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 

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This is version 2.0 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 Biol 6: 530-534

  • DOI: 10.1038/9299
  • Primary Citation of Related Structures:  
    1QFU

  • 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 antibody that recognizes an epitope overlapping the receptor binding site leads to two main conclusions ...

    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
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PROTEIN (HEMAGGLUTININ (HA1 CHAIN))A328Influenza A virus (A/X-31(H3N2))Mutation(s): 0 
Gene Names: HA
UniProt
Find proteins for P03438 (Influenza A virus (strain A/X-31 H3N2))
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Go to UniProtKB:  P03438
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP03438
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
PROTEIN (HEMAGGLUTININ (HA2 CHAIN))B175Influenza A virus (A/X-31(H3N2))Mutation(s): 0 
UniProt
Find proteins for P03437 (Influenza A virus (strain A/Aichi/2/1968 H3N2))
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Go to UniProtKB:  P03437
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UniProt GroupP03437
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
PROTEIN (IMMUNOGLOBULIN IGG1-KAPPA ANTIBODY (LIGHT CHAIN))C [auth L]217Mus musculusMutation(s): 0 
Gene Names: IgkcIgk-C
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UniProt GroupA2NHM3
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
PROTEIN (IMMUNOGLOBULIN IGG1-KAPPA ANTIBODY (HEAVY CHAIN))D [auth H]223Mus musculusMutation(s): 0 
Gene Names: Ighg1Igh-4
UniProt
Find proteins for P01869 (Mus musculus)
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Oligosaccharides

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Entity ID: 5
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseE [auth C]2N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G07375KG
GlyCosmos:  G07375KG
GlyGen:  G07375KG
Entity ID: 6
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseF [auth D]3N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G15407YE
GlyCosmos:  G15407YE
GlyGen:  G15407YE
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
G [auth A],
H [auth A],
I [auth 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

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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