5V2A

Crystal structure of Fab H7.167 in complex with influenza virus hemagglutinin from A/Shanghai/02/2013 (H7N9)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.66 Å
  • R-Value Free: 0.334 
  • R-Value Work: 0.258 
  • R-Value Observed: 0.261 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history. 


Literature

H7N9 influenza virus neutralizing antibodies that possess few somatic mutations.

Thornburg, N.J., Zhang, H., Bangaru, S., Sapparapu, G., Kose, N., Lampley, R.M., Bombardi, R.G., Yu, Y., Graham, S., Branchizio, A., Yoder, S.M., Rock, M.T., Creech, C.B., Edwards, K.M., Lee, D., Li, S., Wilson, I.A., Garcia-Sastre, A., Albrecht, R.A., Crowe, J.E.

(2016) J Clin Invest 126: 1482-1494

  • DOI: 10.1172/JCI85317
  • Structures With Same Primary Citation

  • PubMed Abstract: 

    • Avian H7N9 influenza viruses are group 2 influenza A viruses that have been identified as the etiologic agent for a current major outbreak that began in China in 2013 and may pose a pandemic threat. Here, we examined the human H7-reactive antibody re ...

    Avian H7N9 influenza viruses are group 2 influenza A viruses that have been identified as the etiologic agent for a current major outbreak that began in China in 2013 and may pose a pandemic threat. Here, we examined the human H7-reactive antibody response in 75 recipients of a monovalent inactivated A/Shanghai/02/2013 H7N9 vaccine. After 2 doses of vaccine, the majority of donors had memory B cells that secreted IgGs specific for H7 HA, with dominant responses against single HA subtypes, although frequencies of H7-reactive B cells ranged widely between donors. We isolated 12 naturally occurring mAbs with low half-maximal effective concentrations for binding, 5 of which possessed neutralizing and HA-inhibiting activities. The 5 neutralizing mAbs exhibited narrow breadth of reactivity with influenza H7 strains. Epitope-mapping studies using neutralization escape mutant analysis, deuterium exchange mass spectrometry, and x-ray crystallography revealed that these neutralizing mAbs bind near the receptor-binding pocket on HA. All 5 neutralizing mAbs possessed low numbers of somatic mutations, suggesting the clones arose from naive B cells. The most potent mAb, H7.167, was tested as a prophylactic treatment in a mouse intranasal virus challenge study, and systemic administration of the mAb markedly reduced viral lung titers.

    Organizational Affiliation: 

    Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Hemagglutinin
A
321Influenza A virus (A/chicken/Henan/109/2013(H7N9))Mutation(s): 0 
Gene Names: HA
Find proteins for A0A0R5TXT5 (Influenza A virus)
Go to UniProtKB:  A0A0R5TXT5
Protein Feature View
  • Reference Sequence

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Light chain (kappa) of H7.167 antibody
L
221Homo sapiensMutation(s): 0 
Protein Feature View
  • Reference Sequence

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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Heavy chain of H7.167 antibody
H
220Homo sapiensMutation(s): 0 
Protein Feature View
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Hemagglutinin
B
183Influenza A virus (A/pigeon/Wuxi/0405007G/2013(H7N9))Mutation(s): 0 
Gene Names: HA
Find proteins for A0A097PHH8 (Influenza A virus)
Go to UniProtKB:  A0A097PHH8
Protein Feature View
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG
Download CCD File 
A, H
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N		 Ligand Interaction
BMA
Query on BMA
Download CCD File 
H
BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.66 Å
  • R-Value Free: 0.334 
  • R-Value Work: 0.258 
  • R-Value Observed: 0.261 
  • Space Group: I 21 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 207.276α = 90
b = 207.276β = 90
c = 207.276γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling
PHASERphasing
HKL-2000data reduction

Structure Validation

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View more in-depth experimental data

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR56 AI117675

Revision History 

  • Version 1.0: 2017-04-05
    Type: Initial release
  • Version 1.1: 2017-07-05
    Changes: Source and taxonomy
  • Version 1.2: 2017-09-06
    Changes: Author supporting evidence
  • Version 1.3: 2018-03-07
    Changes: Source and taxonomy
  • Version 1.4: 2019-12-11
    Changes: Author supporting evidence