2FK0

Crystal Structure of a H5N1 influenza virus hemagglutinin.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.95 Å
  • R-Value Free: 0.319 
  • R-Value Work: 0.268 
  • R-Value Observed: 0.269 

wwPDB Validation   3D Report Full Report



Literature

Structure and Receptor Specificity of the Hemagglutinin from an H5N1 Influenza Virus.

Stevens, J.Blixt, O.Tumpey, T.M.Taubenberger, J.K.Paulson, J.C.Wilson, I.A.

(2006) Science 312: 404-410

  • DOI: 10.1126/science.1124513
  • Primary Citation of Related Structures:  
    2FK0

  • PubMed Abstract: 
  • The hemagglutinin (HA) structure at 2.9 angstrom resolution, from a highly pathogenic Vietnamese H5N1 influenza virus, is more related to the 1918 and other human H1 HAs than to a 1997 duck H5 HA. Glycan microarray analysis of this Viet04 HA reveals ...

    The hemagglutinin (HA) structure at 2.9 angstrom resolution, from a highly pathogenic Vietnamese H5N1 influenza virus, is more related to the 1918 and other human H1 HAs than to a 1997 duck H5 HA. Glycan microarray analysis of this Viet04 HA reveals an avian alpha2-3 sialic acid receptor binding preference. Introduction of mutations that can convert H1 serotype HAs to human alpha2-6 receptor specificity only enhanced or reduced affinity for avian-type receptors. However, mutations that can convert avian H2 and H3 HAs to human receptor specificity, when inserted onto the Viet04 H5 HA framework, permitted binding to a natural human alpha2-6 glycan, which suggests a path for this H5N1 virus to gain a foothold in the human population.


    Organizational Affiliation

    Department of Molecular Biology, Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA. jstevens@scripps.edu



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
hemagglutininACEGIKMOQ334Influenza A virus (A/Viet Nam/1203/2004(H5N1))Mutation(s): 0 
Find proteins for Q1KHJ8 (Influenza A virus)
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Go to UniProtKB:  Q1KHJ8
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
hemagglutininBDFHJLNPR181Influenza A virus (A/Viet Nam/1203/2004(H5N1))Mutation(s): 0 
Find proteins for Q1KHG8 (Influenza A virus)
Explore Q1KHG8 
Go to UniProtKB:  Q1KHG8
Protein Feature View
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  • Reference Sequence
Oligosaccharides

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Entity ID: 3
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
S, U, V, W, Y, a, b, c, d, e, f, g, h
2 N-Glycosylation Oligosaccharides Interaction
Entity ID: 4
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
T, X, Z
3 N-Glycosylation Oligosaccharides Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.95 Å
  • R-Value Free: 0.319 
  • R-Value Work: 0.268 
  • R-Value Observed: 0.269 
  • Space Group: P 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 197.943α = 90
b = 197.943β = 90
c = 134.688γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-05-02
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Structure summary