3EFX | pdb_00003efx

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 (Depositor), 0.234 (DCC) 
  • R-Value Work: 
    0.181 (Depositor), 0.182 (DCC) 
  • R-Value Observed: 
    0.184 (Depositor) 

Starting Model: experimental
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This is version 2.3 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: https://doi.org/10.1016/j.str.2004.06.022
  • Primary Citation 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. 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.


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

Macromolecule Content 

  • Total Structure Weight: 124.44 kDa 
  • Atom Count: 8,860 
  • Modeled Residue Count: 961 
  • Deposited Residue Count: 1,030 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Cholera enterotoxin subunit B, Heat-labile enterotoxin B chain103Vibrio choleraeMutation(s): 0 
UniProt
Find proteins for P01556 (Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961))
Explore P01556 
Go to UniProtKB:  P01556
Find proteins for P0CK94 (Escherichia coli)
Explore P0CK94 
Go to UniProtKB:  P0CK94
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP01556P0CK94
Sequence Annotations
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Reference Sequence

Oligosaccharides

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Entity ID: 2
MoleculeChains Length2D Diagram GlycosylationD 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
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 (Depositor), 0.234 (DCC) 
  • R-Value Work:  0.181 (Depositor), 0.182 (DCC) 
  • R-Value Observed: 0.184 (Depositor) 
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

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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
  • Version 2.1: 2023-11-01
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary
  • Version 2.2: 2024-04-10
    Changes: Source and taxonomy
  • Version 2.3: 2024-11-13
    Changes: Structure summary