5K9J

Crystal structure of multidonor HV6-1-class broadly neutralizing Influenza A antibody 56.a.09 isolated following H5 immunization.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.197 

Starting Models: experimental
View more details

wwPDB Validation   3D Report Full Report


This is version 1.3 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
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
56.a.09 heavy chainA [auth H]228Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
56.a.09 light chainB [auth L]212Homo 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: 1.90 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.197 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.79α = 90
b = 103.758β = 90
c = 59.983γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-07-27
    Type: Initial release
  • Version 1.1: 2016-08-10
    Changes: Database references
  • Version 1.2: 2023-09-27
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.3: 2024-10-16
    Changes: Structure summary