5G3L

ESCHERICHIA COLI HEAT LABILE ENTEROTOXIN TYPE IIB B-PENTAMER COMPLEXED WITH SIALYLATED SUGAR


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.72 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.172 

Starting Model: experimental
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This is version 2.1 of the entry. See complete history


Literature

Biochemical and Structural Characterization of the Novel Sialic Acid-Binding Site of Escherichia Coli Heat-Labile Enterotoxin Lt-Iib.

Zalem, D.Ribeiro, J.P.Varrot, A.Lebens, M.Imberty, A.Teneberg, S.

(2016) Biochem J 473: 3923

  • DOI: https://doi.org/10.1042/BCJ20160575
  • Primary Citation of Related Structures:  
    5G3L

  • PubMed Abstract: 

    The structurally related AB 5 -type heat-labile enterotoxins of Escherichia coli and Vibrio cholerae are classified into two major types. The type I group includes cholera toxin (CT) and E. coli LT-I, whereas the type II subfamily comprises LT-IIa, LT-IIb and LT-IIc. The carbohydrate-binding specificities of LT-IIa, LT-IIb and LT-IIc are distinctive from those of cholera toxin and E. coli LT-I. Whereas CT and LT-I bind primarily to the GM1 ganglioside, LT-IIa binds to gangliosides GD1a, GD1b and GM1, LT-IIb binds to the GD1a and GT1b gangliosides, and LT-IIc binds to GM1, GM2, GM3 and GD1a. These previous studies of the binding properties of type II B-subunits have been focused on ganglio core chain gangliosides. To further define the carbohydrate binding specificity of LT-IIb B-subunits, we have investigated its binding to a collection of gangliosides and non-acid glycosphingolipids with different core chains. A high-affinity binding of LT-IIb B-subunits to gangliosides with a neolacto core chain, such as Neu5Gcα3- and Neu5Acα3-neolactohexaosylceramide, and Neu5Gcα3- and Neu5Acα3-neolactooctaosylceramide was detected. An LT-IIb-binding ganglioside was isolated from human small intestine and characterized as Neu5Acα3-neolactohexaosylceramide. The crystal structure of the B-subunit of LT-IIb with the pentasaccharide moiety of Neu5Acα3-neolactotetraosylceramide (Neu5Ac-nLT: Neu5Acα3Galβ4GlcNAcβ3Galβ4Glc) was determined providing the first information for a sialic-binding site in this subfamily, with clear differences from that of CT and LT-I.


  • Organizational Affiliation

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


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
HEAT-LABILE ENTEROTOXIN IIB, B CHAINA [auth D],
B [auth E],
E [auth H]
99Escherichia coli HB101Mutation(s): 0 
UniProt
Find proteins for P43529 (Escherichia coli)
Explore P43529 
Go to UniProtKB:  P43529
Entity Groups  
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UniProt GroupP43529
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
HEAT-LABILE ENTEROTOXIN IIB, B CHAINC [auth F],
D [auth G]
99Escherichia coli HB101Mutation(s): 0 
UniProt
Find proteins for P43529 (Escherichia coli)
Explore P43529 
Go to UniProtKB:  P43529
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP43529
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

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Entity ID: 3
MoleculeChains Length2D Diagram Glycosylation3D Interactions
N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranoseF [auth A],
G [auth B],
H [auth C]
2N/A
Glycosylation Resources
GlyTouCan:  G30207PZ
GlyCosmos:  G30207PZ
GlyGen:  G30207PZ
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.72 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.172 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.564α = 90
b = 68.015β = 90
c = 154.513γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-09-14
    Type: Initial release
  • Version 1.1: 2016-11-09
    Changes: Database references
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Other, Structure summary
  • Version 2.1: 2024-01-10
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary