Biological Assembly 1  

 3D View: Structure | Electron Density | 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: 59.11 kDa 
• Atom Count: 4166 
• Residue Count: 483 
• Unique protein chains: 2

4CQU

H5 (VN1194) Asn186Lys Mutant Haemagglutinin in Complex with Human Receptor Analogue 6'SLN

• DOI: 10.2210/pdb4CQU/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Influenza A virus (A/Vietnam/1194/2004(H5N1))
• Expression System: Gallus gallus
• Mutation(s): Yes 


• Deposited: 2014-02-21 Released: 2014-05-28 
• Deposition Author(s): Xiong, X., Xiao, H., Martin, S.R., Coombs, P.J., Liu, J., Collins, P.J., Vachieri, S.G., Walker, P.A., Lin, Y.P., McCauley, J.W., Gamblin, S.J., Skehel, J.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.48 Å
• R-Value Free: 0.241 
• R-Value Work: 0.204 
• R-Value Observed: 0.206 

Literature

Enhanced Human Receptor Binding by H5 Haemagglutinins.

Xiong, X., Xiao, H., Martin, S.R., Coombs, P.J., Liu, J., Collins, P.J., Vachieri, S.G., Walker, P.A., Lin, Y.P., Mccauley, J.W., Gamblin, S.J., Skehel, J.J.

(2014) Virology 456: 179

• PubMed: 24889237 
• DOI: 10.1016/j.virol.2014.03.008
• Primary Citation of Related Structures:  
  5AJM, 4CQZ, 4CQR, 4CQS, 4CQU, 4CQV, 4CQW, 4CQX, 4CQY, 4CR0


• PubMed Abstract: 
  

Mutant H5N1 influenza viruses have been isolated from humans that have increased human receptor avidity. We have compared the receptor binding properties of these mutants with those of wild-type viruses, and determined the structures of their haemagglutinins in complex with receptor analogues. Mutants from Vietnam bind tighter to human receptor by acquiring basic residues near the receptor binding site. They bind more weakly to avian receptor because they lack specific interactions between Asn-186 and Gln-226. In contrast, a double mutant, Δ133/Ile155Thr, isolated in Egypt has greater avidity for human receptor while retaining wild-type avidity for avian receptor. Despite these increases in human receptor binding, none of the mutants prefers human receptor, unlike aerosol transmissible H5N1 viruses. Nevertheless, mutants with high avidity for both human and avian receptors may be intermediates in the evolution of H5N1 viruses that could infect both humans and poultry.

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Organizational Affiliation: 

MRC National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, UK. Electronic address: [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemagglutinin HA1	A	326	Influenza A virus (A/Vietnam/1194/2004(H5N1))	Mutation(s): 1  Gene Names: HA
Find proteins for Q6DQ34 (Influenza A virus) Explore Q6DQ34  Go to UniProtKB:  Q6DQ34

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemagglutinin HA2	B	166	Influenza A virus (A/Vietnam/1194/2004(H5N1))	Mutation(s): 0  Gene Names: HA
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-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C	2		N-Glycosylation

Entity ID: 4
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
beta-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	D	5		N-Glycosylation

Entity ID: 5
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose	E	2		N/A

Entity ID: 6
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	F	3		N-Glycosylation

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	A	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
MPO	B	3[N-MORPHOLINO]PROPANE SULFONIC ACID C7 H15 N O4 S DVLFYONBTKHTER-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.48 Å
• R-Value Free: 0.241 
• R-Value Work: 0.204 
• R-Value Observed: 0.206 
• Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 101.464	α = 90
b = 101.464	β = 90
c = 452.187	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
xia2	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2014-02-21 
• Released Date: 2014-05-28 
Deposition Author(s): Xiong, X., Xiao, H., Martin, S.R., Coombs, P.J., Liu, J., Collins, P.J., Vachieri, S.G., Walker, P.A., Lin, Y.P., McCauley, J.W., Gamblin, S.J., Skehel, J.J.

Revision History 

• Version 1.0: 2014-05-28
  Type: Initial release
  
• Version 1.1: 2014-06-11
  Changes: Database references
• Version 1.2: 2018-11-07
  Changes: Data collection, Database references, Source and taxonomy, Structure summary
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Other, Structure summary