8FAW

Structure of Hemagglutinin from Influenza A/Victoria/22/2020 in complex with LSTC


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.16 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.201 

Starting Model: experimental
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This is version 1.2 of the entry. See complete history


Literature

Epistasis mediates the evolution of the receptor binding mode in recent human H3N2 hemagglutinin.

Lei, R.Liang, W.Ouyang, W.O.Hernandez Garcia, A.Kikuchi, C.Wang, S.McBride, R.Tan, T.J.C.Sun, Y.Chen, C.Graham, C.S.Rodriguez, L.A.Shen, I.R.Choi, D.Bruzzone, R.Paulson, J.C.Nair, S.K.Mok, C.K.P.Wu, N.C.

(2024) Nat Commun 15: 5175-5175

  • DOI: https://doi.org/10.1038/s41467-024-49487-4
  • Primary Citation of Related Structures:  
    8FAQ, 8FAW

  • PubMed Abstract: 

    The receptor-binding site of influenza A virus hemagglutinin partially overlaps with major antigenic sites and constantly evolves. In this study, we observe that mutations G186D and D190N in the hemagglutinin receptor-binding site have coevolved in two recent human H3N2 clades. X-ray crystallography results show that these mutations coordinately drive the evolution of the hemagglutinin receptor binding mode. Epistasis between G186D and D190N is further demonstrated by glycan binding and thermostability analyses. Immunization and neutralization experiments using mouse and human samples indicate that the evolution of receptor binding mode is accompanied by a change in antigenicity. Besides, combinatorial mutagenesis reveals that G186D and D190N, along with other natural mutations in recent H3N2 strains, alter the compatibility with a common egg-adaptive mutation in seasonal influenza vaccines. Overall, our findings elucidate the role of epistasis in shaping the recent evolution of human H3N2 hemagglutinin and substantiate the high evolvability of its receptor-binding mode.


  • Organizational Affiliation

    Department of Biochemistry, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Hemagglutinin492Influenza A virusMutation(s): 0 
Gene Names: HA
UniProt
Find proteins for A0A6M4ZXR4 (Influenza A virus)
Explore A0A6M4ZXR4 
Go to UniProtKB:  A0A6M4ZXR4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A6M4ZXR4
Glycosylation
Glycosylation Sites: 4
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
B, C
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Entity ID: 3
MoleculeChains Length2D Diagram Glycosylation3D Interactions
N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-beta-D-galactopyranose-(1-4)-beta-D-glucopyranose
D
5N/A
Glycosylation Resources
GlyTouCan:  G83513YI
GlyCosmos:  G83513YI
GlyGen:  G83513YI
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.16 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.201 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 100.349α = 90
b = 100.349β = 90
c = 395.503γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
autoPROCdata reduction
XDSdata scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR00 AI139445
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesDP2 AT011966
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR01 AI167910

Revision History  (Full details and data files)

  • Version 1.0: 2024-06-19
    Type: Initial release
  • Version 1.1: 2024-07-24
    Changes: Database references
  • Version 1.2: 2024-10-23
    Changes: Structure summary