1KEN | pdb_00001ken

INFLUENZA VIRUS HEMAGGLUTININ COMPLEXED WITH AN ANTIBODY THAT PREVENTS THE HEMAGGLUTININ LOW PH FUSOGENIC TRANSITION

PDB DOI: https://doi.org/10.2210/pdb1KEN/pdb

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

Deposited: 2001-11-16 Released: 2002-04-24
Deposition Author(s): Barbey-Martin, C., Gigant, B., Bizebard, T., Calder, L.J., Wharto, S.A., Skehel, J.J., Knossow, M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.50 Å
R-Value Free:
0.323 (Depositor)
R-Value Work:
0.255 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 2.1 of the entry. See complete history.

Literature

An Antibody that Prevents the Hemagglutinin Low pH Fusogenic Transition

Barbey-Martin, C., Gigant, B., Bizebard, T., Calder, L.J., Wharton, S.A., Skehel, J.J., Knossow, M.

(2002) Virology 294: 70-74

PubMed: 11886266 Search on PubMed
DOI: https://doi.org/10.1006/viro.2001.1320
Primary Citation Related Structures:
1KEN

PubMed Abstract:
We have determined the structure of a complex of influenza hemagglutinin (HA) with an antibody that binds simultaneously to the membrane-distal domains of two HA monomers, effectively cross-linking them. The antibody prevents the low pH structural transition of HA that is required for its membrane fusion activity, providing evidence that a rearrangement of HA membrane-distal domains is an essential component of the transition.

Organizational Affiliation

Laboratoire d'Enzymologie et Biochimie Structurales, UPR 9063 CNRS, Bât. 34, CNRS, 91198 Gif-sur-Yvette Cedex, France.

Macromolecule Content

Total Structure Weight: 265.85 kDa
Atom Count: 18,492
Modeled Residue Count: 2,351
Deposited Residue Count: 2,377
Unique protein chains: 4

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
hemagglutinin HA1	A, C, E	328	Influenza A virus (A/X-31(H3N2))	Mutation(s): 0
UniProt
Find proteins for P03438 (Influenza A virus (strain A/X-31 H3N2)) Explore P03438 Go to UniProtKB: P03438
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P03438
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain A Focus chain C Focus chain E
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
hemagglutinin HA2	B, D, F	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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P03437
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
influenza virus infectivity neutralizing antibody (light chain)	G [auth L], I [auth U]	213	Mus musculus	Mutation(s): 0
UniProt
Find proteins for P01837 (Mus musculus) Explore P01837 Go to UniProtKB: P01837
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P01837
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
influenza virus infectivity neutralizing antibody (heavy chain)	H, J [auth T]	221	Mus musculus	Mutation(s): 0
UniProt
Find proteins for P01869 (Mus musculus) Explore P01869 Go to UniProtKB: P01869
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P01869
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	K [auth G], L [auth I], M [auth J]	3		N-Glycosylation	Interactions Focus chain K [auth G] Focus chain L [auth I] Focus chain M [auth J]
Glycosylation Resources
GlyTouCan: G62182OO GlyCosmos: G62182OO GlyGen: G62182OO

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.50 Å
R-Value Free: 0.323 (Depositor)
R-Value Work: 0.255 (Depositor)

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 143.041	α = 90
b = 315.588	β = 90
c = 97.029	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
AMoRE	phasing
CNS	refinement
CCP4	data scaling

Structure Validation

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Entry History

Deposition Data

Released Date: 2002-04-24

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2002-04-24
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 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
Version 2.1: 2024-10-09
Changes: Data collection, Database references, Structure summary