1QFU

INFLUENZA VIRUS HEMAGGLUTININ COMPLEXED WITH A NEUTRALIZING ANTIBODY


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.198 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

A complex of influenza hemagglutinin with a neutralizing antibody that binds outside the virus receptor binding site.

Fleury, D.Barrere, B.Bizebard, T.Daniels, R.S.Skehel, J.J.Knossow, M.

(1999) Nat.Struct.Mol.Biol. 6: 530-534

  • DOI: 10.1038/9299

  • PubMed Abstract: 
  • The structure of a complex of influenza hemagglutinin (HA) with a neutralizing antibody shows that the antibody binds to HA at a distance from the virus receptor binding site. Comparison of the properties of this antibody and its Fab with those of an ...

    The structure of a complex of influenza hemagglutinin (HA) with a neutralizing antibody shows that the antibody binds to HA at a distance from the virus receptor binding site. Comparison of the properties of this antibody and its Fab with those of an antibody that recognizes an epitope overlapping the receptor binding site leads to two main conclusions. First, inhibition of receptor binding is an important component of neutralization. Second, the efficiency of neutralization by the antibodies ranks in the same order as their avidities for HA, and their large size makes these antibodies highly efficient at neutralization, regardless of the location of their epitope in relation to the virus receptor binding site. These observations provide rationales for the range of antibody specificities that are detected in immune sera and for the distribution of sequence changes on the membrane-distal surface of influenza HAs that occur during 'antigenic drift.'


    Related Citations: 
    • Structure of the Haemagglutinin Membrane Glycoprotein of Influenza Virus at 3 Angstroms Resolution
      Wilson, I.A.,Skehel, J.J.,Wiley, D.C.
      (1981) Nature 289: 366
    • Structure of Influenza Virus Haemagglutinin Complexed with a Neutralizing Antibody
      Bizebard, T.,Gigant, B.,Rigolet, P.,Rasmussen, B.,Diat, O.,Boesecke, P.,Wharton, S.A.,Skehel, J.J.,Knossow, M.
      (1995) Nature 376: 92
    • Crystallization and Preliminary X-Ray Diffraction Studies of Complexes between an Influenza Hemagglutinin and Fab Fragments of Two Different Monoclonal Antibodies
      Gigant, B.,Fleury, D.,Bizebard, T.,Skehel, J.J.,Knossow, M.
      (1995) Proteins 23: 115


    Organizational Affiliation

    Laboratoire d'Enzymologie et Biochimie Structurales, UPR 9063, CNRS, Gif-sur-Yvette, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (HEMAGGLUTININ (HA1 CHAIN))
A
328Influenza A virus (strain A/X-31 H3N2)Gene Names: HA
Find proteins for P03438 (Influenza A virus (strain A/X-31 H3N2))
Go to UniProtKB:  P03438
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (HEMAGGLUTININ (HA2 CHAIN))
B
175Influenza A virus (strain A/Aichi/2/1968 H3N2)Gene Names: HA
Find proteins for P03437 (Influenza A virus (strain A/Aichi/2/1968 H3N2))
Go to UniProtKB:  P03437
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (IMMUNOGLOBULIN IGG1-KAPPA ANTIBODY (LIGHT CHAIN))
L
217Mus musculusGene Names: Igkc (Igk-C)
Find proteins for A2NHM3 (Mus musculus)
Go to UniProtKB:  A2NHM3
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (IMMUNOGLOBULIN IGG1-KAPPA ANTIBODY (HEAVY CHAIN))
H
223Mus musculusGene Names: Ighg1 (Igh-4)
Find proteins for P01869 (Mus musculus)
Go to UniProtKB:  P01869
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BMA
Query on BMA

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

Download SDF File 
Download CCD File 
A
2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE
C8 H15 N O6
OVRNDRQMDRJTHS-PVFLNQBWSA-N
 Ligand Interaction
NAG
Query on NAG

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.198 
  • Space Group: P 3 2 1
Unit Cell:
Length (Å)Angle (°)
a = 138.000α = 90.00
b = 138.000β = 90.00
c = 135.000γ = 120.00
Software Package:
Software NamePurpose
X-PLORrefinement
AMoREphasing
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1999-04-16
    Type: Initial release
  • Version 1.1: 2008-04-26
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Non-polymer description, Version format compliance
  • Version 1.3: 2017-03-08
    Type: Derived calculations
  • Version 1.4: 2017-10-04
    Type: Refinement description