Biological Assembly 1  

 3D View: Structure | 1D-3D View | Validation Report | 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: 106.36 kDa 
• Atom Count: 7439 
• Modelled Residue Count: 932 
• Deposited Residue Count: 943 
• Unique protein chains: 4

1QFU

INFLUENZA VIRUS HEMAGGLUTININ COMPLEXED WITH A NEUTRALIZING ANTIBODY

• PDB DOI: 10.2210/pdb1QFU/pdb

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


• Deposited: 1999-04-14 Released: 1999-04-16 
• Deposition Author(s): Fleury, D., Gigant, B., Bizebard, T., Daniels, R.S., Skehel, J.J., Knossow, M.

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Experimental Data Snapshot

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

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

• PubMed: 10360354 
• 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. 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.'

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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

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (HEMAGGLUTININ (HA1 CHAIN))	A	328	Influenza 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)) Explore P03438  Go to UniProtKB:  P03438

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

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (IMMUNOGLOBULIN IGG1-KAPPA ANTIBODY (LIGHT CHAIN))	C [auth L]	217	Mus musculus	Mutation(s): 0  Gene Names: Igkc, Igk-C
UniProt
Find proteins for A2NHM3 (Mus musculus) Explore A2NHM3  Go to UniProtKB:  A2NHM3

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (IMMUNOGLOBULIN IGG1-KAPPA ANTIBODY (HEAVY CHAIN))	D [auth H]	223	Mus musculus	Mutation(s): 0  Gene Names: Ighg1, Igh-4
UniProt
Find proteins for P01869 (Mus musculus) Explore P01869  Go to UniProtKB:  P01869

Oligosaccharides

Help

Entity ID: 5
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	E [auth C]	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G07375KG GlyCosmos:  G07375KG GlyGen:  G07375KG

Entity ID: 6
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	F [auth D]	3		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE GlyCosmos:  G15407YE GlyGen:  G15407YE

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	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 = 138	α = 90
b = 138	β = 90
c = 135	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: 1999-04-14 
• Released Date: 1999-04-16 
Deposition Author(s): Fleury, D., Gigant, B., Bizebard, T., Daniels, R.S., Skehel, J.J., Knossow, M.

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