5ELF

Cholera toxin El Tor B-pentamer in complex with A-pentasaccharide

PDB DOI: https://doi.org/10.2210/pdb5ELF/pdb

Classification: TOXIN
Organism(s): Vibrio cholerae O1 biovar El Tor str. N16961
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: 1.55 Å
R-Value Free:
0.220 (Depositor), 0.230 (DCC)
R-Value Work:
0.179 (Depositor), 0.190 (DCC)
R-Value Observed:
0.181 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.2 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: 125.38 kDa
Atom Count: 10,185
Modelled Residue Count: 1,030
Deposited Residue Count: 1,030
Unique protein chains: 1

Macromolecules

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(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 biovar El Tor str. N16961	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 LOADING

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)]alpha-D-glucopyranose	K, M, P, Q	5		N/A	Interactions Focus chain K Focus chain M Focus chain P Focus chain Q Interactions & Density Focus chain K Focus chain M Focus chain P Focus chain Q
Glycosylation Resources
GlyTouCan: G75772UP GlyCosmos: G75772UP GlyGen: G75772UP

Entity ID: 3
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)]beta-D-glucopyranose	L, N, O	5		N/A	Interactions Focus chain L Focus chain N Focus chain O Interactions & Density Focus chain L Focus chain N Focus chain O
Glycosylation Resources
GlyTouCan: G62121FH GlyCosmos: G62121FH GlyGen: G62121FH

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PG4 Query on PG4 Download Ideal Coordinates CCD File SDF format, chain NA [auth F] MOL2 format, chain NA [auth F] mmCIF format, chain NA [auth F]	NA [auth F]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain NA [auth F] Interactions & Density Focus chain NA [auth F]
GLC Query on GLC Download Ideal Coordinates CCD File SDF format, chain IA [auth D] SDF format, chain OA [auth G] MOL2 format, chain IA [auth D] MOL2 format, chain OA [auth G] mmCIF format, chain IA [auth D] mmCIF format, chain OA [auth G]	IA [auth D], OA [auth G]	alpha-D-glucopyranose C₆ H₁₂ O₆ WQZGKKKJIJFFOK-DVKNGEFBSA-N		Interactions Focus chain IA [auth D] Focus chain OA [auth G] Interactions & Density Focus chain IA [auth D] Focus chain OA [auth G]
FUC Query on FUC Download Ideal Coordinates CCD File SDF format, chain PA [auth H] SDF format, chain X [auth B] MOL2 format, chain PA [auth H] MOL2 format, chain X [auth B] mmCIF format, chain PA [auth H] mmCIF format, chain X [auth B]	PA [auth H], X [auth B]	alpha-L-fucopyranose C₆ H₁₂ O₅ SHZGCJCMOBCMKK-SXUWKVJYSA-N		Interactions Focus chain PA [auth H] Focus chain X [auth B] Interactions & Density Focus chain PA [auth H] Focus chain X [auth B]
BCN Query on BCN Download Ideal Coordinates CCD File SDF format, chain BA [auth C] SDF format, chain CA [auth C] SDF format, chain FA [auth D] SDF format, chain GA [auth D] SDF format, chain JA [auth E] SDF format, chain LA [auth E] SDF format, chain S [auth A] SDF format, chain U [auth A] SDF format, chain V [auth B] SDF format, chain Y [auth B] MOL2 format, chain BA [auth C] MOL2 format, chain CA [auth C] MOL2 format, chain FA [auth D] MOL2 format, chain GA [auth D] MOL2 format, chain JA [auth E] MOL2 format, chain LA [auth E] MOL2 format, chain S [auth A] MOL2 format, chain U [auth A] MOL2 format, chain V [auth B] MOL2 format, chain Y [auth B] mmCIF format, chain BA [auth C] mmCIF format, chain CA [auth C] mmCIF format, chain FA [auth D] mmCIF format, chain GA [auth D] mmCIF format, chain JA [auth E] mmCIF format, chain LA [auth E] mmCIF format, chain S [auth A] mmCIF format, chain U [auth A] mmCIF format, chain V [auth B] mmCIF format, chain Y [auth B]	BA [auth C] CA [auth C] FA [auth D] GA [auth D] JA [auth E] BA [auth C], CA [auth C], FA [auth D], GA [auth D], JA [auth E], LA [auth E], S [auth A], U [auth A], V [auth B], Y [auth B]	BICINE C₆ H₁₃ N O₄ FSVCELGFZIQNCK-UHFFFAOYSA-N		Interactions Focus chain BA [auth C] Focus chain CA [auth C] Focus chain FA [auth D] Focus chain GA [auth D] Focus chain JA [auth E] Focus chain LA [auth E] Focus chain S [auth A] Focus chain U [auth A] Focus chain V [auth B] Focus chain Y [auth B] Interactions & Density Focus chain BA [auth C] Focus chain CA [auth C] Focus chain FA [auth D] Focus chain GA [auth D] Focus chain JA [auth E] Focus chain LA [auth E] Focus chain S [auth A] Focus chain U [auth A] Focus chain V [auth B] Focus chain Y [auth B]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain DA [auth C] SDF format, chain EA [auth D] SDF format, chain HA [auth D] SDF format, chain KA [auth E] SDF format, chain MA [auth E] SDF format, chain R [auth A] SDF format, chain T [auth A] SDF format, chain W [auth B] SDF format, chain Z [auth B] MOL2 format, chain AA [auth C] MOL2 format, chain DA [auth C] MOL2 format, chain EA [auth D] MOL2 format, chain HA [auth D] MOL2 format, chain KA [auth E] MOL2 format, chain MA [auth E] MOL2 format, chain R [auth A] MOL2 format, chain T [auth A] MOL2 format, chain W [auth B] MOL2 format, chain Z [auth B] mmCIF format, chain AA [auth C] mmCIF format, chain DA [auth C] mmCIF format, chain EA [auth D] mmCIF format, chain HA [auth D] mmCIF format, chain KA [auth E] mmCIF format, chain MA [auth E] mmCIF format, chain R [auth A] mmCIF format, chain T [auth A] mmCIF format, chain W [auth B] mmCIF format, chain Z [auth B]	AA [auth C] DA [auth C] EA [auth D] HA [auth D] KA [auth E] AA [auth C], DA [auth C], EA [auth D], HA [auth D], KA [auth E], MA [auth E], R [auth A], T [auth A], W [auth B], Z [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain AA [auth C] Focus chain DA [auth C] Focus chain EA [auth D] Focus chain HA [auth D] Focus chain KA [auth E] Focus chain MA [auth E] Focus chain R [auth A] Focus chain T [auth A] Focus chain W [auth B] Focus chain Z [auth B] Interactions & Density Focus chain AA [auth C] Focus chain DA [auth C] Focus chain EA [auth D] Focus chain HA [auth D] Focus chain KA [auth E] Focus chain MA [auth E] Focus chain R [auth A] Focus chain T [auth A] Focus chain W [auth B] Focus chain Z [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.55 Å
R-Value Free: 0.220 (Depositor), 0.230 (DCC)
R-Value Work: 0.179 (Depositor), 0.190 (DCC)
R-Value Observed: 0.181 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.626	α = 90
b = 84.72	β = 90
c = 195.68	γ = 90

Software Package:

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

Structure Validation

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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 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: Data collection, Database references, Derived calculations, Refinement description, Structure summary
Version 2.2: 2024-10-23
Changes: Structure summary

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Help and Resources

5ELF

Cholera toxin El Tor B-pentamer in complex with A-pentasaccharide

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