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: 3.387 Å
  • R-Value Free: 0.346 
  • R-Value Work: 0.291 

wwPDB Validation 3D Report Full Report


This is version 1.1 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:  

  • 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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
31.b.09 Heavy Fv
A, H
227N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
31.b.09 Light Fv
B, L
219N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Hemagglutinin
F, I
505Influenza A virus (strain swl A/California/04/2009 H1N1)Mutation(s): 0 
Gene Names: HA
Find proteins for C3W5S1 (Influenza A virus (strain swl A/California/04/2009 H1N1))
Go to UniProtKB:  C3W5S1
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BMA
Query on BMA

Download SDF File 
Download CCD File 
I
BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
I
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.387 Å
  • R-Value Free: 0.346 
  • R-Value Work: 0.291 
  • Space Group: P 6 2 2
Unit Cell:
Length (Å)Angle (°)
a = 208.648α = 90.00
b = 208.648β = 90.00
c = 252.031γ = 120.00
Software Package:
Software NamePurpose
HKL-2000data reduction
PDB_EXTRACTdata extraction
PHASERphasing
HKL-2000data scaling
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-12-28
    Type: Initial release
  • Version 1.1: 2017-05-24
    Type: Structure summary