5ELC | pdb_00005elc

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

• PDB DOI: https://doi.org/10.2210/pdb5ELC/pdb

• Classification: TOXIN
• Organism(s): Vibrio cholerae O1
• Expression System: Vibrio
• Mutation(s): No 


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

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 
  0.260 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.221 (Depositor), 0.224 (DCC) 
• R-Value Observed: 
  0.223 (Depositor) 

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 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.
Department of Biology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia.
The National Institute of Chemistry, Ljubljana, Slovenia.

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Biological Assembly 2  

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

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 124.88 kDa 
• Atom Count: 9,536 
• Modeled Residue Count: 1,030 
• Deposited Residue Count: 1,030 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cholera enterotoxin subunit B	A, B, C, D, E, F, G, H, I, J	103	Vibrio cholerae O1	Mutation(s): 0  Gene Names: ctxB, toxB, VC_1456
UniProt
Find proteins for P01556 (Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)) Explore P01556  Go to UniProtKB:  P01556

Oligosaccharides

Help  

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-L-fucopyranose-(1-2)-beta-D-galactopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-alpha-D-glucopyranose	K, O, Q, S	4		N/A
Glycosylation Resources
GlyTouCan: G82236PZ GlyCosmos: G82236PZ GlyGen: G82236PZ

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-L-fucopyranose-(1-2)-beta-D-galactopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-alpha-D-glucopyranose	L, M, R	5		N/A
Glycosylation Resources
GlyTouCan: G82236PZ GlyCosmos: G82236PZ GlyGen: G82236PZ

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-L-fucopyranose-(1-2)-beta-D-galactopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranose	N, P	4		N/A
Glycosylation Resources
GlyTouCan: G00052MO GlyCosmos: G00052MO GlyGen: G00052MO

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FUC	NA [auth F]	alpha-L-fucopyranose C6 H12 O5 SHZGCJCMOBCMKK-SXUWKVJYSA-N
BCN	CA [auth C], EA [auth C], FA [auth D], HA [auth D], KA [auth E], MA [auth E], U [auth A], W [auth A], X [auth B], Z [auth B]	BICINE C6 H13 N O4 FSVCELGFZIQNCK-UHFFFAOYSA-N
CA	AA [auth B], BA [auth C], DA [auth C], GA [auth D], IA [auth D], JA [auth E], LA [auth E], T [auth A], V [auth A], Y [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Biologically Interesting Molecules (External Reference) 

2 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900124	K, O, Q, S	Lewis Y antigen, alpha anomer	Oligosaccharide / Antigen

Entity ID: 4
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900054	N, P	Lewis Y antigen, beta anomer	Oligosaccharide / Antigen

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free:  0.260 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.221 (Depositor), 0.224 (DCC) 
• R-Value Observed: 0.223 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.667	α = 90
b = 80.916	β = 96.07
c = 95.77	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: 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
• Version 2.1: 2024-01-10
  Changes: Data collection, Database references, Refinement description, Structure summary
• Version 2.2: 2024-11-20
  Changes: Structure summary