4BH0

H5 (tyTy) Influenza Virus Haemagglutinin in Complex with Human Receptor Analogue 6'-SLN


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.36 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.214 

wwPDB Validation   3D Report Full Report



Literature

Receptor Binding by a Ferret-Transmissible H5 Avian Influenza Virus

Xiong, X.Coombs, P.J.R Martin, S.Liu, J.Xiao, H.Mccauley, J.W.Locher, K.Walker, P.A.Collins, P.J.Kawaoka, Y.Skehel, J.J.Gamblin, S.J.

(2013) Nature 497: 392

  • DOI: 10.1038/nature12144
  • Primary Citation of Related Structures:  
    4BH2, 4BH3, 4BH4, 4BGW, 4BGX, 4BH0, 4BH1, 4BGY, 4BGZ

  • PubMed Abstract: 
  • Cell-surface-receptor binding by influenza viruses is a key determinant of their transmissibility, both from avian and animal species to humans as well as from human to human. Highly pathogenic avian H5N1 viruses that are a threat to public health ha ...

    Cell-surface-receptor binding by influenza viruses is a key determinant of their transmissibility, both from avian and animal species to humans as well as from human to human. Highly pathogenic avian H5N1 viruses that are a threat to public health have been observed to acquire affinity for human receptors, and transmissible-mutant-selection experiments have identified a virus that is transmissible in ferrets, the generally accepted experimental model for influenza in humans. Here, our quantitative biophysical measurements of the receptor-binding properties of haemagglutinin (HA) from the transmissible mutant indicate a small increase in affinity for human receptor and a marked decrease in affinity for avian receptor. From analysis of virus and HA binding data we have derived an algorithm that predicts virus avidity from the affinity of individual HA-receptor interactions. It reveals that the transmissible-mutant virus has a 200-fold preference for binding human over avian receptors. The crystal structure of the transmissible-mutant HA in complex with receptor analogues shows that it has acquired the ability to bind human receptor in the same folded-back conformation as seen for HA from the 1918, 1957 (ref. 4), 1968 (ref. 5) and 2009 (ref. 6) pandemic viruses. This binding mode is substantially different from that by which non-transmissible wild-type H5 virus HA binds human receptor. The structure of the complex also explains how the change in preference from avian to human receptors arises from the Gln226Leu substitution, which facilitates binding to human receptor but restricts binding to avian receptor. Both features probably contribute to the acquisition of transmissibility by this mutant virus.


    Organizational Affiliation

    MRC National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, UK.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
HEMAGGLUTININACE327Influenza A virus (A/turkey/Turkey/1/2005(H5N1))Mutation(s): 0 
Gene Names: HA
Find proteins for Q207Z6 (Influenza A virus)
Explore Q207Z6 
Go to UniProtKB:  Q207Z6
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
HEMAGGLUTININBDF166Influenza A virus (A/turkey/Turkey/1/2005(H5N1))Mutation(s): 0 
Gene Names: HA
Find proteins for Q207Z6 (Influenza A virus)
Explore Q207Z6 
Go to UniProtKB:  Q207Z6
Protein Feature View
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  • Reference Sequence
Oligosaccharides

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Entity ID: 3
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose
G
2 N/A Oligosaccharides Interaction
Entity ID: 4
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
H, I
3 N/A Oligosaccharides Interaction
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

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A, C, E
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
PO4
Query on PO4

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A, C, E
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 4
IDChainsNameType/Class2D Diagram3D Interactions
PRD_900046
Query on PRD_900046
H, I6'-sialyl-N-acetyllactosamineOligosaccharide /  Glycan component

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.36 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.214 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.346α = 90
b = 228.296β = 114.01
c = 71.267γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-04-24
    Type: Initial release
  • Version 1.1: 2013-05-08
    Changes: Database references
  • Version 1.2: 2013-05-15
    Changes: Database references
  • Version 1.3: 2013-05-22
    Changes: Database references
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Other, Structure summary