5ELB

Cholera toxin classical B-pentamer in complex with Lewis-y


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.08 Å
  • R-Value Free: 0.155 
  • R-Value Work: 0.120 
  • R-Value Observed: 0.122 

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Ligand Structure Quality Assessment 


This is version 2.0 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: 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 ...

    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
MoleculeChainsSequence LengthOrganismDetailsImage
Cholera enterotoxin B subunit
A, B, C, D, E, F, G, H, I, J
A, B, C, D, E, F, G, H, I, J
103Vibrio cholerae O1Mutation(s): 0 
Gene Names: ctxBEN12_07055ERS013160_03498ERS013165_03981ERS013197_06217ERS013202_03762ERS013206_03003ERS013207_03244ERS013212_03447
UniProt
Find proteins for Q57193 (Vibrio cholerae)
Explore Q57193 
Go to UniProtKB:  Q57193
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ57193
Protein Feature View
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
alpha-L-fucopyranose-(1-2)-beta-D-galactopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-alpha-D-glucopyranose
K, L, M, N, O, P, Q, R
K, L, M, N, O, P, Q, R
4N/A Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G82236PZ
GlyCosmos:  G82236PZ
GlyGen:  G82236PZ
Entity ID: 3
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
alpha-L-fucopyranose-(1-2)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-3)-alpha-L-fucopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranoseS, T 5N/AN/A Oligosaccharides Interaction
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GLA
Query on GLA

Download Ideal Coordinates CCD File 
BB [auth G],
DA [auth B],
EB [auth H],
GB [auth I],
IA [auth C],
BB [auth G],
DA [auth B],
EB [auth H],
GB [auth I],
IA [auth C],
IB [auth J],
QA [auth D],
W [auth A],
WA [auth E],
YA [auth F]
alpha-D-galactopyranose
C6 H12 O6
WQZGKKKJIJFFOK-PHYPRBDBSA-N
 Ligand Interaction
GAL
Query on GAL

Download Ideal Coordinates CCD File 
CA [auth B],
CB [auth G],
DB [auth H],
FB [auth I],
HA [auth C],
CA [auth B],
CB [auth G],
DB [auth H],
FB [auth I],
HA [auth C],
HB [auth J],
PA [auth D],
V [auth A],
VA [auth E],
ZA [auth F]
beta-D-galactopyranose
C6 H12 O6
WQZGKKKJIJFFOK-FPRJBGLDSA-N
 Ligand Interaction
BCN
Query on BCN

Download Ideal Coordinates CCD File 
BA [auth B],
FA [auth B],
KA [auth C],
LA [auth C],
MA [auth D],
BA [auth B],
FA [auth B],
KA [auth C],
LA [auth C],
MA [auth D],
OA [auth D],
SA [auth E],
UA [auth E],
X [auth A],
Z [auth A]
BICINE
C6 H13 N O4
FSVCELGFZIQNCK-UHFFFAOYSA-N
 Ligand Interaction
PEG
Query on PEG

Download Ideal Coordinates CCD File 
AB [auth G]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download Ideal Coordinates CCD File 
AA [auth B],
EA [auth B],
GA [auth C],
JA [auth C],
NA [auth D],
AA [auth B],
EA [auth B],
GA [auth C],
JA [auth C],
NA [auth D],
RA [auth D],
TA [auth E],
U [auth A],
XA [auth E],
Y [auth A]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 2
IDChainsNameType/Class2D Diagram3D Interactions
PRD_900124
Query on PRD_900124
K, L, M, N, O, P, Q, RLewis Y antigen, alpha anomerOligosaccharide / Antigen Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.08 Å
  • R-Value Free: 0.155 
  • R-Value Work: 0.120 
  • R-Value Observed: 0.122 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.333α = 90
b = 98.984β = 90
c = 152.019γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata 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: 2016-03-30
    Type: Initial release
  • Version 1.1: 2016-04-27
    Changes: Database references
  • Version 1.2: 2017-10-11
    Changes: Derived calculations
  • Version 1.3: 2018-11-21
    Changes: Data collection, Source and taxonomy
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary