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


This is version 2.1 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: https://doi.org/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. 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.'


  • Organizational Affiliation

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


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PROTEIN (HEMAGGLUTININ (HA1 CHAIN))328Influenza A virus (A/X-31(H3N2))Mutation(s): 0 
UniProt
Find proteins for P03438 (Influenza A virus (strain A/X-31 H3N2))
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Go to UniProtKB:  P03438
Entity Groups  
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UniProt GroupP03438
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
PROTEIN (HEMAGGLUTININ (HA2 CHAIN))175Influenza A virus (A/X-31(H3N2))Mutation(s): 0 
UniProt
Find proteins for P03437 (Influenza A virus (strain A/Aichi/2/1968 H3N2))
Explore P03437 
Go to UniProtKB:  P03437
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UniProt GroupP03437
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
PROTEIN (IMMUNOGLOBULIN IGG1-KAPPA ANTIBODY (LIGHT CHAIN))C [auth L]217Mus musculusMutation(s): 0 
UniProt
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UniProt GroupA2NHM3
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
PROTEIN (IMMUNOGLOBULIN IGG1-KAPPA ANTIBODY (HEAVY CHAIN))D [auth H]223Mus musculusMutation(s): 0 
UniProt
Find proteins for P01869 (Mus musculus)
Explore P01869 
Go to UniProtKB:  P01869
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UniProt GroupP01869
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Oligosaccharides

Help

Entity ID: 5
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseE [auth C]2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G07375KG
GlyCosmos:  G07375KG
GlyGen:  G07375KG
Entity ID: 6
MoleculeChains Length2D Diagram Glycosylation3D 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
Glycosylation Resources
GlyTouCan:  G15407YE
GlyCosmos:  G15407YE
GlyGen:  G15407YE
Small Molecules
Ligands 1 Unique
IDChains Name / 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
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  (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
  • Version 2.1: 2023-12-27
    Changes: Data collection, Database references, Structure summary