6AOQ

Crystal structure of the A/Brisbane/10/2007 (H3N2) influenza virus hemagglutinin apo form


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.218 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

A structural explanation for the low effectiveness of the seasonal influenza H3N2 vaccine.

Wu, N.C.Zost, S.J.Thompson, A.J.Oyen, D.Nycholat, C.M.McBride, R.Paulson, J.C.Hensley, S.E.Wilson, I.A.

(2017) PLoS Pathog 13: e1006682-e1006682

  • DOI: 10.1371/journal.ppat.1006682
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • The effectiveness of the annual influenza vaccine has declined in recent years, especially for the H3N2 component, and is a concern for global public health. A major cause for this lack in effectiveness has been attributed to the egg-based vaccine pr ...

    The effectiveness of the annual influenza vaccine has declined in recent years, especially for the H3N2 component, and is a concern for global public health. A major cause for this lack in effectiveness has been attributed to the egg-based vaccine production process. Substitutions on the hemagglutinin glycoprotein (HA) often arise during virus passaging that change its antigenicity and hence vaccine effectiveness. Here, we characterize the effect of a prevalent substitution, L194P, in egg-passaged H3N2 viruses. X-ray structural analysis reveals that this substitution surprisingly increases the mobility of the 190-helix and neighboring regions in antigenic site B, which forms one side of the receptor binding site (RBS) and is immunodominant in recent human H3N2 viruses. Importantly, the L194P substitution decreases binding and neutralization by an RBS-targeted broadly neutralizing antibody by three orders of magnitude and significantly changes the HA antigenicity as measured by binding of human serum antibodies. The receptor binding mode and specificity are also altered to adapt to avian receptors during egg passaging. Overall, these findings help explain the low effectiveness of the seasonal vaccine against H3N2 viruses, and suggest that alternative approaches should be accelerated for producing influenza vaccines as well as isolating clinical isolates.


    Organizational Affiliation

    The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA, United States of America.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Hemagglutinin HA1 chain
A
323Influenza A virus (A/Brisbane/10/2007(H3N2))Mutation(s): 1 
Gene Names: HA
Find proteins for B2VNK2 (Influenza A virus)
Go to UniProtKB:  B2VNK2
Protein Feature View
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Hemagglutinin HA2 chain
B
174Influenza A virus (A/Brisbane/10/2007(H3N2))Mutation(s): 0 
Gene Names: HA
Find proteins for C3PR70 (Influenza A virus)
Go to UniProtKB:  C3PR70
Protein Feature View
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download CCD File 
A, B
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
BMA
Query on BMA

Download CCD File 
A
BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
 Ligand Interaction
MAN
Query on MAN

Download CCD File 
A
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.218 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 100.614α = 90
b = 100.614β = 90
c = 382.62γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data processing
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2017-08-16 
  • Released Date: 2017-10-18 
  • Deposition Author(s): Wu, N.C., Wilson, I.A.

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR56 AI117675
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR56 AI127371
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR01 AI114730

Revision History 

  • Version 1.0: 2017-10-18
    Type: Initial release
  • Version 1.1: 2017-11-08
    Changes: Database references
  • Version 1.2: 2019-12-11
    Changes: Author supporting evidence