5VJL

Crystal structure of H7 hemagglutinin mutant (V186K, K193T, G228S) from the influenza virus A/Shanghai/2/2013 (H7N9) with LSTc

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.221 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history. 


Literature

Three mutations switch H7N9 influenza to human-type receptor specificity.

de Vries, R.P., Peng, W., Grant, O.C., Thompson, A.J., Zhu, X., Bouwman, K.M., de la Pena, A.T.T., van Breemen, M.J., Ambepitiya Wickramasinghe, I.N., de Haan, C.A.M., Yu, W., McBride, R., Sanders, R.W., Woods, R.J., Verheije, M.H., Wilson, I.A., Paulson, J.C.

(2017) PLoS Pathog 13: e1006390-e1006390

  • DOI: 10.1371/journal.ppat.1006390
  • Primary Citation of Related Structures:  
    5VJK, 5VJL, 5VJM

  • PubMed Abstract: 

    • The avian H7N9 influenza outbreak in 2013 resulted from an unprecedented incidence of influenza transmission to humans from infected poultry. The majority of human H7N9 isolates contained a hemagglutinin (HA) mutation (Q226L) that has previously been associated with a switch in receptor specificity from avian-type (NeuAcα2-3Gal) to human-type (NeuAcα2-6Gal), as documented for the avian progenitors of the 1957 (H2N2) and 1968 (H3N2) human influenza pandemic viruses ...

    The avian H7N9 influenza outbreak in 2013 resulted from an unprecedented incidence of influenza transmission to humans from infected poultry. The majority of human H7N9 isolates contained a hemagglutinin (HA) mutation (Q226L) that has previously been associated with a switch in receptor specificity from avian-type (NeuAcα2-3Gal) to human-type (NeuAcα2-6Gal), as documented for the avian progenitors of the 1957 (H2N2) and 1968 (H3N2) human influenza pandemic viruses. While this raised concern that the H7N9 virus was adapting to humans, the mutation was not sufficient to switch the receptor specificity of H7N9, and has not resulted in sustained transmission in humans. To determine if the H7 HA was capable of acquiring human-type receptor specificity, we conducted mutation analyses. Remarkably, three amino acid mutations conferred a switch in specificity for human-type receptors that resembled the specificity of the 2009 human H1 pandemic virus, and promoted binding to human trachea epithelial cells.

    Organizational Affiliation: 

    Departments of Molecular Medicine, & Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, United States of America.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Hemagglutinin HA1A325Influenza A virus (A/Shanghai/02/2013(H7N9))Mutation(s): 3 
Gene Names: HA
UniProt
Find proteins for R4NN21 (Influenza A virus)
Explore R4NN21 
Go to UniProtKB:  R4NN21
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupR4NN21
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Hemagglutinin HA2B183Influenza A virus (A/Shanghai/02/2013(H7N9))Mutation(s): 0 
Gene Names: HA
UniProt
Find proteins for R4NN21 (Influenza A virus)
Explore R4NN21 
Go to UniProtKB:  R4NN21
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupR4NN21
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SIA
Query on SIA
Download Ideal Coordinates CCD File 
C [auth A]N-acetyl-alpha-neuraminic acid
C11 H19 N O9
SQVRNKJHWKZAKO-YRMXFSIDSA-N		 Ligand Interaction
NAG
Query on NAG
Download Ideal Coordinates CCD File 
E [auth A],
F [auth A],
G [auth B]		2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N		 Ligand Interaction
MOH
Query on MOH
Download Ideal Coordinates CCD File 
D [auth A]METHANOL
C H4 O
OKKJLVBELUTLKV-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.221 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 116.375α = 90
b = 116.375β = 90
c = 296.008γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


View more in-depth experimental data

Entry History 

Deposition Data

  • Deposited Date: 2017-04-19 
  • Released Date: 2017-05-24 
    • Deposition Author(s): Zhu, X., Wilson, I.A.

Revision History  (Full details and data files)

  • Version 1.0: 2017-05-24
    Type: Initial release
  • Version 1.1: 2017-05-31
    Changes: Data collection
  • Version 1.2: 2017-06-28
    Changes: Database references
  • Version 1.3: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary