5ELC

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
R-Value Work: 0.221
R-Value Observed: 0.223

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.1 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

PubMed: 27082955 Search on PubMedSearch on PubMed Central
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.

Macromolecule Content

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

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cholera enterotoxin subunit B	A, B, C, D, E 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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P01556
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D 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	Interactions Focus chain K Focus chain O Focus chain Q Focus chain S Interactions & Density Focus chain K Focus chain O Focus chain Q Focus chain S
Glycosylation Resources
GlyTouCan: G82236PZ GlyCosmos: G82236PZ GlyGen: G82236PZ

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D 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	Interactions Focus chain L Focus chain M Focus chain R Interactions & Density Focus chain L Focus chain M Focus chain R
Glycosylation Resources
GlyTouCan: G82236PZ GlyCosmos: G82236PZ GlyGen: G82236PZ

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D 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	Interactions Focus chain N Focus chain P Interactions & Density Focus chain N Focus chain P
Glycosylation Resources
GlyTouCan: G00052MO GlyCosmos: G00052MO GlyGen: G00052MO

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FUC Query on FUC Download Ideal Coordinates CCD File SDF format, chain NA [auth F] MOL2 format, chain NA [auth F]	NA [auth F]	alpha-L-fucopyranose C₆ H₁₂ O₅ SHZGCJCMOBCMKK-SXUWKVJYSA-N		Interactions Focus chain NA [auth F] Interactions & Density Focus chain NA [auth F]
BCN Query on BCN Download Ideal Coordinates CCD File SDF format, chain CA [auth C] SDF format, chain FA [auth D] SDF format, chain HA [auth D] SDF format, chain KA [auth E] SDF format, chain U [auth A] SDF format, chain Z [auth B] SDF format, chain EA [auth C] SDF format, chain MA [auth E] SDF format, chain W [auth A] SDF format, chain X [auth B] MOL2 format, chain CA [auth C] MOL2 format, chain FA [auth D] MOL2 format, chain HA [auth D] MOL2 format, chain KA [auth E] MOL2 format, chain U [auth A] MOL2 format, chain Z [auth B] MOL2 format, chain EA [auth C] MOL2 format, chain MA [auth E] MOL2 format, chain W [auth A] MOL2 format, chain X [auth B]	CA [auth C] EA [auth C] FA [auth D] HA [auth D] KA [auth E] 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		Interactions Focus chain CA [auth C] Focus chain EA [auth C] Focus chain FA [auth D] Focus chain HA [auth D] Focus chain KA [auth E] Focus chain MA [auth E] Focus chain U [auth A] Focus chain W [auth A] Focus chain X [auth B] Focus chain Z [auth B] Interactions & Density Focus chain CA [auth C] Focus chain EA [auth C] Focus chain FA [auth D] Focus chain HA [auth D] Focus chain KA [auth E] Focus chain MA [auth E] Focus chain U [auth A] Focus chain W [auth A] Focus chain X [auth B] Focus chain Z [auth B]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain BA [auth C] SDF format, chain DA [auth C] SDF format, chain JA [auth E] SDF format, chain LA [auth E] SDF format, chain T [auth A] SDF format, chain V [auth A] SDF format, chain Y [auth B] SDF format, chain GA [auth D] SDF format, chain IA [auth D] MOL2 format, chain AA [auth B] MOL2 format, chain BA [auth C] MOL2 format, chain DA [auth C] MOL2 format, chain JA [auth E] MOL2 format, chain LA [auth E] MOL2 format, chain T [auth A] MOL2 format, chain V [auth A] MOL2 format, chain Y [auth B] MOL2 format, chain GA [auth D] MOL2 format, chain IA [auth D]	AA [auth B] BA [auth C] DA [auth C] GA [auth D] IA [auth D] 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		Interactions Focus chain AA [auth B] Focus chain BA [auth C] Focus chain DA [auth C] Focus chain GA [auth D] Focus chain IA [auth D] Focus chain JA [auth E] Focus chain LA [auth E] Focus chain T [auth A] Focus chain V [auth A] Focus chain Y [auth B] Interactions & Density Focus chain AA [auth B] Focus chain BA [auth C] Focus chain DA [auth C] Focus chain GA [auth D] Focus chain IA [auth D] Focus chain JA [auth E] Focus chain LA [auth E] Focus chain T [auth A] Focus chain V [auth A] Focus chain Y [auth B]

Biologically Interesting Molecules (External Reference) 2 Unique

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

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free: 0.260
R-Value Work: 0.221
R-Value Observed: 0.223
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

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2016-03-30

Deposition Author(s):

Heggelund, J.E.

Burschowsky, D.

Krengel, U.

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: 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

Prepare Data

Validate Data

Deposit Data

Help and Resources

5ELC

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

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

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Expand

Entity ID: 2

Glycosylation Resources

Entity ID: 3

Glycosylation Resources

Entity ID: 4

Glycosylation Resources

Entity ID: 2

Entity ID: 4

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)