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 

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This is version 2.0 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
  • Primary Citation of Related Structures:  
    5V2A

  • 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 response in 75 recipients of a monovalent inactivated A/Shanghai/02/2013 H7N9 vaccine ...

    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
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
HemagglutininA321Influenza A virus (A/chicken/Henan/109/2013(H7N9))Mutation(s): 0 
Gene Names: HA
UniProt
Find proteins for A0A0R5TXT5 (Influenza A virus)
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Go to UniProtKB:  A0A0R5TXT5
Entity Groups  
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UniProt GroupA0A0R5TXT5
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
HemagglutininB183Influenza A virus (A/pigeon/Wuxi/0405007G/2013(H7N9))Mutation(s): 0 
Gene Names: HA
UniProt
Find proteins for A0A097PHH8 (Influenza A virus)
Explore A0A097PHH8 
Go to UniProtKB:  A0A097PHH8
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UniProt GroupA0A097PHH8
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Light chain (kappa) of H7.167 antibodyC [auth L]221Homo sapiensMutation(s): 0 
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Heavy chain of H7.167 antibodyD [auth H]220Homo sapiensMutation(s): 0 
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Oligosaccharides

Help

Entity ID: 5
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseE [auth C]3N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G15407YE
GlyCosmos:  G15407YE
GlyGen:  G15407YE
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
F [auth A],
G [auth A]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-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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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  (Full details and data files)

  • 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
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary