antibody m336 in complex with MERS Co-V RBD

Structural highlights

4xak is a 6 chain structure with sequence from Betacoronavirus england 1 and Human. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	,
Gene:	S, 3 (Betacoronavirus England 1)
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[SPIKE_CVEMC] S1 attaches the virion to the cell membrane by interacting with host DPP4, initiating the infection.^[1] S2 is a class I viral fusion protein. Under the current model, the protein has at least 3 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 plasma cell membranes (By similarity).

Publication Abstract from PubMed

The MERS-CoV is an emerging virus, which already infected more than 1,300 humans with high ( approximately 36%) mortality. Here, we show that m336, an exceptionally potent human anti-MERS-CoV antibody, is almost germline with only one somatic mutation in the heavy chain. The structure of Fab m336 in complex with the MERS-CoV receptor-binding domain reveals that its IGHV1-69-derived heavy chain provides more than 85% binding surface and that its epitope almost completely overlaps with the receptor-binding site. Analysis of antibodies from 69 healthy humans suggests an important role of the V(D)J recombination-generated junctional and allele-specific residues for achieving high affinity of binding at such low levels of somatic hypermutation. Our results also have important implications for development of vaccine immunogens based on the newly identified m336 epitope as well as for elucidation of mechanisms of neutralization by m336-like antibodies and their elicitation in vivo.

Junctional and allele-specific residues are critical for MERS-CoV neutralization by an exceptionally potent germline-like antibody.,Ying T, Prabakaran P, Du L, Shi W, Feng Y, Wang Y, Wang L, Li W, Jiang S, Dimitrov DS, Zhou T Nat Commun. 2015 Sep 15;6:8223. doi: 10.1038/ncomms9223. PMID:26370782^[2]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Raj VS, Mou H, Smits SL, Dekkers DH, Muller MA, Dijkman R, Muth D, Demmers JA, Zaki A, Fouchier RA, Thiel V, Drosten C, Rottier PJ, Osterhaus AD, Bosch BJ, Haagmans BL. Dipeptidyl peptidase 4 is a functional receptor for the emerging human coronavirus-EMC. Nature. 2013 Mar 14;495(7440):251-4. doi: 10.1038/nature12005. PMID:23486063 doi:http://dx.doi.org/10.1038/nature12005
↑ Ying T, Prabakaran P, Du L, Shi W, Feng Y, Wang Y, Wang L, Li W, Jiang S, Dimitrov DS, Zhou T. Junctional and allele-specific residues are critical for MERS-CoV neutralization by an exceptionally potent germline-like antibody. Nat Commun. 2015 Sep 15;6:8223. doi: 10.1038/ncomms9223. PMID:26370782 doi:http://dx.doi.org/10.1038/ncomms9223

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 See Also
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/4xak"

@@ Line 1: / Line 1: @@
 ==Crystal structure of potent neutralizing antibody m336 in complex with MERS Co-V RBD==
 <StructureSection load='4xak' size='340' side='right' caption='[[4xak]], [[Resolution|resolution]] 2.45&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4xak]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4XAK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4XAK FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4xak]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Betacoronavirus_england_1 Betacoronavirus england 1] and [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4XAK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4XAK 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=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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4xak FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xak OCA], [http://pdbe.org/4xak PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4xak RCSB], [http://www.ebi.ac.uk/pdbsum/4xak PDBsum]</span></td></tr>
+<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">S, 3 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1263720 Betacoronavirus England 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=4xak FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xak OCA], [http://pdbe.org/4xak PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4xak RCSB], [http://www.ebi.ac.uk/pdbsum/4xak PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4xak ProSAT]</span></td></tr>
 </table>
 == Function ==
@@ Line 17: / Line 19: @@
 </div>
 <div class="pdbe-citations 4xak" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[3D structures of antibody|3D structures of antibody]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
+[[Category: Betacoronavirus england 1]]
+[[Category: Human]]
 [[Category: Dimtrov, D S]]
 [[Category: Ying, T]]

4xak

From Proteopedia

Revision as of 16:17, 16 November 2017

Crystal structure of potent neutralizing antibody m336 in complex with MERS Co-V RBD

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox