5ELD

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

PDB DOI: https://doi.org/10.2210/pdb5ELD/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: 1.40 Å
R-Value Free:
0.193 (Depositor), 0.200 (DCC)
R-Value Work:
0.171 (Depositor), 0.180 (DCC)
R-Value Observed:
0.172 (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: 63.23 kDa
Atom Count: 5,418
Modelled Residue Count: 515
Deposited Residue Count: 515
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 B subunit	A, B, C, D, E	103	Vibrio cholerae O1	Mutation(s): 0 Gene Names: ctxB
UniProt
Find proteins for D6R7L2 (Vibrio cholerae O1) Explore D6R7L2 Go to UniProtKB: D6R7L2
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	D6R7L2
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)]2-acetamido-2-deoxy-alpha-D-glucopyranose	F, G, H, I	5		N/A	Interactions Focus chain F Focus chain G Focus chain H Focus chain I Interactions & Density Focus chain F Focus chain G Focus chain H Focus chain I
Glycosylation Resources
GlyTouCan: G62623TF GlyCosmos: G62623TF GlyGen: G62623TF

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MES Query on MES Download Ideal Coordinates CCD File SDF format, chain M [auth C] MOL2 format, chain M [auth C] mmCIF format, chain M [auth C]	M [auth C]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C₆ H₁₃ N O₄ S SXGZJKUKBWWHRA-UHFFFAOYSA-N		Interactions Focus chain M [auth C] Interactions & Density Focus chain M [auth C]
GAL Query on GAL Download Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain O [auth C] SDF format, chain S [auth E] MOL2 format, chain K [auth A] MOL2 format, chain O [auth C] MOL2 format, chain S [auth E] mmCIF format, chain K [auth A] mmCIF format, chain O [auth C] mmCIF format, chain S [auth E]	K [auth A], O [auth C], S [auth E]	beta-D-galactopyranose C₆ H₁₂ O₆ WQZGKKKJIJFFOK-FPRJBGLDSA-N		Interactions Focus chain K [auth A] Focus chain O [auth C] Focus chain S [auth E] Interactions & Density Focus chain K [auth A] Focus chain O [auth C] Focus chain S [auth E]
GLA Query on GLA Download Ideal Coordinates CCD File SDF format, chain T [auth E] MOL2 format, chain T [auth E] mmCIF format, chain T [auth E]	T [auth E]	alpha-D-galactopyranose C₆ H₁₂ O₆ WQZGKKKJIJFFOK-PHYPRBDBSA-N		Interactions Focus chain T [auth E] Interactions & Density Focus chain T [auth E]
PGE Query on PGE Download Ideal Coordinates CCD File SDF format, chain N [auth C] SDF format, chain Q [auth D] SDF format, chain R [auth E] MOL2 format, chain N [auth C] MOL2 format, chain Q [auth D] MOL2 format, chain R [auth E] mmCIF format, chain N [auth C] mmCIF format, chain Q [auth D] mmCIF format, chain R [auth E]	N [auth C], Q [auth D], R [auth E]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain N [auth C] Focus chain Q [auth D] Focus chain R [auth E] Interactions & Density Focus chain N [auth C] Focus chain Q [auth D] Focus chain R [auth E]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain P [auth D] MOL2 format, chain J [auth A] MOL2 format, chain P [auth D] mmCIF format, chain J [auth A] mmCIF format, chain P [auth D]	J [auth A], P [auth D]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain P [auth D] Interactions & Density Focus chain J [auth A] Focus chain P [auth D]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain L [auth B] MOL2 format, chain L [auth B] mmCIF format, chain L [auth B]	L [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain L [auth B] Interactions & Density Focus chain L [auth B]

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900128 Query on PRD_900128	F, G, H, I	Blood group A Lewis Y antigen, alpha anomer	Oligosaccharide / Antigen		Interactions Focus chain F Focus chain G Focus chain H Focus chain I Interactions & Density Focus chain F Focus chain G Focus chain H Focus chain I

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.40 Å
R-Value Free: 0.193 (Depositor), 0.200 (DCC)
R-Value Work: 0.171 (Depositor), 0.180 (DCC)
R-Value Observed: 0.172 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.7	α = 90
b = 69.806	β = 90
c = 134.735	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
MOLREP	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 1.2: 2016-05-11
Changes: Source and taxonomy
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: Advisory, Data collection, Database references, Refinement description, Structure summary
Version 2.2: 2024-10-23
Changes: Structure summary