9BT5 | pdb_00009bt5

The crystal structure of the HA1 domain of hemagglutinin from A/Shanghai/02/2013 (H7N9) bound to H7-235 Fab


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 
    0.251 (Depositor), 0.250 (DCC) 
  • R-Value Work: 
    0.195 (Depositor), 0.194 (DCC) 
  • R-Value Observed: 
    0.198 (Depositor) 

Starting Model: experimental
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Literature

Pan-H7 influenza human antibody virus neutralization depends on avidity and steric hindrance.

Gilchuk, I.M.Dong, J.Irving, R.P.Buchman, C.D.Armstrong, E.Turner, H.L.Li, S.Ward, A.B.Carnahan, R.H.Crowe Jr., J.E.

(2025) JCI Insight 10

  • DOI: https://doi.org/10.1172/jci.insight.186182
  • Primary Citation of Related Structures:  
    9BT5

  • PubMed Abstract: 

    H7N9 avian influenza virus is a zoonotic influenza virus of public health concern, with a 39% mortality rate in humans. H7N9-specific prevention or treatments for humans have not been approved. We previously isolated a human monoclonal antibody (mAb) designated H7-235 that broadly reacts to diverse H7 viruses and neutralizes H7N9 viruses in vitro. Here, we report the crystal structure of H7 HA1 bound to the fragment antigen-binding region (Fab) of recombinant H7-235 (rH7-235). The crystal structure revealed that rH7-235 recognizes residues near but outside of the receptor binding site (RBS). Nevertheless, the rH7-235 IgG potently inhibits hemagglutination mediated by H7N9 viruses due to avidity effect and Fc steric hindrance. This mAb prophylactically protects mice against weight loss and death caused by challenge with lethal H7N9 viruses in vivo. rH7-235 mAb neutralizing activity alone is sufficient for protection when used at high dosed in a prophylactic setting. This study provides insights into mechanisms of viral neutralization by protective broadly reactive anti-H7 antibodies informing the rational design of therapeutics and vaccines against H7N9 influenza virus.


  • Organizational Affiliation
    • The Vanderbilt Center for Antibody Therapeutics, Vanderbilt University Medical Center, Nashville, United States of America.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
HemagglutininA,
D [auth B]
217Influenza A virus (A/Shanghai/02/2013(H7N9))Mutation(s): 0 
Gene Names: HA
UniProt
Find proteins for R4NN21 (Influenza A virus)
Explore R4NN21 
Go to UniProtKB:  R4NN21
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupR4NN21
Glycosylation
Glycosylation Sites: 1
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Monoclonal antibody H7-235 heavy chainB [auth C],
E
228Homo sapiensMutation(s): 0 
Entity Groups  
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Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Monoclonal antibody H7-235 light chainC [auth D],
F
219Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free:  0.251 (Depositor), 0.250 (DCC) 
  • R-Value Work:  0.195 (Depositor), 0.194 (DCC) 
  • R-Value Observed: 0.198 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 240.603α = 90
b = 95.053β = 95.85
c = 99.265γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling

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 States--

Revision History  (Full details and data files)

  • Version 1.0: 2025-06-25
    Type: Initial release
  • Version 1.1: 2025-07-23
    Changes: Database references