4MHI

Crystal structure of a H5N1 influenza virus hemagglutinin from A/goose/Guangdong/1/96


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.595 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.189 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

A Unique and Conserved Neutralization Epitope in H5N1 Influenza Viruses Identified by an Antibody against the A/Goose/Guangdong/1/96 Hemagglutinin.

Zhu, X.Guo, Y.H.Jiang, T.Wang, Y.D.Chan, K.H.Li, X.F.Yu, W.McBride, R.Paulson, J.C.Yuen, K.Y.Qin, C.F.Che, X.Y.Wilson, I.A.

(2013) J.Virol. 87: 12619-12635

  • DOI: 10.1128/JVI.01577-13
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Despite substantial efforts to control and contain H5N1 influenza viruses, bird flu viruses continue to spread and evolve. Neutralizing antibodies against conserved epitopes on the viral hemagglutinin (HA) could confer immunity to the diverse H5N1 vi ...

    Despite substantial efforts to control and contain H5N1 influenza viruses, bird flu viruses continue to spread and evolve. Neutralizing antibodies against conserved epitopes on the viral hemagglutinin (HA) could confer immunity to the diverse H5N1 virus strains and provide information for effective vaccine design. Here, we report the characterization of a broadly neutralizing murine monoclonal antibody, H5M9, to most H5N1 clades and subclades that was elicited by immunization with viral HA of A/Goose/Guangdong/1/96 (H5N1), the immediate precursor of the current dominant strains of H5N1 viruses. The crystal structures of the Fab' fragment of H5M9 in complexes with H5 HAs of A/Vietnam/1203/2004 and A/Goose/Guangdong/1/96 reveal a conserved epitope in the HA1 vestigial esterase subdomain that is some distance from the receptor binding site and partially overlaps antigenic site C of H3 HA. Further epitope characterization by selection of escape mutants and epitope mapping by flow cytometry analysis of site-directed mutagenesis of HA with a yeast cell surface display identified four residues that are critical for H5M9 binding. D53, Y274, E83a, and N276 are all conserved in H5N1 HAs and are not in H5 epitopes identified by other mouse or human antibodies. Antibody H5M9 is effective in protection of H5N1 virus both prophylactically and therapeutically and appears to neutralize by blocking both virus receptor binding and postattachment steps. Thus, the H5M9 epitope identified here should provide valuable insights into H5N1 vaccine design and improvement, as well as antibody-based therapies for treatment of H5N1 infection.


    Organizational Affiliation

    Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Hemagglutinin HA1 chain
A, C, E, G, I, K, M, O, Q
334Influenza A virus (strain A/Goose/Guangdong/1/1996 H5N1 genotype Gs/Gd)Mutation(s): 0 
Gene Names: HA
Find proteins for Q9Q0U6 (Influenza A virus (strain A/Goose/Guangdong/1/1996 H5N1 genotype Gs/Gd))
Go to UniProtKB:  Q9Q0U6
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Hemagglutinin HA2 chain
B, D, F, H, J, L, N, P, R
182Influenza A virus (strain A/Goose/Guangdong/1/1996 H5N1 genotype Gs/Gd)Mutation(s): 0 
Gene Names: HA
Find proteins for Q9Q0U6 (Influenza A virus (strain A/Goose/Guangdong/1/1996 H5N1 genotype Gs/Gd))
Go to UniProtKB:  Q9Q0U6
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MAN
Query on MAN

Download SDF File 
Download CCD File 
Q
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
A, C, E, G, I, K, M, O, Q, R
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.595 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.189 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 72.482α = 90.00
b = 225.728β = 98.97
c = 211.633γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling
HKL-2000data collection
PHASERphasing
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2013-08-29 
  • Released Date: 2013-10-02 
  • Deposition Author(s): Zhu, X., Wilson, I.A.

Revision History 

  • Version 1.0: 2013-10-02
    Type: Initial release
  • Version 1.1: 2013-11-20
    Type: Database references