Biological Assembly 1  

 3D View: Structure | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Cyclic - C3  (3D View)
Global Stoichiometry: Hetero 6-mer - A3B3 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 57.36 kDa 
• Atom Count: 4258 
• Modelled Residue Count: 483 
• Deposited Residue Count: 492 
• Unique protein chains: 2

4BGW

Crystal Structure of H5 (VN1194) Influenza Haemagglutinin

• DOI: 10.2210/pdb4BGW/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Influenza A virus (A/Vietnam/1194/2004(H5N1))
• Mutation(s): No 


• Deposited: 2013-03-29 Released: 2013-04-24 
• Deposition Author(s): Xiong, X., Coombs, P., Martin, S.R., Liu, J., Xiao, H., McCauley, J.W., Locher, K., Walker, P.A., Collins, P.J., Kawaoka, Y., Skehel, J.J., Gamblin, S.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.48 Å
• R-Value Free: 0.258 
• R-Value Work: 0.208 
• R-Value Observed: 0.210 

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

• PubMed: 23615615 
• DOI: 10.1038/nature12144
• Primary Citation of Related Structures:  
  4BGW, 4BGX, 4BGY, 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 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HEMAGGLUTININ	A	326	Influenza A virus (A/Vietnam/1194/2004(H5N1))	Mutation(s): 0  Gene Names: HA
UniProt
Find proteins for Q6DQ34 (Influenza A virus) Explore Q6DQ34  Go to UniProtKB:  Q6DQ34

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
HEMAGGLUTININ	B	166	Influenza A virus (A/Vietnam/1194/2004(H5N1))	Mutation(s): 0  Gene Names: HA
UniProt
Find proteins for Q6DQ34 (Influenza A virus) Explore Q6DQ34  Go to UniProtKB:  Q6DQ34

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose	C	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G79924RM GlyCosmos:  G79924RM GlyGen:  G79924RM

Entity ID: 4
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	D	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EPE	F [auth B]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C8 H18 N2 O4 S JKMHFZQWWAIEOD-UHFFFAOYSA-N
NAG (Subject of Investigation/LOI)	E [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.48 Å
• R-Value Free: 0.258 
• R-Value Work: 0.208 
• R-Value Observed: 0.210 
• Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 101.24	α = 90
b = 101.24	β = 90
c = 451.32	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Ligand Structure Quality Assessment  

Entry History 

Deposition Data

• Deposited Date: 2013-03-29 
• Released Date: 2013-04-24 
Deposition Author(s): Xiong, X., Coombs, P., Martin, S.R., Liu, J., Xiao, H., McCauley, J.W., Locher, K., Walker, P.A., Collins, P.J., Kawaoka, Y., Skehel, J.J., Gamblin, S.J.

Revision History  

• Version 1.0: 2013-04-24
  Type: Initial release
  
• Version 1.1: 2013-05-01
  Changes: Structure summary
• Version 1.2: 2013-05-08
  Changes: Database references, Refinement description
• Version 1.3: 2013-05-15
  Changes: Database references
• Version 1.4: 2013-05-22
  Changes: Database references
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Other, Structure summary