2GHW | pdb_00002ghw

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 (Depositor), 0.270 (DCC) 
  • R-Value Work: 
    0.248 (Depositor), 0.263 (DCC) 
  • R-Value Observed: 
    0.251 (Depositor) 

Starting Models: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.4 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 Biological Chem 281: 34610-34616

  • DOI: https://doi.org/10.1074/jbc.M603275200
  • Primary Citation 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.

Macromolecule Content 

  • Total Structure Weight: 98.85 kDa 
  • Atom Count: 7,089 
  • Modeled Residue Count: 842 
  • Deposited Residue Count: 900 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  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
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UniProt GroupP59594
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  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
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free:  0.295 (Depositor), 0.270 (DCC) 
  • R-Value Work:  0.248 (Depositor), 0.263 (DCC) 
  • R-Value Observed: 0.251 (Depositor) 
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

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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
  • Version 1.4: 2024-11-20
    Changes: Structure summary