4K62

Structure of an avian influenza H5 hemagglutinin from the influenza virus A/Indonesia/5/2005


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.235 
  • R-Value Observed: 0.238 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

An airborne transmissible avian influenza H5 hemagglutinin seen at the atomic level.

Zhang, W.Shi, Y.Lu, X.Shu, Y.Qi, J.Gao, G.F.

(2013) Science 340: 1463-1467

  • DOI: https://doi.org/10.1126/science.1236787
  • Primary Citation of Related Structures:  
    4K62, 4K63, 4K64, 4K65, 4K66, 4K67

  • PubMed Abstract: 

    Recent studies have identified several mutations in the hemagglutinin (HA) protein that allow the highly pathogenic avian H5N1 influenza A virus to transmit between mammals by airborne route. Here, we determined the complex structures of wild-type and mutant HAs derived from an Indonesia H5N1 virus bound to either avian or human receptor sialic acid analogs. A cis/trans conformational change in the glycosidic linkage of the receptor analog was observed, which explains how the H5N1 virus alters its receptor-binding preference. Furthermore, the mutant HA possessed low affinities for both avian and human receptors. Our findings provide a structural and biophysical basis for the H5N1 adaptation to acquire human, but maintain avian, receptor-binding properties.


  • Organizational Affiliation

    CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Hemagglutinin
A, C, E, G
321Influenza A virus (A/Indonesia/5/2005(H5N1))Mutation(s): 0 
Gene Names: HA
UniProt
Find proteins for A8HWY8 (Influenza A virus)
Explore A8HWY8 
Go to UniProtKB:  A8HWY8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA8HWY8
Glycosylation
Glycosylation Sites: 1
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
164Influenza A virus (A/Indonesia/5/2005(H5N1))Mutation(s): 0 
Gene Names: HA
UniProt
Find proteins for A8HWY8 (Influenza A virus)
Explore A8HWY8 
Go to UniProtKB:  A8HWY8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA8HWY8
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
I [auth A],
J [auth C]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.235 
  • R-Value Observed: 0.238 
  • Space Group: P 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.507α = 90
b = 70.507β = 90
c = 489.563γ = 120
Software Package:
Software NamePurpose
ADSCdata collection
PHASERphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-05-22
    Type: Initial release
  • Version 1.1: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Database references, Derived calculations, Structure summary
  • Version 1.2: 2022-08-24
    Changes: Database references, Structure summary
  • Version 1.3: 2023-11-08
    Changes: Data collection, Refinement description