5ELB

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

PDB DOI: https://doi.org/10.2210/pdb5ELB/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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.08 Å
R-Value Free: 0.155
R-Value Work: 0.120
R-Value Observed: 0.122

Starting Model: experimental
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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: 129.14 kDa
Atom Count: 11,575
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 B subunit	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, EN12_07055, ERS013160_03498, ERS013165_03981, ERS013197_06217, ERS013202_03762, ERS013206_03003, ERS013207_03244, ERS013212_03447
UniProt
Find proteins for Q57193 (Vibrio cholerae) Explore Q57193 Go to UniProtKB: Q57193
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q57193
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, L, M, N, O K, L, M, N, O, P, Q, R	4		N/A	Interactions Focus chain K Focus chain L Focus chain M Focus chain N Focus chain O Focus chain P Focus chain Q Focus chain R Interactions & Density Focus chain K Focus chain L Focus chain M Focus chain N Focus chain O Focus chain P Focus chain Q Focus chain R
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)-2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-3)-alpha-L-fucopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose	S, T	5	N/A	N/A	Interactions Focus chain S Focus chain T Interactions & Density Focus chain S Focus chain T

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GLA Query on GLA Download Ideal Coordinates CCD File SDF format, chain BB [auth G] SDF format, chain DA [auth B] SDF format, chain EB [auth H] SDF format, chain GB [auth I] SDF format, chain IA [auth C] SDF format, chain IB [auth J] SDF format, chain QA [auth D] SDF format, chain W [auth A] SDF format, chain WA [auth E] SDF format, chain YA [auth F] MOL2 format, chain BB [auth G] MOL2 format, chain DA [auth B] MOL2 format, chain EB [auth H] MOL2 format, chain GB [auth I] MOL2 format, chain IA [auth C] MOL2 format, chain IB [auth J] MOL2 format, chain QA [auth D] MOL2 format, chain W [auth A] MOL2 format, chain WA [auth E] MOL2 format, chain YA [auth F] mmCIF format, chain BB [auth G] mmCIF format, chain DA [auth B] mmCIF format, chain EB [auth H] mmCIF format, chain GB [auth I] mmCIF format, chain IA [auth C] mmCIF format, chain IB [auth J] mmCIF format, chain QA [auth D] mmCIF format, chain W [auth A] mmCIF format, chain WA [auth E] mmCIF format, chain YA [auth F]	BB [auth G] DA [auth B] EB [auth H] GB [auth I] IA [auth C] BB [auth G], DA [auth B], EB [auth H], GB [auth I], IA [auth C], IB [auth J], QA [auth D], W [auth A], WA [auth E], YA [auth F]	alpha-D-galactopyranose C₆ H₁₂ O₆ WQZGKKKJIJFFOK-PHYPRBDBSA-N		Interactions Focus chain BB [auth G] Focus chain DA [auth B] Focus chain EB [auth H] Focus chain GB [auth I] Focus chain IA [auth C] Focus chain IB [auth J] Focus chain QA [auth D] Focus chain W [auth A] Focus chain WA [auth E] Focus chain YA [auth F] Interactions & Density Focus chain BB [auth G] Focus chain DA [auth B] Focus chain EB [auth H] Focus chain GB [auth I] Focus chain IA [auth C] Focus chain IB [auth J] Focus chain QA [auth D] Focus chain W [auth A] Focus chain WA [auth E] Focus chain YA [auth F]
GAL Query on GAL Download Ideal Coordinates CCD File SDF format, chain CA [auth B] SDF format, chain CB [auth G] SDF format, chain DB [auth H] SDF format, chain FB [auth I] SDF format, chain HA [auth C] SDF format, chain HB [auth J] SDF format, chain PA [auth D] SDF format, chain VA [auth E] SDF format, chain ZA [auth F] SDF format, chain V [auth A] MOL2 format, chain CA [auth B] MOL2 format, chain CB [auth G] MOL2 format, chain DB [auth H] MOL2 format, chain FB [auth I] MOL2 format, chain HA [auth C] MOL2 format, chain HB [auth J] MOL2 format, chain PA [auth D] MOL2 format, chain VA [auth E] MOL2 format, chain ZA [auth F] MOL2 format, chain V [auth A] mmCIF format, chain CA [auth B] mmCIF format, chain CB [auth G] mmCIF format, chain DB [auth H] mmCIF format, chain FB [auth I] mmCIF format, chain HA [auth C] mmCIF format, chain HB [auth J] mmCIF format, chain PA [auth D] mmCIF format, chain VA [auth E] mmCIF format, chain ZA [auth F] mmCIF format, chain V [auth A]	CA [auth B] CB [auth G] DB [auth H] FB [auth I] HA [auth C] CA [auth B], CB [auth G], DB [auth H], FB [auth I], HA [auth C], HB [auth J], PA [auth D], V [auth A], VA [auth E], ZA [auth F]	beta-D-galactopyranose C₆ H₁₂ O₆ WQZGKKKJIJFFOK-FPRJBGLDSA-N		Interactions Focus chain CA [auth B] Focus chain CB [auth G] Focus chain DB [auth H] Focus chain FB [auth I] Focus chain HA [auth C] Focus chain HB [auth J] Focus chain PA [auth D] Focus chain V [auth A] Focus chain VA [auth E] Focus chain ZA [auth F] Interactions & Density Focus chain CA [auth B] Focus chain CB [auth G] Focus chain DB [auth H] Focus chain FB [auth I] Focus chain HA [auth C] Focus chain HB [auth J] Focus chain PA [auth D] Focus chain V [auth A] Focus chain VA [auth E] Focus chain ZA [auth F]
BCN Query on BCN Download Ideal Coordinates CCD File SDF format, chain BA [auth B] SDF format, chain FA [auth B] SDF format, chain KA [auth C] SDF format, chain LA [auth C] SDF format, chain MA [auth D] SDF format, chain SA [auth E] SDF format, chain UA [auth E] SDF format, chain X [auth A] SDF format, chain Z [auth A] SDF format, chain OA [auth D] MOL2 format, chain BA [auth B] MOL2 format, chain FA [auth B] MOL2 format, chain KA [auth C] MOL2 format, chain LA [auth C] MOL2 format, chain MA [auth D] MOL2 format, chain SA [auth E] MOL2 format, chain UA [auth E] MOL2 format, chain X [auth A] MOL2 format, chain Z [auth A] MOL2 format, chain OA [auth D] mmCIF format, chain BA [auth B] mmCIF format, chain FA [auth B] mmCIF format, chain KA [auth C] mmCIF format, chain LA [auth C] mmCIF format, chain MA [auth D] mmCIF format, chain SA [auth E] mmCIF format, chain UA [auth E] mmCIF format, chain X [auth A] mmCIF format, chain Z [auth A] mmCIF format, chain OA [auth D]	BA [auth B] FA [auth B] KA [auth C] LA [auth C] MA [auth D] BA [auth B], FA [auth B], KA [auth C], LA [auth C], MA [auth D], OA [auth D], SA [auth E], UA [auth E], X [auth A], Z [auth A]	BICINE C₆ H₁₃ N O₄ FSVCELGFZIQNCK-UHFFFAOYSA-N		Interactions Focus chain BA [auth B] Focus chain FA [auth B] Focus chain KA [auth C] Focus chain LA [auth C] Focus chain MA [auth D] Focus chain OA [auth D] Focus chain SA [auth E] Focus chain UA [auth E] Focus chain X [auth A] Focus chain Z [auth A] Interactions & Density Focus chain BA [auth B] Focus chain FA [auth B] Focus chain KA [auth C] Focus chain LA [auth C] Focus chain MA [auth D] Focus chain OA [auth D] Focus chain SA [auth E] Focus chain UA [auth E] Focus chain X [auth A] Focus chain Z [auth A]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain AB [auth G] MOL2 format, chain AB [auth G] mmCIF format, chain AB [auth G]	AB [auth G]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain AB [auth G] Interactions & Density Focus chain AB [auth G]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain EA [auth B] SDF format, chain JA [auth C] SDF format, chain NA [auth D] SDF format, chain RA [auth D] SDF format, chain TA [auth E] SDF format, chain U [auth A] SDF format, chain XA [auth E] SDF format, chain Y [auth A] SDF format, chain GA [auth C] MOL2 format, chain AA [auth B] MOL2 format, chain EA [auth B] MOL2 format, chain JA [auth C] MOL2 format, chain NA [auth D] MOL2 format, chain RA [auth D] MOL2 format, chain TA [auth E] MOL2 format, chain U [auth A] MOL2 format, chain XA [auth E] MOL2 format, chain Y [auth A] MOL2 format, chain GA [auth C] mmCIF format, chain AA [auth B] mmCIF format, chain EA [auth B] mmCIF format, chain JA [auth C] mmCIF format, chain NA [auth D] mmCIF format, chain RA [auth D] mmCIF format, chain TA [auth E] mmCIF format, chain U [auth A] mmCIF format, chain XA [auth E] mmCIF format, chain Y [auth A] mmCIF format, chain GA [auth C]	AA [auth B] EA [auth B] GA [auth C] JA [auth C] NA [auth D] AA [auth B], EA [auth B], GA [auth C], JA [auth C], NA [auth D], RA [auth D], TA [auth E], U [auth A], XA [auth E], Y [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain AA [auth B] Focus chain EA [auth B] Focus chain GA [auth C] Focus chain JA [auth C] Focus chain NA [auth D] Focus chain RA [auth D] Focus chain TA [auth E] Focus chain U [auth A] Focus chain XA [auth E] Focus chain Y [auth A] Interactions & Density Focus chain AA [auth B] Focus chain EA [auth B] Focus chain GA [auth C] Focus chain JA [auth C] Focus chain NA [auth D] Focus chain RA [auth D] Focus chain TA [auth E] Focus chain U [auth A] Focus chain XA [auth E] Focus chain Y [auth A]

Biologically Interesting Molecules (External Reference) 1 Unique

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.08 Å
R-Value Free: 0.155
R-Value Work: 0.120
R-Value Observed: 0.122
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.333	α = 90
b = 98.984	β = 90
c = 152.019	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
PHASER	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: 2017-10-11
Changes: Derived calculations
Version 1.3: 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, Derived calculations, Refinement description, Structure summary