Experimental Data Snapshot

  • Resolution: 2.00 Å
  • R-Value Work: 0.171 
  • R-Value Observed: 0.171 

wwPDB Validation   3D Report Full Report

This is version 2.1 of the entry. See complete history


Structural studies of receptor binding by cholera toxin mutants.

Merritt, E.A.Sarfaty, S.Jobling, M.G.Chang, T.Holmes, R.K.Hirst, T.R.Hol, W.G.

(1997) Protein Sci 6: 1516-1528

  • DOI: https://doi.org/10.1002/pro.5560060716
  • Primary Citation of Related Structures:  
    1CT1, 2CHB

  • PubMed Abstract: 

    The wide range of receptor binding affinities reported to result from mutations at residue Gly 33 of the cholera toxin B-pentamer (CTB) has been most puzzling. For instance, introduction of an aspartate at this position abolishes receptor binding, whereas substitution by arginine retains receptor affinity despite the larger side chain. We now report the structure determination and 2.3-A refinement of the CTB mutant Gly 33-->Arg complexed with the GM1 oligosaccharide, as well as the 2.2-A refinement of a Gly 33-->Asp mutant of the closely related Escherichia coli heat-labile enterotoxin B-pentamer (LTB). Two of the five receptor binding sites in the Gly 33-->Arg CTB mutant are occupied by bound GM1 oligosaccharide; two other sites are involved in a reciprocal toxin:toxin interaction; one site is unoccupied. We further report a higher resolution (2.0 A) determination and refinement of the wild-type CTB:GM1 oligosaccharide complex in which all five oligosaccharides are seen to be bound in essentially identical conformations. Saccharide conformation and binding interactions are very similar in both the CTB wild-type and Gly 33-->Arg mutant complexes. The protein conformation observed for the binding-deficient Gly 33-->Asp mutant of LTB does not differ substantially from that seen in the toxin:saccharide complexes. The critical nature of the side chain of residue 33 is apparently due to a limited range of subtle rearrangements available to both the toxin and the saccharide to accommodate receptor binding. The intermolecular interactions seen in the CTB (Gly 33-->Arg) complex with oligosaccharide suggest that the affinity of this mutant for the receptor is close to the self-affinity corresponding to the toxin:toxin binding interaction that has now been observed in crystal structures of three CTB mutants.

  • Organizational Affiliation

    Department of Biological Structure, University of Washington, Seattle 98195-7742, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
B [auth E],
C [auth F],
D [auth G],
E [auth H]
104Vibrio choleraeMutation(s): 0 
Find proteins for P01556 (Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961))
Explore P01556 
Go to UniProtKB:  P01556
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01556
Sequence Annotations
  • Reference Sequence


Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-galactopyranose-(1-4)-[N-acetyl-alpha-neuraminic acid-(2-3)]beta-D-galactopyranoseF [auth A],
H [auth C]
Glycosylation Resources
GlyTouCan:  G50886AE
GlyCosmos:  G50886AE
GlyGen:  G50886AE
Entity ID: 3
MoleculeChains Length2D Diagram Glycosylation3D Interactions
beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-galactopyranose-(1-4)-[N-acetyl-alpha-neuraminic acid-(2-3)]beta-D-galactopyranose-(1-4)-beta-D-glucopyranoseG [auth B],
Glycosylation Resources
GlyTouCan:  G48558GR
GlyCosmos:  G48558GR
GlyGen:  G48558GR
Experimental Data & Validation

Experimental Data

  • Resolution: 2.00 Å
  • R-Value Work: 0.171 
  • R-Value Observed: 0.171 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 101.9α = 90
b = 67.58β = 105.69
c = 80.47γ = 90
Software Package:
Software NamePurpose
XENGENdata collection
MACROdata reduction
X-PLORmodel building
XENGENdata reduction
MACROdata scaling

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1997-12-03
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Other, Structure summary
  • Version 2.1: 2023-08-09
    Changes: Database references, Refinement description, Structure summary