5VTX

Crystal structure of the A/Hong Kong/1/1968 (H3N2) influenza virus hemagglutinin G225M/L226T/S228A mutant apo form

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.196 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history. 

Literature

Diversity of Functionally Permissive Sequences in the Receptor-Binding Site of Influenza Hemagglutinin.

Wu, N.C., Xie, J., Zheng, T., Nycholat, C.M., Grande, G., Paulson, J.C., Lerner, R.A., Wilson, I.A.

(2017) Cell Host Microbe 21: 742-753.e8

  • DOI: 10.1016/j.chom.2017.05.011
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    • Influenza A virus hemagglutinin (HA) initiates viral entry by engaging host receptor sialylated glycans via its receptor-binding site (RBS). The amino acid sequence of the RBS naturally varies across avian and human influenza virus subtypes and is al ...

    Influenza A virus hemagglutinin (HA) initiates viral entry by engaging host receptor sialylated glycans via its receptor-binding site (RBS). The amino acid sequence of the RBS naturally varies across avian and human influenza virus subtypes and is also evolvable. However, functional sequence diversity in the RBS has not been fully explored. Here, we performed a large-scale mutational analysis of the RBS of A/WSN/33 (H1N1) and A/Hong Kong/1/1968 (H3N2) HAs. Many replication-competent mutants not yet observed in nature were identified, including some that could escape from an RBS-targeted broadly neutralizing antibody. This functional sequence diversity is made possible by pervasive epistasis in the RBS 220-loop and can be buffered by avidity in viral receptor binding. Overall, our study reveals that the HA RBS can accommodate a much greater range of sequence diversity than previously thought, which has significant implications for the complex evolutionary interrelationships between receptor specificity and immune escape.

    Organizational Affiliation: 

    Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Hemagglutinin HA1 chain
A, C, E
323Influenza A virus (strain A/Hong Kong/1/1968 H3N2)Mutation(s): 3 
Gene Names: HA
Find proteins for Q91MA7 (Influenza A virus (strain A/Hong Kong/1/1968 H3N2))
Go to UniProtKB:  Q91MA7
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Hemagglutinin HA2 chain
B, D, F
174Influenza A virus (strain A/Hong Kong/1/1968 H3N2)Mutation(s): 0 
Gene Names: HA
Find proteins for Q91MA7 (Influenza A virus (strain A/Hong Kong/1/1968 H3N2))
Go to UniProtKB:  Q91MA7
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MAN
Query on MAN
Download SDF File 
Download CCD File 
E
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
BMA
Query on BMA
Download SDF File 
Download CCD File 
A, C, E
BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
 Ligand Interaction
NAG
Query on NAG
Download SDF File 
Download CCD File 
A, C, D, E, F
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.196 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 208.587α = 90.00
b = 131.060β = 97.98
c = 72.252γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
REFMACrefinement
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History & Funding Information

Deposition Data

  • Deposited Date: 2017-05-18 
  • Released Date: 2017-06-28 
  • Deposition Author(s): Wu, N.C., Wilson, I.A.
Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious DiseasesUnited StatesR56 AI117675
National Institutes of Health/National Institute Of Allergy and Infectious DiseasesUnited StatesR01 AI114730

Revision History 

  • Version 1.0: 2017-06-28
    Type: Initial release
  • Version 1.1: 2017-09-20
    Type: Author supporting evidence, Refinement description