4K66

Structure of an airborne transmissible avian influenza H5 hemagglutinin mutant from the influenza virus A/Indonesia/5/2005 complexed with avian receptor analog LSTa


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.219 
  • R-Value Observed: 0.221 

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Ligand Structure Quality Assessment 


This is version 2.0 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 

  • DOI: 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 ...

    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)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
HemagglutininA, C, E, G321Influenza A virus (A/Indonesia/5/2005(H5N1))Mutation(s): 4 
Gene Names: HA
UniProt
Find proteins for A8HWY8 (Influenza A virus)
Explore A8HWY8 
Go to UniProtKB:  A8HWY8
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
HemagglutininB, D, F, H164Influenza 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
Protein Feature View
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 3
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranoseI, J2N/A Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G30207PZ
GlyCosmos:  G30207PZ
GlyGen:  G30207PZ
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG (Subject of Investigation/LOI)
Query on NAG

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.219 
  • R-Value Observed: 0.221 
  • Space Group: P 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.605α = 90
b = 70.605β = 90
c = 490.126γ = 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: 2013-05-29
    Changes: Refinement description
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Structure summary