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 

wwPDB Validation 3D Report Full Report


This is version 1.2 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: 10.1074/jbc.M603275200
  • Structures With Same Primary Citation

  • 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 gly ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Spike glycoprotein
A, C
203Severe acute respiratory syndrome-related coronavirusMutation(s): 0 
Gene Names: S2
Find proteins for P59594 (Human SARS coronavirus)
Go to UniProtKB:  P59594
Protein Feature View
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
anti-sars scFv antibody, 80R
B, D
247Homo sapiensMutation(s): 0 
Gene Names: scFv
Find proteins for Q65ZC9 (Homo sapiens)
Go to UniProtKB:  Q65ZC9
Protein Feature View
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download CCD File 
A, C
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
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 

  • 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