4BGY

H5 (VN1194) Influenza Virus Haemagglutinin in Complex with Avian Receptor Analogue 3'-SLN


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.68 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.202 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Receptor Binding by a Ferret-Transmissible H5 Avian Influenza Virus.

Xiong, X.Coombs, P.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:  4BGW, 4BGX, 4BGZ, 4BH0, 4BH1, 4BH2, 4BH3, 4BH4

  • 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

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HEMAGGLUTININ
A
326Influenza A virus (A/Vietnam/1194/2004(H5N1))Gene Names: HA
Find proteins for Q6DQ34 (Influenza A virus (A/Vietnam/1194/2004(H5N1)))
Go to UniProtKB:  Q6DQ34
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
HEMAGGLUTININ
B
166Influenza A virus (A/Vietnam/1194/2004(H5N1))Gene Names: HA
Find proteins for Q6DQ34 (Influenza A virus (A/Vietnam/1194/2004(H5N1)))
Go to UniProtKB:  Q6DQ34
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EPE
Query on EPE

Download SDF File 
Download CCD File 
B
4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
HEPES
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
 Ligand Interaction
GAL
Query on GAL

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Download CCD File 
A
BETA-D-GALACTOSE
C6 H12 O6
WQZGKKKJIJFFOK-FPRJBGLDSA-N
 Ligand Interaction
NAG
Query on NAG

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Download CCD File 
A, B
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
SIA
Query on SIA

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Download CCD File 
A
O-SIALIC ACID
C11 H19 N O9
SQVRNKJHWKZAKO-YRMXFSIDSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.68 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.202 
  • Space Group: H 3 2
Unit Cell:
Length (Å)Angle (°)
a = 101.403α = 90.00
b = 101.403β = 90.00
c = 449.997γ = 120.00
Software Package:
Software NamePurpose
SCALAdata scaling
MOSFLMdata reduction
PHASERphasing
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-04-24
    Type: Initial release
  • Version 1.1: 2013-05-08
    Type: Database references, Refinement description
  • Version 1.2: 2013-05-15
    Type: Database references
  • Version 1.3: 2013-05-22
    Type: Database references