Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

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

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 122.67 kDa 
• Atom Count: 9841 
• Modelled Residue Count: 1030 
• Deposited Residue Count: 1030 
• Unique protein chains: 1

6HJD

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

• PDB DOI: 10.2210/pdb6HJD/pdb

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


• Deposited: 2018-09-03 Released: 2019-08-14 
• Deposition Author(s): Krengel, U., Heim, J.B.
• Funding Organization(s): Research Council of Norway

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.54 Å
• R-Value Free: 0.224 
• R-Value Work: 0.193 
• R-Value Observed: 0.194 

Literature

Crystal structures of cholera toxin in complex with fucosylated receptors point to importance of secondary binding site.

Heim, J.B., Hodnik, V., Heggelund, J.E., Anderluh, G., Krengel, U.

(2019) Sci Rep 9: 12243-12243

• PubMed: 31439922 
• DOI: 10.1038/s41598-019-48579-2
• Primary Citation of Related Structures:  
  6HJD, 6HMW, 6HMY


• PubMed Abstract: 
  

Cholera is a life-threatening diarrhoeal disease caused by the human pathogen Vibrio cholerae. Infection occurs after ingestion of the bacteria, which colonize the human small intestine and secrete their major virulence factor - the cholera toxin (CT). The GM1 ganglioside is considered the primary receptor of the CT, but recent studies suggest that also fucosylated receptors such as histo-blood group antigens are important for cellular uptake and toxicity. Recently, a special focus has been on the histo-blood group antigen Lewis ^x (Le ^x ), however, where and how the CT binds to Le ^x remains unclear. Here we report the high-resolution crystal structure (1.5 Å) of the receptor-binding B-subunits of the CT bound to the Le ^x trisaccharide, and complementary quantitative binding data for CT holotoxins. Le ^x , and also L-fucose alone, bind to the secondary binding site of the toxin, distinct from the GM1 binding site. In contrast, fucosyl-GM1 mainly binds to the primary binding site due to high-affinity interactions of its GM1 core. Le ^x is the first histo-blood group antigen of non-secretor phenotype structurally investigated in complex with CT. Together with the quantitative binding data, this allows unique insight into why individuals with non-secretor phenotype are more prone to severe cholera than so-called 'secretors'.

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Organizational Affiliation: 

Department of Chemistry, University of Oslo, P.O. Box 1033, NO-0315, Blindern, Norway. [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cholera toxin B subunit	A, B, C, D, E, F, G, H, I, J	103	Vibrio cholerae	Mutation(s): 0  Gene Names: ctxB
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	Chain Length	2D Diagram	Glycosylation
alpha-L-fucopyranose-(1-3)-[beta-D-galactopyranose-(1-4)]2-acetamido-2-deoxy-alpha-D-glucopyranose	K, L, N, P, Q, R	3		N/A
Glycosylation Resources
GlyTouCan:  G51591NI GlyCosmos:  G51591NI GlyGen:  G51591NI

Entity ID: 3
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
alpha-L-fucopyranose-(1-3)-[beta-D-galactopyranose-(1-4)]2-acetamido-2-deoxy-beta-D-glucopyranose	M, O	3		N/A
Glycosylation Resources
GlyTouCan:  G00051MO GlyCosmos:  G00051MO GlyGen:  G00051MO

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FUC (Subject of Investigation/LOI)	DA [auth F]	alpha-L-fucopyranose C6 H12 O5 SHZGCJCMOBCMKK-SXUWKVJYSA-N
BCN	CA [auth F], FA [auth G], GA [auth G], JA [auth I], KA [auth I], MA [auth J], T [auth A], V [auth B], Y [auth D], Z [auth D]	BICINE C6 H13 N O4 FSVCELGFZIQNCK-UHFFFAOYSA-N
CA	AA [auth E], BA [auth F], EA [auth G], HA [auth H], IA [auth I], LA [auth J], S [auth A], U [auth B], W [auth C], X [auth D]	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_900120	K, L, N, P, Q, R	Lewis X antigen, alpha anomer	Oligosaccharide / Antigen		Ligand Interaction

Entity ID: 3
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900119	M, O	Lewis X antigen, beta anomer	Oligosaccharide / Antigen		Ligand Interaction

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.54 Å
• R-Value Free: 0.224 
• R-Value Work: 0.193 
• R-Value Observed: 0.194 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.965	α = 90
b = 108.291	β = 90
c = 115.621	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
Coot	model building
xia2	data reduction
DIALS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2018-09-03 
• Released Date: 2019-08-14 
Deposition Author(s): Krengel, U., Heim, J.B.

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Funding Organization	Location	Grant Number
Research Council of Norway	Norway	247730

Revision History  

• Version 1.0: 2019-08-14
  Type: Initial release
  
• Version 1.1: 2019-10-02
  Changes: Data collection, Database references
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary