3EFX

Novel binding site identified in a hybrid between cholera toxin and heat-labile enterotoxin, 1.9A crystal structure reveals the details


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.94 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.184 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

Novel binding site identified in a hybrid between cholera toxin and heat-labile enterotoxin: 1.9 A crystal structure reveals the details

Holmner, A.Lebens, M.Teneberg, S.Angstrom, J.Okvist, M.Krengel, U.

(2004) Structure 12: 1655-1667

  • DOI: 10.1016/j.str.2004.06.022
  • Primary Citation of Related Structures:  
    3EFX

  • PubMed Abstract: 
  • A hybrid between the B subunits of cholera toxin and Escherichia coli heat-labile enterotoxin has been described, which exhibits a novel binding specificity to blood group A and B type 2 determinants. In the present investigation, we have determined the crystal structure of this protein hybrid, termed LCTBK, in complex with the blood group A pentasaccharide GalNAcalpha3(Fucalpha2)Galbeta4(Fucalpha3)GlcNAcbeta, confirming not only the novel binding specificity but also a distinct new oligosaccharide binding site ...

    A hybrid between the B subunits of cholera toxin and Escherichia coli heat-labile enterotoxin has been described, which exhibits a novel binding specificity to blood group A and B type 2 determinants. In the present investigation, we have determined the crystal structure of this protein hybrid, termed LCTBK, in complex with the blood group A pentasaccharide GalNAcalpha3(Fucalpha2)Galbeta4(Fucalpha3)GlcNAcbeta, confirming not only the novel binding specificity but also a distinct new oligosaccharide binding site. Binding studies revealed that the new specificity can be ascribed to a single mutation (S4N) introduced into the sequence of Escherichia coli heat-labile enterotoxin. At a resolution of 1.9 A, the new binding site is resolved in excellent detail. Main features include a complex network of water molecules, which is well preserved by the parent toxins, and an unexpectedly modest contribution to binding by the critical residue Asn4, which interacts with the ligand only via a single water molecule.


    Related Citations: 
    • Novel binding site identified in a hybrid between cholera toxin and heat-labile enterotoxin: 1.9 A crystal structure reveals the details
      Holmner, A., Lebens, M., Teneberg, S., Angstrom, J., Okvist, M., Krengel, U.
      (2007) Structure 15: 253

    Organizational Affiliation

    Department of Chemistry and Bioscience, Chalmers University of Technology, PO Box 462, SE-40530 Göteborg, Sweden. asa.holmner@chembio.chalmers.se



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Cholera enterotoxin subunit B, Heat-labile enterotoxin B chain103Vibrio choleraeMutation(s): 0 
UniProt
Find proteins for P0CK94 (Escherichia coli)
Explore P0CK94 
Go to UniProtKB:  P0CK94
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 GroupsP01556P0CK94
Protein Feature View
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
alpha-L-fucopyranose-(1-2)-[2-acetamido-2-deoxy-alpha-D-galactopyranose-(1-3)]beta-D-galactopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]beta-D-glucopyranose
K [auth A],
L [auth B],
M [auth C],
N,
O,
K [auth A],
L [auth B],
M [auth C],
N,
O,
P,
Q,
R,
S,
T
5N/A Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G62121FH
GlyCosmos:  G62121FH
GlyGen:  G62121FH
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.94 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.184 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 110.2α = 90
b = 70.1β = 92.9
c = 137.4γ = 90
Software Package:
Software NamePurpose
MAR345dtbdata collection
AMoREphasing
REFMACrefinement
XDSdata reduction
XSCALEdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-09-23
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2015-06-24
    Changes: Source and taxonomy
  • Version 1.3: 2015-09-02
    Changes: Source and taxonomy
  • Version 1.4: 2020-01-29
    Changes: Data collection, Database references, Derived calculations, Source and taxonomy
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary