5K9O

Crystal structure of multidonor HV1-18+HD3-9 class broadly neutralizing Influenza A antibody 31.b.09 in complex with Hemagglutinin H1 A/California/04/2009


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.39 Å
  • R-Value Free: 0.346 
  • R-Value Work: 0.291 
  • R-Value Observed: 0.294 

Starting Models: experimental
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wwPDB Validation   3D Report Full Report


This is version 2.2 of the entry. See complete history


Literature

Vaccine-Induced Antibodies that Neutralize Group 1 and Group 2 Influenza A Viruses.

Joyce, M.G.Wheatley, A.K.Thomas, P.V.Chuang, G.Y.Soto, C.Bailer, R.T.Druz, A.Georgiev, I.S.Gillespie, R.A.Kanekiyo, M.Kong, W.P.Leung, K.Narpala, S.N.Prabhakaran, M.S.Yang, E.S.Zhang, B.Zhang, Y.Asokan, M.Boyington, J.C.Bylund, T.Darko, S.Lees, C.R.Ransier, A.Shen, C.H.Wang, L.Whittle, J.R.Wu, X.Yassine, H.M.Santos, C.Matsuoka, Y.Tsybovsky, Y.Baxa, U.Mullikin, J.C.Subbarao, K.Douek, D.C.Graham, B.S.Koup, R.A.Ledgerwood, J.E.Roederer, M.Shapiro, L.Kwong, P.D.Mascola, J.R.McDermott, A.B.

(2016) Cell 166: 609-623

  • DOI: https://doi.org/10.1016/j.cell.2016.06.043
  • Primary Citation of Related Structures:  
    5K9J, 5K9K, 5K9O, 5K9Q, 5KAN, 5KAQ

  • PubMed Abstract: 

    Antibodies capable of neutralizing divergent influenza A viruses could form the basis of a universal vaccine. Here, from subjects enrolled in an H5N1 DNA/MIV-prime-boost influenza vaccine trial, we sorted hemagglutinin cross-reactive memory B cells and identified three antibody classes, each capable of neutralizing diverse subtypes of group 1 and group 2 influenza A viruses. Co-crystal structures with hemagglutinin revealed that each class utilized characteristic germline genes and convergent sequence motifs to recognize overlapping epitopes in the hemagglutinin stem. All six analyzed subjects had sequences from at least one multidonor class, and-in half the subjects-multidonor-class sequences were recovered from >40% of cross-reactive B cells. By contrast, these multidonor-class sequences were rare in published antibody datasets. Vaccination with a divergent hemagglutinin can thus increase the frequency of B cells encoding broad influenza A-neutralizing antibodies. We propose the sequence signature-quantified prevalence of these B cells as a metric to guide universal influenza A immunization strategies.


  • Organizational Affiliation

    Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
31.b.09 Heavy FvA,
D [auth H]
227Homo sapiensMutation(s): 0 
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Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
31.b.09 Light FvB,
F [auth L]
219Homo sapiensMutation(s): 0 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
HemagglutininC [auth F],
E [auth I]
505Influenza A virus (A/California/04/2009(H1N1))Mutation(s): 0 
Gene Names: HA
UniProt
Find proteins for C3W5S1 (Influenza A virus (strain swl A/California/04/2009 H1N1))
Explore C3W5S1 
Go to UniProtKB:  C3W5S1
Entity Groups  
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UniProt GroupC3W5S1
Glycosylation
Glycosylation Sites: 1
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

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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-glucopyranoseG [auth C]3N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE
GlyCosmos:  G15407YE
GlyGen:  G15407YE
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.39 Å
  • R-Value Free: 0.346 
  • R-Value Work: 0.291 
  • R-Value Observed: 0.294 
  • Space Group: P 6 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 208.648α = 90
b = 208.648β = 90
c = 252.031γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-12-28
    Type: Initial release
  • Version 1.1: 2017-05-24
    Changes: Structure summary
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2023-09-27
    Changes: Data collection, Database references, Refinement description, Structure summary
  • Version 2.2: 2024-10-09
    Changes: Structure summary