6NB6

SARS-CoV complex with human neutralizing S230 antibody Fab fragment (state 1)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.2 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Unexpected Receptor Functional Mimicry Elucidates Activation of Coronavirus Fusion.

Walls, A.C.Xiong, X.Park, Y.J.Tortorici, M.A.Snijder, J.Quispe, J.Cameroni, E.Gopal, R.Dai, M.Lanzavecchia, A.Zambon, M.Rey, F.A.Corti, D.Veesler, D.

(2019) Cell 176: 1026-1039.e15

  • DOI: 10.1016/j.cell.2018.12.028
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Recent outbreaks of severe acute respiratory syndrome and Middle East respiratory syndrome, along with the threat of a future coronavirus-mediated pandemic, underscore the importance of finding ways to combat these viruses. The trimeric spike transme ...

    Recent outbreaks of severe acute respiratory syndrome and Middle East respiratory syndrome, along with the threat of a future coronavirus-mediated pandemic, underscore the importance of finding ways to combat these viruses. The trimeric spike transmembrane glycoprotein S mediates entry into host cells and is the major target of neutralizing antibodies. To understand the humoral immune response elicited upon natural infections with coronaviruses, we structurally characterized the SARS-CoV and MERS-CoV S glycoproteins in complex with neutralizing antibodies isolated from human survivors. Although the two antibodies studied blocked attachment to the host cell receptor, only the anti-SARS-CoV S antibody triggered fusogenic conformational changes via receptor functional mimicry. These results provide a structural framework for understanding coronavirus neutralization by human antibodies and shed light on activation of coronavirus membrane fusion, which takes place through a receptor-driven ratcheting mechanism.


    Organizational Affiliation

    Humabs Biomed SA, Vir Biotechnology, 6500 Bellinzona, Switzerland.,Institute for Research in Biomedicine, Faculty of Biomedical Sciences, Università della Svizzera italiana, 6500 Bellinzona, Switzerland.,Crick Worldwide Influenza Centre, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK.,National Infection Service, Public Health England, London NW9 5HT, UK.,Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA.,Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA; Institute Pasteur & CNRS UMR 3569, Unité de Virologie Structurale, 75015, Paris, France.,Institute Pasteur & CNRS UMR 3569, Unité de Virologie Structurale, 75015, Paris, France.,Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA. Electronic address: dveesler@uw.edu.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Spike glycoprotein
A, B, C
1263Human SARS coronavirusMutation(s): 0 
Gene Names: S
Find proteins for P59594 (Human SARS coronavirus)
Go to UniProtKB:  P59594
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
S230 heavy chain
H, I
127N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
S230 light chain
L, M
112N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MAN
Query on MAN

Download SDF File 
Download CCD File 
A, B, C
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
BMA
Query on BMA

Download SDF File 
Download CCD File 
A, B, C
BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
A, B, C
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.2 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM120553

Revision History 

  • Version 1.0: 2019-02-06
    Type: Initial release
  • Version 1.1: 2019-02-20
    Type: Data collection, Database references
  • Version 1.2: 2019-03-06
    Type: Data collection, Database references
  • Version 1.3: 2020-01-08
    Type: Author supporting evidence