1QFU

INFLUENZA VIRUS HEMAGGLUTININ COMPLEXED WITH A NEUTRALIZING ANTIBODY


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.198 

wwPDB Validation 3D Report Full Report



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 Biol 6: 530-534

  • DOI: 10.1038/9299
  • Structures With Same Primary Citation

  • 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 influenza virus haemagglutinin complexed with a neutralizing antibody.
      Bizebard, T., Gigant, B., Rigolet, P., Rasmussen, B., Diat, O., Bosecke, 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
    • Structure of the haemagglutinin membrane glycoprotein of influenza virus at 3 A resolution.
      Wilson, I.A., Skehel, J.J., Wiley, D.C.
      (1981) Nature 289: 366

    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))A328Influenza A virus (A/X-31(H3N2))Mutation(s): 0 
Gene Names: HA
Find proteins for P03438 (Influenza A virus (strain A/X-31 H3N2))
Explore P03438 
Go to UniProtKB:  P03438
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (HEMAGGLUTININ (HA2 CHAIN))B175Influenza A virus (A/X-31(H3N2))Mutation(s): 0 
Find proteins for P03437 (Influenza A virus (strain A/Aichi/2/1968 H3N2))
Explore P03437 
Go to UniProtKB:  P03437
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (IMMUNOGLOBULIN IGG1-KAPPA ANTIBODY (LIGHT CHAIN))L217Mus musculusMutation(s): 0 
Gene Names: IgkcIgk-C
Find proteins for A2NHM3 (Mus musculus)
Explore A2NHM3 
Go to UniProtKB:  A2NHM3
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (IMMUNOGLOBULIN IGG1-KAPPA ANTIBODY (HEAVY CHAIN))H223Mus musculusMutation(s): 0 
Gene Names: Ighg1Igh-4
Find proteins for P01869 (Mus musculus)
Explore P01869 
Go to UniProtKB:  P01869
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Oligosaccharides
Entity ID: 5
MoleculeChainsChain Length2D Diagram Glycosylation
2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
C
2 N-Glycosylation
Entity ID: 6
MoleculeChainsChain Length2D Diagram Glycosylation
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
D
3 N-Glycosylation
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download CCD File 
A, B
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: 2.80 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.198 
  • Space Group: P 3 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 138α = 90
b = 138β = 90
c = 135γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
X-PLORrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1999-04-16
    Type: Initial release
  • Version 1.1: 2008-04-26
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.3: 2017-03-08
    Changes: Derived calculations
  • Version 1.4: 2017-10-04
    Changes: Refinement description
  • Version 1.5: 2019-11-27
    Changes: Database references, Derived calculations
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary