4NM8

Crystal structure of broadly neutralizing antibody CR8043 bound to H3 influenza hemagglutinin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.0041 Å
  • R-Value Free: 0.292 
  • R-Value Work: 0.240 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

A common solution to group 2 influenza virus neutralization.

Friesen, R.H.Lee, P.S.Stoop, E.J.Hoffman, R.M.Ekiert, D.C.Bhabha, G.Yu, W.Juraszek, J.Koudstaal, W.Jongeneelen, M.Korse, H.J.Ophorst, C.Brinkman-van der Linden, E.C.Throsby, M.Kwakkenbos, M.J.Bakker, A.Q.Beaumont, T.Spits, H.Kwaks, T.Vogels, R.Ward, A.B.Goudsmit, J.Wilson, I.A.

(2014) Proc.Natl.Acad.Sci.USA 111: 445-450

  • DOI: 10.1073/pnas.1319058110
  • Primary Citation of Related Structures:  4NM4

  • PubMed Abstract: 
  • The discovery and characterization of broadly neutralizing antibodies (bnAbs) against influenza viruses have raised hopes for the development of monoclonal antibody (mAb)-based immunotherapy and the design of universal influenza vaccines. Only one hu ...

    The discovery and characterization of broadly neutralizing antibodies (bnAbs) against influenza viruses have raised hopes for the development of monoclonal antibody (mAb)-based immunotherapy and the design of universal influenza vaccines. Only one human bnAb (CR8020) specifically recognizing group 2 influenza A viruses has been previously characterized that binds to a highly conserved epitope at the base of the hemagglutinin (HA) stem and has neutralizing activity against H3, H7, and H10 viruses. Here, we report a second group 2 bnAb, CR8043, which was derived from a different germ-line gene encoding a highly divergent amino acid sequence. CR8043 has in vitro neutralizing activity against H3 and H10 viruses and protects mice against challenge with a lethal dose of H3N2 and H7N7 viruses. The crystal structure and EM reconstructions of the CR8043-H3 HA complex revealed that CR8043 binds to a site similar to the CR8020 epitope but uses an alternative angle of approach and a distinct set of interactions. The identification of another antibody against the group 2 stem epitope suggests that this conserved site of vulnerability has great potential for design of therapeutics and vaccines.


    Organizational Affiliation

    Crucell Vaccine Institute, Janssen Center of Excellence for Immunoprophylaxis, 2333 CN, Leiden, The Netherlands.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Hemagglutinin HA1 Chain
A, C, E
323Influenza A virus (strain A/Hong Kong/1/1968 H3N2)Gene Names: HA
Find proteins for Q91MA7 (Influenza A virus (strain A/Hong Kong/1/1968 H3N2))
Go to UniProtKB:  Q91MA7
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Hemagglutinin HA2 Chain
B, D, F
176Influenza A virus (strain A/Hong Kong/1/1968 H3N2)Gene Names: HA
Find proteins for Q91MA7 (Influenza A virus (strain A/Hong Kong/1/1968 H3N2))
Go to UniProtKB:  Q91MA7
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Antibody CR8043, Light Chain
L, M, N
220Homo sapiensGene Names: IGKC
Find proteins for P01834 (Homo sapiens)
Go to UniProtKB:  P01834
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Antibody CR8043, Heavy Chain
H, I, J
230Homo sapiensN/A
Find proteins for S6C4S0 (Homo sapiens)
Go to UniProtKB:  S6C4S0
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download SDF File 
Download CCD File 
A, B, C, D, E, F
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.0041 Å
  • R-Value Free: 0.292 
  • R-Value Work: 0.240 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 241.491α = 90.00
b = 142.355β = 133.46
c = 170.725γ = 90.00
Software Package:
Software NamePurpose
Blu-Icedata collection
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-12-25
    Type: Initial release
  • Version 1.1: 2014-01-22
    Type: Database references
  • Version 1.2: 2017-06-21
    Type: Database references, Source and taxonomy, Structure summary
  • Version 1.3: 2017-12-06
    Type: Database references