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


Ligand Structure Quality Assessment 


This is version 1.5 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
HemagglutininA,
B [auth C],
E [auth B]
512Influenza A virus (A/Hong Kong/1-4-MA21-1/1968(H3N2))Mutation(s): 0 
Gene Names: HA
UniProt
Find proteins for E1AFM4 (Influenza A virus)
Explore E1AFM4 
Go to UniProtKB:  E1AFM4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupE1AFM4
Glycosylation
Glycosylation Sites: 6
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
ANTIBODY 31.A.83 FAB HEAVY CHAINC [auth F],
F [auth H],
H [auth Q]
236Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
ANTIBODY 31.A.83 FAB LIGHT CHAIND [auth G],
G [auth L],
I [auth R]
214Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
AA [auth B]
J [auth A]
K [auth A]
L [auth A]
M [auth A]
AA [auth B],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
N [auth A],
O [auth A],
P [auth C],
Q [auth C],
R [auth C],
S [auth C],
T [auth C],
U [auth C],
V [auth B],
W [auth B],
X [auth B],
Y [auth B],
Z [auth B]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
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



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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
  • Version 1.5: 2024-10-30
    Changes: Advisory, Data collection, Database references, Structure summary