2GHW

Crystal structure of SARS spike protein receptor binding domain in complex with a neutralizing antibody, 80R


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.295 
  • R-Value Work: 0.248 
  • R-Value Observed: 0.251 

Starting Models: experimental
View more details

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structural basis of neutralization by a human anti-severe acute respiratory syndrome spike protein antibody, 80R.

Hwang, W.C.Lin, Y.Santelli, E.Sui, J.Jaroszewski, L.Stec, B.Farzan, M.Marasco, W.A.Liddington, R.C.

(2006) J Biol Chem 281: 34610-34616

  • DOI: https://doi.org/10.1074/jbc.M603275200
  • Primary Citation of Related Structures:  
    2GHV, 2GHW

  • PubMed Abstract: 

    Severe acute respiratory syndrome (SARS) is a newly emerged infectious disease that caused pandemic spread in 2003. The etiological agent of SARS is a novel coronavirus (SARS-CoV). The coronaviral surface spike protein S is a type I transmembrane glycoprotein that mediates initial host binding via the cell surface receptor angiotensin-converting enzyme 2 (ACE2), as well as the subsequent membrane fusion events required for cell entry. Here we report the crystal structure of the S1 receptor binding domain (RBD) in complex with a neutralizing antibody, 80R, at 2.3 A resolution, as well as the structure of the uncomplexed S1 RBD at 2.2 A resolution. We show that the 80R-binding epitope on the S1 RBD overlaps very closely with the ACE2-binding site, providing a rationale for the strong binding and broad neutralizing ability of the antibody. We provide a structural basis for the differential effects of certain mutations in the spike protein on 80R versus ACE2 binding, including escape mutants, which should facilitate the design of immunotherapeutics to treat a future SARS outbreak. We further show that the RBD of S1 forms dimers via an extensive interface that is disrupted in receptor- and antibody-bound crystal structures, and we propose a role for the dimer in virus stability and infectivity.


  • Organizational Affiliation

    Infectious and Inflammatory Disease Center, Burnham Institute for Medical Research, La Jolla, California 92037, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Spike glycoprotein
A, C
203Severe acute respiratory syndrome-related coronavirusMutation(s): 0 
Gene Names: S
UniProt
Find proteins for P59594 (Severe acute respiratory syndrome coronavirus)
Explore P59594 
Go to UniProtKB:  P59594
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP59594
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
anti-sars scFv antibody, 80R
B, D
247Homo sapiensMutation(s): 0 
UniProt
Find proteins for Q65ZC9 (Homo sapiens)
Explore Q65ZC9 
Go to UniProtKB:  Q65ZC9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ65ZC9
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.295 
  • R-Value Work: 0.248 
  • R-Value Observed: 0.251 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 47.453α = 90
b = 175.902β = 96.55
c = 67.561γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
Blu-Icedata collection
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-09-19
    Type: Initial release
  • Version 1.1: 2008-05-05
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-08-30
    Changes: Data collection, Database references, Derived calculations, Refinement description