5ELD

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

• PDB DOI: https://doi.org/10.2210/pdb5ELD/pdb

• Classification: TOXIN
• Organism(s): Vibrio cholerae O1
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2015-11-04 Released: 2016-03-30 
• Deposition Author(s): Heggelund, J.E., Burschowsky, D., Krengel, U.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 0.193 
• R-Value Work: 0.171 
• R-Value Observed: 0.172 

Starting Model: experimental

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

• PubMed: 27082955 
• 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Cyclic - C5  (Explore in 3D)
Global Stoichiometry: Homo 5-mer - A5 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 63.23 kDa 
• Atom Count: 5,418 
• Modelled Residue Count: 515 
• Deposited Residue Count: 515 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cholera enterotoxin B subunit	A, B, C, D, E	103	Vibrio cholerae O1	Mutation(s): 0  Gene Names: ctxB
UniProt
Find proteins for D6R7L2 (Vibrio cholerae O1) Explore D6R7L2  Go to UniProtKB:  D6R7L2

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D 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	F, G, H, I	5		N/A
Glycosylation Resources
GlyTouCan:  G62623TF GlyCosmos:  G62623TF GlyGen:  G62623TF

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MES	M [auth C]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C6 H13 N O4 S SXGZJKUKBWWHRA-UHFFFAOYSA-N
GLA	T [auth E]	alpha-D-galactopyranose C6 H12 O6 WQZGKKKJIJFFOK-PHYPRBDBSA-N
GAL	K [auth A], O [auth C], S [auth E]	beta-D-galactopyranose C6 H12 O6 WQZGKKKJIJFFOK-FPRJBGLDSA-N
PGE	N [auth C], Q [auth D], R [auth E]	TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N
PEG	J [auth A], P [auth D]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
NA	L [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900128	F, G, H, I	Blood group A Lewis Y antigen, alpha anomer	Oligosaccharide / Antigen

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 0.193 
• R-Value Work: 0.171 
• R-Value Observed: 0.172 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.7	α = 90
b = 69.806	β = 90
c = 134.735	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-03-30 
Deposition Author(s): Heggelund, J.E., Burschowsky, D., Krengel, U.

Revision History  

• Version 1.0: 2016-03-30
  Type: Initial release
  
• Version 1.1: 2016-04-27
  Changes: Database references
• Version 1.2: 2016-05-11
  Changes: Source and taxonomy
• 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: Advisory, Data collection, Database references, Refinement description, Structure summary
• Version 2.2: 2024-10-23
  Changes: Structure summary