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 

Starting Model: experimental
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This is version 2.1 of the entry. See complete history


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: https://doi.org/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 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
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
hemagglutinin
A, C, E, G, I
A, C, E, G, I, K, M, O, Q
334Influenza A virus (A/Viet Nam/1203/2004(H5N1))Mutation(s): 0 
UniProt
Find proteins for Q1KHJ8 (Influenza A virus)
Explore Q1KHJ8 
Go to UniProtKB:  Q1KHJ8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ1KHJ8
Glycosylation
Glycosylation Sites: 2
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
hemagglutinin
B, D, F, H, J
B, D, F, H, J, L, N, P, R
181Influenza A virus (A/Viet Nam/1203/2004(H5N1))Mutation(s): 0 
UniProt
Find proteins for Q1KHG8 (Influenza A virus)
Explore Q1KHG8 
Go to UniProtKB:  Q1KHG8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ1KHG8
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

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Entity ID: 3
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
AA [auth a],
BA [auth b],
CA [auth c],
DA [auth d],
EA [auth e],
AA [auth a],
BA [auth b],
CA [auth c],
DA [auth d],
EA [auth e],
FA [auth f],
GA [auth g],
HA [auth h],
S,
U,
V,
W,
Y
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Entity ID: 4
MoleculeChains 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
3N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE
GlyCosmos:  G15407YE
GlyGen:  G15407YE
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

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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
  • Version 2.1: 2023-08-30
    Changes: Data collection, Database references, Refinement description, Structure summary