3BGF

X-ray crystal structure of the SARS coronavirus spike receptor binding domain in complex with F26G19 Fab


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.234 
  • R-Value Observed: 0.237 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural insights into immune recognition of the severe acute respiratory syndrome coronavirus S protein receptor binding domain.

Pak, J.E.Sharon, C.Satkunarajah, M.Auperin, T.C.Cameron, C.M.Kelvin, D.J.Seetharaman, J.Cochrane, A.Plummer, F.A.Berry, J.D.Rini, J.M.

(2009) J Mol Biol 388: 815-823

  • DOI: 10.1016/j.jmb.2009.03.042
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • The spike (S) protein of the severe acute respiratory syndrome coronavirus (SARS-CoV) is responsible for host cell attachment and fusion of the viral and host cell membranes. Within S the receptor binding domain (RBD) mediates the interaction with an ...

    The spike (S) protein of the severe acute respiratory syndrome coronavirus (SARS-CoV) is responsible for host cell attachment and fusion of the viral and host cell membranes. Within S the receptor binding domain (RBD) mediates the interaction with angiotensin-converting enzyme 2 (ACE2), the SARS-CoV host cell receptor. Both S and the RBD are highly immunogenic and both have been found to elicit neutralizing antibodies. Reported here is the X-ray crystal structure of the RBD in complex with the Fab of a neutralizing mouse monoclonal antibody, F26G19, elicited by immunization with chemically inactivated SARS-CoV. The RBD-F26G19 Fab complex represents the first example of the structural characterization of an antibody elicited by an immune response to SARS-CoV or any fragment of it. The structure reveals that the RBD surface recognized by F26G19 overlaps significantly with the surface recognized by ACE2 and, as such, suggests that F26G19 likely neutralizes SARS-CoV by blocking the virus-host cell interaction.


    Organizational Affiliation

    Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Spike protein S1
A, S
193Severe 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
F26G19 Fab
C, L
212Mus musculusMutation(s): 0 
Find proteins for Q7TS98 (Mus musculus)
Go to UniProtKB:  Q7TS98
Protein Feature View
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
F26G19 Fab
B, H
220Mus musculusMutation(s): 0 
Find proteins for Q8CGS2 (Mus musculus)
Go to UniProtKB:  Q8CGS2
Protein Feature View
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.234 
  • R-Value Observed: 0.237 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 183.688α = 90
b = 73.365β = 90
c = 110.782γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
CBASSdata collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2007-11-26 
  • Released Date: 2008-12-02 
  • Deposition Author(s): Pak, J.E., Rini, J.M.

Revision History 

  • Version 1.0: 2008-12-02
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-10-25
    Changes: Refinement description