5KAQ

Crystal structure of broadly neutralizing Influenza A antibody 31.a.83 in complex with Hemagglutinin Hong Kong 1968.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.51 Å
  • R-Value Free: 0.313 
  • R-Value Work: 0.270 
  • R-Value Observed: 0.272 

wwPDB Validation   3D Report Full Report


This is version 1.4 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: 10.1016/j.cell.2016.06.043
  • Primary Citation of Related Structures:  
    5K9K, 5K9O, 5K9Q, 5K9J, 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 a ...

    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. Electronic address: adrian.mcdermott@nih.gov.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
HemagglutininABC512Influenza A virus (A/Hong Kong/1-4-MA21-1/1968(H3N2))Mutation(s): 0 
Gene Names: HA
Find proteins for E1AFM4 (Influenza A virus)
Explore E1AFM4 
Go to UniProtKB:  E1AFM4
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
ANTIBODY 31.A.83 FAB HEAVY CHAINFHQ236Homo sapiensMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
ANTIBODY 31.A.83 FAB LIGHT CHAINGLR214Homo sapiensMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download CCD File 
A, B, C
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: 3.51 Å
  • R-Value Free: 0.313 
  • R-Value Work: 0.270 
  • R-Value Observed: 0.272 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 279.435α = 90
b = 154.283β = 116.86
c = 157.937γ = 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 

  • Version 1.0: 2017-02-22
    Type: Initial release
  • Version 1.1: 2017-03-01
    Changes: Structure summary
  • Version 1.2: 2017-03-22
    Changes: Source and taxonomy
  • Version 1.3: 2017-04-19
    Changes: Structure summary
  • Version 1.4: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary