5ELE

Cholera toxin El Tor B-pentamer in complex with A Lewis-y


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.185 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 2.2 of the entry. See complete history


Literature

High-Resolution Crystal Structures Elucidate the Molecular Basis of Cholera Blood Group Dependence.

Heggelund, J.E.Burschowsky, D.Bjrnestad, V.A.Hodnik, V.Anderluh, G.Krengel, U.

(2016) PLoS Pathog 12: e1005567-e1005567

  • DOI: https://doi.org/10.1371/journal.ppat.1005567
  • Primary Citation of Related Structures:  
    5ELB, 5ELC, 5ELD, 5ELE, 5ELF

  • PubMed Abstract: 

    Cholera is the prime example of blood-group-dependent diseases, with individuals of blood group O experiencing the most severe symptoms. The cholera toxin is the main suspect to cause this relationship. We report the high-resolution crystal structures (1.1-1.6 Å) of the native cholera toxin B-pentamer for both classical and El Tor biotypes, in complexes with relevant blood group determinants and a fragment of its primary receptor, the GM1 ganglioside. The blood group A determinant binds in the opposite orientation compared to previously published structures of the cholera toxin, whereas the blood group H determinant, characteristic of blood group O, binds in both orientations. H-determinants bind with higher affinity than A-determinants, as shown by surface plasmon resonance. Together, these findings suggest why blood group O is a risk factor for severe cholera.


  • Organizational Affiliation

    Department of Chemistry, University of Oslo, Blindern, Norway.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cholera enterotoxin subunit B
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J
103Vibrio cholerae O1Mutation(s): 0 
Gene Names: ctxBtoxBVC_1456
UniProt
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
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  • Reference Sequence
Oligosaccharides

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Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D 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)]2-acetamido-2-deoxy-alpha-D-glucopyranose
K, L, M
5N/A
Glycosylation Resources
GlyTouCan:  G62623TF
GlyCosmos:  G62623TF
GlyGen:  G62623TF
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
1PE
Query on 1PE

Download Ideal Coordinates CCD File 
JA [auth F]PENTAETHYLENE GLYCOL
C10 H22 O6
JLFNLZLINWHATN-UHFFFAOYSA-N
NAG
Query on NAG

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KA [auth G]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
FUC
Query on FUC

Download Ideal Coordinates CCD File 
IA [auth F],
LA [auth H],
MA [auth I],
O [auth A]
alpha-L-fucopyranose
C6 H12 O5
SHZGCJCMOBCMKK-SXUWKVJYSA-N
BCN
Query on BCN

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AA [auth D]
CA [auth D]
EA [auth E]
GA [auth E]
P [auth A]
AA [auth D],
CA [auth D],
EA [auth E],
GA [auth E],
P [auth A],
R [auth A],
S [auth B],
U [auth B],
W [auth C],
Y [auth C]
BICINE
C6 H13 N O4
FSVCELGFZIQNCK-UHFFFAOYSA-N
CA
Query on CA

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BA [auth D]
DA [auth D]
FA [auth E]
HA [auth E]
N [auth A]
BA [auth D],
DA [auth D],
FA [auth E],
HA [auth E],
N [auth A],
Q [auth A],
T [auth B],
V [auth B],
X [auth C],
Z [auth C]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.185 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.543α = 90
b = 82.973β = 90
c = 196.555γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-03-30
    Type: Initial release
  • Version 1.1: 2016-04-27
    Changes: Database references
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2024-01-10
    Changes: Data collection, Database references, Refinement description, Structure summary
  • Version 2.2: 2024-11-13
    Changes: Structure summary