4CYV

Structure of the A_mallard_Sweden_51_2002 H10 Avian Haemmaglutinin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.216 

Starting Model: experimental
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This is version 2.1 of the entry. See complete history


Literature

Receptor Binding by H10 Influenza Viruses.

Vachieri, S.G.Xiong, X.Collins, P.J.Walker, P.A.Martin, S.R.Haire, L.F.Zhang, Y.Mccauley, J.W.Gamblin, S.J.Skehel, J.J.

(2014) Nature 511: 475

  • DOI: https://doi.org/10.1038/nature13443
  • Primary Citation of Related Structures:  
    4CYV, 4CYW, 4CYZ, 4CZ0, 4D00

  • PubMed Abstract: 

    H10N8 follows H7N9 and H5N1 as the latest in a line of avian influenza viruses that cause serious disease in humans and have become a threat to public health. Since December 2013, three human cases of H10N8 infection have been reported, two of whom are known to have died. To gather evidence relating to the epidemic potential of H10 we have determined the structure of the haemagglutinin of a previously isolated avian H10 virus and we present here results relating especially to its receptor-binding properties, as these are likely to be major determinants of virus transmissibility. Our results show, first, that the H10 virus possesses high avidity for human receptors and second, from the crystal structure of the complex formed by avian H10 haemagglutinin with human receptor, it is clear that the conformation of the bound receptor has characteristics of both the 1918 H1N1 pandemic virus and the human H7 viruses isolated from patients in 2013 (ref. 3). We conclude that avian H10N8 virus has sufficient avidity for human receptors to account for its infection of humans but that its preference for avian receptors should make avian-receptor-rich human airway mucins an effective block to widespread infection. In terms of surveillance, particular attention will be paid to the detection of mutations in the receptor-binding site of the H10 haemagglutinin that decrease its avidity for avian receptor, and could enable it to be more readily transmitted between humans.


  • Organizational Affiliation

    1] MRC National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, UK [2].


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
HEMAGGLUTININ
A, C, E
324Influenza A virus (A/mallard/Sweden/51/2002(H10N2))Mutation(s): 0 
UniProt
Find proteins for E0YNJ7 (Influenza A virus)
Explore E0YNJ7 
Go to UniProtKB:  E0YNJ7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupE0YNJ7
Glycosylation
Glycosylation Sites: 2
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
HEMAGGLUTININ
B, D, F
172Influenza A virus (A/mallard/Sweden/51/2002(H10N2))Mutation(s): 0 
UniProt
Find proteins for E0YNJ7 (Influenza A virus)
Explore E0YNJ7 
Go to UniProtKB:  E0YNJ7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupE0YNJ7
Glycosylation
Glycosylation Sites: 2
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 3
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
G, I, K
5N-Glycosylation
Glycosylation Resources
GlyTouCan:  G22768VO
GlyCosmos:  G22768VO
GlyGen:  G22768VO
Entity ID: 4
MoleculeChains Length2D Diagram Glycosylation3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
H
3N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE
GlyCosmos:  G15407YE
GlyGen:  G15407YE
Entity ID: 5
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
J
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
BA [auth E]
L [auth A]
M [auth A]
Q [auth B]
U [auth C]
BA [auth E],
L [auth A],
M [auth A],
Q [auth B],
U [auth C],
Z [auth D]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
AA [auth D]
CA [auth E]
DA [auth E]
EA [auth E]
FA [auth F]
AA [auth D],
CA [auth E],
DA [auth E],
EA [auth E],
FA [auth F],
GA [auth F],
HA [auth F],
IA [auth F],
N [auth A],
O [auth A],
P [auth A],
R [auth B],
S [auth B],
T [auth B],
V [auth C],
W [auth C],
X [auth C],
Y [auth C]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.216 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.612α = 90
b = 227.989β = 110.32
c = 68.716γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-06-11
    Type: Initial release
  • Version 1.1: 2014-06-25
    Changes: Atomic model, Derived calculations, Other
  • Version 1.2: 2014-07-30
    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
  • Version 2.1: 2023-12-20
    Changes: Data collection, Database references, Refinement description, Structure summary