7T1V

Crystal structure of an equine H7 hemagglutinin from A/equine/NY/49/73 (H7N7) in complex with 3'-GcLN


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.218 

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Literature

N -Glycolylneuraminic Acid Binding of Avian and Equine H7 Influenza A Viruses.

Spruit, C.M.Zhu, X.Tomris, I.Rios-Carrasco, M.Han, A.X.Broszeit, F.van der Woude, R.Bouwman, K.M.Luu, M.M.T.Matsuno, K.Sakoda, Y.Russell, C.A.Wilson, I.A.Boons, G.J.de Vries, R.P.

(2022) J Virol 96: e0212021-e0212021

  • DOI: https://doi.org/10.1128/jvi.02120-21
  • Primary Citation of Related Structures:  
    7T1V

  • PubMed Abstract: 

    Influenza A viruses (IAV) initiate infection by binding to glycans with terminal sialic acids on the cell surface. Hosts of IAV variably express two major forms of sialic acid, N -acetylneuraminic acid (NeuAc) and N -glycolylneuraminic acid (NeuGc). NeuGc is produced in most mammals, including horses and pigs, but is absent in humans, ferrets, and birds. The only known naturally occurring IAV that exclusively bind NeuGc are extinct highly pathogenic equine H7N7 viruses. We determined the crystal structure of a representative equine H7 hemagglutinin (HA) in complex with NeuGc and observed high similarity in the receptor-binding domain with an avian H7 HA. To determine the molecular basis for NeuAc and NeuGc specificity, we performed systematic mutational analyses, based on the structural insights, on two distant avian H7 HAs and an H15 HA. We found that the A135E mutation is key for binding α2,3-linked NeuGc but does not abolish NeuAc binding. The additional mutations S128T, I130V, T189A, and K193R converted the specificity from NeuAc to NeuGc. We investigated the residues at positions 128, 130, 135, 189, and 193 in a phylogenetic analysis of avian and equine H7 HAs. This analysis revealed a clear distinction between equine and avian residues. The highest variability was observed at key position 135, of which only the equine glutamic acid led to NeuGc binding. These results demonstrate that genetically distinct H7 and H15 HAs can be switched from NeuAc to NeuGc binding and vice versa after the introduction of several mutations, providing insights into the adaptation of H7 viruses to NeuGc receptors. IMPORTANCE Influenza A viruses cause millions of cases of severe illness and deaths annually. To initiate infection and replicate, the virus first needs to bind to a structure on the cell surface, like a key fitting in a lock. For influenza A viruses, these "keys" (receptors) on the cell surface are chains of sugar molecules (glycans). The terminal sugar on these glycans is often either N -acetylneuraminic acid (NeuAc) or N -glycolylneuraminic acid (NeuGc). Most influenza A viruses bind NeuAc, but a small minority bind NeuGc. NeuGc is present in species like horses, pigs, and mice but not in humans, ferrets, and birds. Here, we investigated the molecular determinants of NeuGc specificity and the origin of viruses that bind NeuGc.


  • Organizational Affiliation

    Department of Chemical Biology & Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, Utrecht Universitygrid.5477.1, Utrecht, the Netherlands.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Hemagglutinin HA1 chain
A, C, E
334Influenza A virus (A/equine/New York/49/1973(H7N7))Mutation(s): 0 
Gene Names: HA
UniProt
Find proteins for A0A348FV55 (Influenza A virus)
Explore A0A348FV55 
Go to UniProtKB:  A0A348FV55
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A348FV55
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Hemagglutinin HA2 chain
B, D, F
186Influenza A virus (A/equine/New York/49/1973(H7N7))Mutation(s): 0 
Gene Names: HA
UniProt
Find proteins for A0A348FV55 (Influenza A virus)
Explore A0A348FV55 
Go to UniProtKB:  A0A348FV55
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A348FV55
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 3
MoleculeChains Length2D Diagram Glycosylation3D Interactions
N-glycolyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
G
3N/A
Glycosylation Resources
GlyTouCan:  G08169IN
GlyCosmos:  G08169IN
GlyGen:  G08169IN
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
N-glycolyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose
I, K
2N/A
Glycosylation Resources
GlyTouCan:  G38557KR
GlyCosmos:  G38557KR
GlyGen:  G38557KR
Entity ID: 6
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
J, L
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.218 
  • Space Group: P 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 112.753α = 90
b = 112.753β = 90
c = 130.187γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Bill & Melinda Gates FoundationUnited StatesOPP1170236

Revision History  (Full details and data files)

  • Version 1.0: 2022-01-12
    Type: Initial release
  • Version 1.1: 2022-02-02
    Changes: Database references
  • Version 1.2: 2022-03-23
    Changes: Database references
  • Version 1.3: 2023-10-18
    Changes: Data collection, Refinement description