Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Cyclic - C3  (3D View)
Global Stoichiometry: Hetero 6-mer - A3B 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 58.85 kDa 
• Atom Count: 4584 
• Residue Count: 490 
• Unique protein chains: 2

6AOR

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

• DOI: 10.2210/pdb6AOR/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Influenza A virus (A/Brisbane/10/2007(H3N2))
• Expression System: Trichoplusia ni
• Mutation(s): Yes 


• Deposited: 2017-08-16 Released: 2017-10-18 
• Deposition Author(s): Wu, N.C., Wilson, I.A.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.196 
• R-Value Work: 0.169 
• R-Value Observed: 0.170 

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

• PubMed: 29059230 
• 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 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Hemagglutinin HA1 chain	A	323	Influenza A virus (A/Brisbane/10/2007(H3N2))	Mutation(s): 1  Gene Names: HA
Find proteins for B2VNK2 (Influenza A virus) Go to UniProtKB:  B2VNK2

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
Hemagglutinin HA2 chain	B	174	Influenza A virus (A/Brisbane/10/2007(H3N2))	Mutation(s): 0  Gene Names: HA
Find proteins for C3PR70 (Influenza A virus) Go to UniProtKB:  C3PR70

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	A, B	N-ACETYL-D-GLUCOSAMINE C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
BMA	A	BETA-D-MANNOSE C6 H12 O6 WQZGKKKJIJFFOK-RWOPYEJCSA-N
MAN	A	ALPHA-D-MANNOSE C6 H12 O6 WQZGKKKJIJFFOK-PQMKYFCFSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.196 
• R-Value Work: 0.169 
• R-Value Observed: 0.170 
• Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 100.556	α = 90
b = 100.556	β = 90
c = 384.183	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data processing
HKL-2000	data scaling
PHASER	phasing

Structure Validation

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.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	R56 AI117675
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	R56 AI127371
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	R01 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