7PRS

Crystal Structure of the B subunit of heat labile enterotoxin LT-IIc from Escherichia coli in complex with Sialyl-lacto-N-neotetraose d


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.188 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Characterization of the ganglioside recognition profile of Escherichia coli heat-labile enterotoxin LT-IIc.

Zalem, D.Juhas, M.Terrinoni, M.King-Lyons, N.Lebens, M.Varrot, A.Connell, T.D.Teneberg, S.

(2022) Glycobiology 32: 391-403

  • DOI: https://doi.org/10.1093/glycob/cwab133
  • Primary Citation of Related Structures:  
    7PRP, 7PRS

  • PubMed Abstract: 

    The heat-labile enterotoxins of Escherichia coli and cholera toxin of Vibrio cholerae are related in structure and function. Each of these oligomeric toxins is comprised of one A polypeptide and five B polypeptides. The B-subunits bind to gangliosides, which are followed by uptake into the intoxicated cell and activation of the host's adenylate cyclase by the A-subunits. There are two antigenically distinct groups of these toxins. Group I includes cholera toxin and type I heat-labile enterotoxin of E. coli; group II contains the type II heat-labile enterotoxins of E. coli. Three variants of type II toxins, designated LT-IIa, LT-IIb and LT-IIc have been described. Earlier studies revealed the crystalline structure of LT-IIb. Herein the carbohydrate binding specificity of LT-IIc B-subunits was investigated by glycosphingolipid binding studies on thin-layer chromatograms and in microtiter wells. Binding studies using a large variety of glycosphingolipids showed that LT-IIc binds with high affinity to gangliosides with a terminal Neu5Acα3Gal or Neu5Gcα3Gal, e.g. the gangliosides GM3, GD1a and Neu5Acα3-/Neu5Gcα3--neolactotetraosylceramide and Neu5Acα3-/Neu5Gcα3-neolactohexaosylceramide. The crystal structure of LT-IIc B-subunits alone and with bound LSTd/sialyl-lacto-N-neotetraose d pentasaccharide uncovered the molecular basis of the ganglioside recognition. These studies revealed common and unique functional structures of the type II family of heat-labile enterotoxins.


  • Organizational Affiliation

    Department of Medical Biochemistry and Cell Biology, Sahlgrenska Academy, Institute of Biomedicine, University of Gothenburg, Sweden.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Heat-labile enterotoxin IIA, B chain104Escherichia coliMutation(s): 0 
Gene Names: LT-IIc1 BGQM13_12885HVV37_03950HVV78_10285HVW37_13205
UniProt
Find proteins for H6W8F2 (Escherichia coli)
Explore H6W8F2 
Go to UniProtKB:  H6W8F2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupH6W8F2
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

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Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-beta-D-galactopyranose-(1-4)-alpha-D-glucopyranoseK [auth DaD]5N/A
Entity ID: 3
MoleculeChains Length2D Diagram Glycosylation3D Interactions
N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-beta-D-galactopyranoseL [auth GaG],
N [auth JaJ]
4N/A
Glycosylation Resources
GlyTouCan:  G69440RD
GlyCosmos:  G69440RD
GlyGen:  G69440RD
Entity ID: 4
MoleculeChains Length2D Diagram Glycosylation3D Interactions
N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseM [auth HaH]3N/A
Glycosylation Resources
GlyTouCan:  G00065MO
GlyCosmos:  G00065MO
GlyGen:  G00065MO
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SIA (Subject of Investigation/LOI)
Query on SIA

Download Ideal Coordinates CCD File 
S [auth III],
T [auth JJJ],
U [auth KKK],
V [auth LLL]
N-acetyl-alpha-neuraminic acid
C11 H19 N O9
SQVRNKJHWKZAKO-YRMXFSIDSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
O [auth DDD],
P [auth EEE],
Q [auth FFF],
R [auth HHH]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.188 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.09α = 90
b = 121.269β = 90
c = 126.732γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data

  • Released Date: 2022-02-02 
  • Deposition Author(s): Varrot, A.

Funding OrganizationLocationGrant Number
European CommissionEuropean Union653706

Revision History  (Full details and data files)

  • Version 1.0: 2022-02-02
    Type: Initial release
  • Version 1.1: 2022-05-04
    Changes: Database references
  • Version 1.2: 2024-01-31
    Changes: Data collection, Derived calculations, Refinement description
  • Version 1.3: 2024-11-20
    Changes: Structure summary