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: 2.3 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.185 

wwPDB Validation 3D Report Full Report


This is version 1.4 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.USA 97: 8433-8438

  • DOI: 10.1073/pnas.060022997
  • Primary Citation of Related Structures:  

  • 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 p ...

    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

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ANTIBODY S-20-4, FAB FRAGMENT, LIGHT CHAIN
L
210N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
ANTIBODY S-20-4, FAB FRAGMENT, HEAVY CHAIN
H
216N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MGS
Query on MGS

Download SDF File 
Download CCD File 
H
1,2-O-DIMETHYL-4-[2,4-DIHYDROXY-BUTYRAMIDO]-4,6-DIDEOXY-ALPHA-D-MANNOPYRANOSIDE
C12 H23 N O7
NGGZJRAGGXAXNO-DZXYHILESA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
MGSKd: 2600 nM BINDINGMOAD
MGSKd: 2600 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.185 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 45.570α = 90.00
b = 113.090β = 100.57
c = 46.240γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
REFMACrefinement
AMoREphasing
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2000-08-02
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2016-10-26
    Type: Non-polymer description
  • Version 1.4: 2018-02-07
    Type: Experimental preparation