Biological Assembly 1  

 3D View: Structure | Ligand Interaction

Global Symmetry: Cyclic - C3  (3D View)
Global Stoichiometry: Hetero 12-mer - A3B3C3D3 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 104.24 kDa 
• Atom Count: 7357 
• Residue Count: 921 
• Unique protein chains: 4

1EO8

INFLUENZA VIRUS HEMAGGLUTININ COMPLEXED WITH A NEUTRALIZING ANTIBODY

• DOI: 10.2210/pdb1EO8/pdb

• Classification: Viral protein/Immune system
• Organism(s): Influenza A virus (A/X-31(H3N2)), Mus musculus
• Mutation(s): No 


• Deposited: 2000-03-22 Released: 2000-04-12 
• Deposition Author(s): Fleury, D., Gigant, B., Daniels, R.S., Skehel, J.J., Knossow, M., Bizebard, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.298 
• R-Value Work: 0.196 

Literature

Structural evidence for recognition of a single epitope by two distinct antibodies.

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

(2000) Proteins 40: 572-578

• PubMed: 10899782 
• Primary Citation of Related Structures:  
  1EO8


• PubMed Abstract: 
  

The structure of a complex between the hemagglutinin of influenza virus and the Fab of a neutralizing antibody was determined by X-ray crystallography at 2.8 A resolution. This antibody and another which has only 56% sequence identity bind to the same epitope with very similar affinities and in the same orientation. One third of the interactions is conserved in the two complexes; a significant proportion of the interactions that differ are established by residues of the H3 complementarity-determining regions (CDR) which adopt distinct conformations in the two antibodies. This demonstrates that there is a definite flexibility in the selection of antibodies that bind to a given epitope, despite the high affinity of their complexes. This flexibility allows the humoral immune response to be redundant, a feature that may be useful in achieving longer lasting protection against evolving viral pathogens.

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Related Citations: 

• 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

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Organizational Affiliation: 

Laboratoire d'Enzymologie et Biochimie Structurales, CNRS, France.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HEMAGGLUTININ (HA1 CHAIN)	A	328	Influenza 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

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
HEMAGGLUTININ (HA2 CHAIN)	B	175	Influenza 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

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
ANTIBODY (LIGHT CHAIN)	L	210	Mus musculus	Mutation(s): 0

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
ANTIBODY (HEAVY CHAIN)	H	217	Mus musculus	Mutation(s): 0

Oligosaccharides

Help

Entity ID: 5
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C	3		N-Glycosylation

Entity ID: 6
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	D	2		N-Glycosylation

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	A, 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: 0.298 
• R-Value Work: 0.196 
• Space Group: P 3 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 138.15	α = 90
b = 138.15	β = 90
c = 129.5	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing
X-PLOR	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2000-03-22 
• Released Date: 2000-04-12 
Deposition Author(s): Fleury, D., Gigant, B., Daniels, R.S., Skehel, J.J., Knossow, M., Bizebard, T.

Revision History 

• Version 1.0: 2000-04-12
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.3: 2017-10-04
  Changes: Refinement description
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Structure summary