6BKN

Crystal structure of the A/Wyoming/3/2003 (H3N2) influenza virus hemagglutinin apo form

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.185 
  • R-Value Work: 0.167 
  • R-Value Observed: 0.168 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history. 


Literature

A complex epistatic network limits the mutational reversibility in the influenza hemagglutinin receptor-binding site.

Wu, N.C., Thompson, A.J., Xie, J., Lin, C.W., Nycholat, C.M., Zhu, X., Lerner, R.A., Paulson, J.C., Wilson, I.A.

(2018) Nat Commun 9: 1264-1264

  • DOI: 10.1038/s41467-018-03663-5
  • Structures With Same Primary Citation

  • PubMed Abstract: 

    • The hemagglutinin (HA) receptor-binding site (RBS) in human influenza A viruses is critical for attachment to host cells, which imposes a functional constraint on its natural evolution. On the other hand, being part of the major antigenic sites, the ...

    The hemagglutinin (HA) receptor-binding site (RBS) in human influenza A viruses is critical for attachment to host cells, which imposes a functional constraint on its natural evolution. On the other hand, being part of the major antigenic sites, the HA RBS of human H3N2 viruses needs to constantly mutate to evade the immune system. From large-scale mutagenesis experiments, we here show that several of the natural RBS substitutions become integrated into an extensive epistatic network that prevents substitution reversion. X-ray structural analysis reveals the mechanistic consequences as well as changes in the mode of receptor binding. Further studies are necessary to elucidate whether such entrenchment limits future options for immune escape or adversely affect long-term viral fitness.

    Organizational Affiliation: 

    The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA. wilson@scripps.edu.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Hemagglutinin
A
323Influenza A virus (A/Wyoming/3e/2003(H3))Mutation(s): 1 
Gene Names: HA
Find proteins for A4GYF9 (Influenza A virus)
Go to UniProtKB:  A4GYF9
Protein Feature View
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Hemagglutinin
B
174Influenza A virus (A/Nymc X-149C6(Puerto Rico/8/1934-Wyoming/03/2003)(H3N2))Mutation(s): 0 
Gene Names: HA
Find proteins for B4UPH9 (Influenza A virus)
Go to UniProtKB:  B4UPH9
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: 1.85 Å
  • R-Value Free: 0.185 
  • R-Value Work: 0.167 
  • R-Value Observed: 0.168 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 100.334α = 90
b = 100.333β = 90
c = 385.597γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data processing
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report


View more in-depth experimental data

Entry History & Funding Information

Deposition Data

  • Deposited Date: 2017-11-09 
  • Released Date: 2018-02-28 
    • 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: 2018-02-28
    Type: Initial release
  • Version 1.1: 2018-04-11
    Changes: Data collection, Database references
  • Version 1.2: 2019-12-11
    Changes: Author supporting evidence