1F4X

CRYSTAL STRUCTURE OF AN ANTI-CARBOHYDRATE ANTIBODY DIRECTED AGAINST VIBRIO CHOLERAE O1 IN COMPLEX WITH ANTIGEN


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.185 

wwPDB Validation   3D Report Full Report


This is version 1.5 of the entry. See complete history


Literature

Crystal structure of an anti-carbohydrate antibody directed against Vibrio cholerae O1 in complex with antigen: molecular basis for serotype specificity.

Villeneuve, S.Souchon, H.Riottot, M.M.Mazie, J.C.Lei, P.Glaudemans, C.P.Kovac, P.Fournier, J.M.Alzari, P.M.

(2000) Proc Natl Acad Sci U S A 97: 8433-8438

  • DOI: https://doi.org/10.1073/pnas.060022997
  • Primary Citation of Related Structures:  
    1F4W, 1F4X, 1F4Y

  • PubMed Abstract: 

    The crystal structure of the murine Fab S-20-4 from a protective anti-cholera Ab specific for the lipopolysaccharide Ag of the Ogawa serotype has been determined in its unliganded form and in complex with synthetic fragments of the Ogawa O-specific polysaccharide (O-SP). The upstream terminal O-SP monosaccharide is shown to be the primary antigenic determinant. Additional perosamine residues protrude outwards from the Ab surface and contribute only marginally to the binding affinity and specificity. A complementary water-excluding hydrophobic interface and five Ab-Ag hydrogen bonds are crucial for carbohydrate recognition. The structure reported here explains the serotype specificity of anti-Ogawa Abs and provides a rational basis toward the development of a synthetic carbohydrate-based anti-cholera vaccine.


  • Organizational Affiliation

    Unité de Biochimie Structurale (Centre National de la Recherche Scientifique, Unité de Recherche Associée 2185), Laboratoire d'Ingénierie des Anticorps, Institut Pasteur, Paris, France.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ANTIBODY S-20-4, FAB FRAGMENT, LIGHT CHAINA [auth L]210Mus musculusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
ANTIBODY S-20-4, FAB FRAGMENT, HEAVY CHAINB [auth H]216Mus musculusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MGS
Query on MGS

Download Ideal Coordinates CCD File 
C [auth H]methyl 4,6-dideoxy-4-{[(2R)-2,4-dihydroxybutanoyl]amino}-2-O-methyl-alpha-D-mannopyranoside
C12 H23 N O7
NGGZJRAGGXAXNO-DZXYHILESA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
MGS PDBBind:  1F4X Kd: 2600 (nM) from 1 assay(s)
Binding MOAD:  1F4X Kd: 2600 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.185 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.57α = 90
b = 113.09β = 100.57
c = 46.24γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMACrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2000-08-02
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2016-10-26
    Changes: Non-polymer description
  • Version 1.4: 2018-02-07
    Changes: Experimental preparation
  • Version 1.5: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Derived calculations, Structure summary