2WV6 | pdb_00002wv6

Crystal structure of the cholera toxin-like B-subunit from Citrobacter freundii to 1.9 angstrom


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 
    0.211 (Depositor), 0.214 (DCC) 
  • R-Value Work: 
    0.174 (Depositor), 0.177 (DCC) 
  • R-Value Observed: 
    0.176 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.4 of the entry. See complete history

Literature

Carbohydrate Binding Specificities and Crystal Structure of the Cholera Toxin-Like B-Subunit from Citrobacter Freundii.

Jansson, L.Angstrom, J.Lebens, M.Imberty, A.Varrot, A.Teneberg, S.

(2010) Biochimie 92: 482

  • DOI: https://doi.org/10.1016/j.biochi.2010.02.010
  • Primary Citation Related Structures: 
    2WV6

  • PubMed Abstract: 

    Enterotoxigenic Escherichia coli and Vibrio cholerae are well known causative agents of severe diarrheal diseases. Both pathogens produce AB(5) toxins, with one enzymatically active A-subunit and a pentamer of receptor-binding B-subunits. The primary receptor for both B-subunits is the GM1 ganglioside (Galbeta3GalNAcbeta4(NeuAcalpha3)Galbeta4GlcbetaCer), but the B-subunits from porcine isolates of E. coli also bind neolacto-(Galbeta4GlcNAcbeta-)terminated glycoconjugates and the B-subunits from human isolates of E. coli (hLTB) have affinity for blood group A type 2-(GalNAcalpha3(Fucalpha2)Galbeta4GlcNAcbeta-)terminated glycoconjugates. A B-subunit with 73% sequence identity to the B-subunits of cholera toxin and the heat-labile toxin of E. coli is produced by certain strains of enteropathogenic E. coli and by Citrobacter freundii. This C. freundii B-subunit (CFXB) has now been expressed in V. cholerae, and isolated in high yields. Glycosphingolipid binding studies show that CFXB binds to the GM1 ganglioside with high affinity. In addition, CFXB has high affinity for both neolacto-terminated and blood group A type 2-terminated glycoconjugates. The crystal structure of the pentameric arrangement of C. freundii B-subunits display high structural similarity with related proteins from E. coli and V. cholerae and oligosaccharide binding sites can be identified on the protein surface. Small changes in the 88-95 loop connecting the GM1 and blood group A binding sites explains the minor changes in affinity seen for these two ligands. However, the enhanced affinity of CFXB for neolacto-terminated structures can be sought in the Lys34Tyr substitution affording additional hydrogen bond interactions between the tyrosyl side chain and the GlcNAcbeta3Galb4Glcbeta1 segment of neolactotetraosylceramide via bridging water molecules.


  • Organizational Affiliation
    • Institute of Biomedicine, Department of Medical Biochemistry and Cell Biology, University of Gothenburg, PO Box 440, SE-40530 Göteborg, Sweden.

Macromolecule Content 

  • Total Structure Weight: 117.95 kDa 
  • Atom Count: 8,064 
  • Modeled Residue Count: 938 
  • Deposited Residue Count: 1,030 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
CFXB103Citrobacter freundiiMutation(s): 0 
UniProt
Find proteins for Q8GAV5 (Citrobacter freundii)
Explore Q8GAV5 
Go to UniProtKB:  Q8GAV5
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8GAV5
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GOL

Query on GOL



Download:Ideal Coordinates CCD File
L [auth E]
M [auth E]
N [auth G]
P [auth I]
Q [auth I]
L [auth E],
M [auth E],
N [auth G],
P [auth I],
Q [auth I],
S [auth K],
U [auth L],
V [auth M]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO

Query on EDO



Download:Ideal Coordinates CCD File
K [auth D],
O [auth H],
R [auth J],
T [auth L]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free:  0.211 (Depositor), 0.214 (DCC) 
  • R-Value Work:  0.174 (Depositor), 0.177 (DCC) 
  • R-Value Observed: 0.176 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 131.05α = 90
b = 100.94β = 122.24
c = 83.27γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-10-27
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description
  • Version 1.4: 2024-11-20
    Changes: Structure summary