2VIR

INFLUENZA VIRUS HEMAGGLUTININ COMPLEXED WITH A NEUTRALIZING ANTIBODY

• PDB DOI: https://doi.org/10.2210/pdb2VIR/pdb
• Entry: 2VIR supersedes: 1VIR

• Classification: COMPLEX (HEMAGGLUTININ/IMMUNOGLOBULIN)
• Organism(s): Mus musculus, Influenza A virus (A/X-31(H3N2))
• Mutation(s): Yes 


• Deposited: 1997-12-22 Released: 1998-04-29 
• Deposition Author(s): Bizebard, T., Fleury, D., Gigant, B., Wharton, S.A., Skehel, J.J., Knossow, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.25 Å
• R-Value Free: 0.249 
• R-Value Work: 0.198 
• R-Value Observed: 0.198 

Literature

Antigen distortion allows influenza virus to escape neutralization.

Fleury, D., Wharton, S.A., Skehel, J.J., Knossow, M., Bizebard, T.

(1998) Nat Struct Biol 5: 119-123

• PubMed: 9461077 
• DOI: https://doi.org/10.1038/nsb0298-119
• Primary Citation of Related Structures:  
  2VIR, 2VIS, 2VIT, 2VIU


• PubMed Abstract: 
  

  The structure of the hemagglutinin (HA) of a mutant influenza virus that escapes neutralization by a monoclonal antibody shows that the mutation causes changes in HA structure which avoid an energetically less favorable conformation. However, the structure of the mutant HA.Fab complex indicates that the antibody binds selectively to mutant HA in a wild type-like distorted conformation. The association of an antibody with a less favored HA conformation represents an alternative to previously described mechanisms of escape from neutralization by antibodies.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A2B1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 77.74 kDa 
• Atom Count: 5,339 
• Modelled Residue Count: 698 
• Deposited Residue Count: 713 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
IMMUNOGLOBULIN (IGG1, LAMBDA)	A	210	Mus musculus	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
IMMUNOGLOBULIN (IGG1, LAMBDA)	B	221	Mus musculus	Mutation(s): 0
UniProt
Find proteins for Q99LC4 (Mus musculus) Explore Q99LC4  Go to UniProtKB:  Q99LC4

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
HEMAGGLUTININ	C	282	Influenza A virus (A/X-31(H3N2))	Mutation(s): 3
UniProt
Find proteins for P03437 (Influenza A virus (strain A/Aichi/2/1968 H3N2)) Explore P03437  Go to UniProtKB:  P03437

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	D [auth A], E [auth A], F [auth C]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.25 Å
• R-Value Free: 0.249 
• R-Value Work: 0.198 
• R-Value Observed: 0.198 
• Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.5	α = 90
b = 85.5	β = 90
c = 515	γ = 120

Software Package:

Software Name	Purpose
HKL	data collection
X-PLOR	model building
X-PLOR	refinement
HKL	data reduction
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1998-04-29 
Deposition Author(s): Bizebard, T., Fleury, D., Gigant, B., Wharton, S.A., Skehel, J.J., Knossow, M.
• This entry supersedes: 1VIR

Revision History  

• Version 1.0: 1998-04-29
  Type: Initial release
  
• Version 1.1: 2008-03-25
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-06-05
  Changes: Data collection, Database references, Derived calculations, Other
• Version 1.4: 2024-10-23
  Changes: Structure summary