8Q6I | pdb_00008q6i

Cholera holotoxin variant (chimera with E. coli heat-labile enterotoxin, 1 C-terminal substitution)

PDB DOI: https://doi.org/10.2210/pdb8Q6I/pdb

Classification: TOXIN
Organism(s): Vibrio cholerae O1
Expression System: Vibrio natriegens
Mutation(s): Yes

Deposited: 2023-08-11 Released: 2025-02-12
Deposition Author(s): Mojica, N., Cordara, G., Kersten, F., Heim, J.B., Krengel, U.
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.60 ?
R-Value Free:
0.222 (Depositor), 0.230 (DCC)
R-Value Work:
0.185 (Depositor), 0.194 (DCC)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Cholera toxin variants

Kersten, F., Serrano, A., Mojica, N., Cordara, G., Heim, J.B., Tatulian, S.A., Krengel, U., Teter, K.

To be published.

Macromolecule Content

Total Structure Weight: 86.64 kDa
Atom Count: 6,874
Modelled Residue Count: 742
Deposited Residue Count: 755
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cholera enterotoxin subunit A	A	240	Vibrio cholerae O1	Mutation(s): 1 Gene Names: ctxA, toxA, VC_1457
UniProt
Find proteins for P01555 (Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)) Explore P01555 Go to UniProtKB: P01555
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P01555
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Cholera enterotoxin subunit B	B [auth D], C [auth E], D [auth F], E [auth G], F [auth H]	103	Vibrio cholerae O1	Mutation(s): 2 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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain L [auth D] SDF format, chain O [auth E] MOL2 format, chain L [auth D] MOL2 format, chain O [auth E] mmCIF format, chain L [auth D] mmCIF format, chain O [auth E]	L [auth D], O [auth E]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain L [auth D] Focus chain O [auth E] Interactions & Density Focus chain L [auth D] Focus chain O [auth E]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain I [auth D] SDF format, chain J [auth D] SDF format, chain K [auth D] SDF format, chain M [auth E] SDF format, chain N [auth E] SDF format, chain P [auth F] SDF format, chain Q [auth G] SDF format, chain R [auth G] SDF format, chain S [auth G] SDF format, chain T [auth H] SDF format, chain U [auth H] MOL2 format, chain I [auth D] MOL2 format, chain J [auth D] MOL2 format, chain K [auth D] MOL2 format, chain M [auth E] MOL2 format, chain N [auth E] MOL2 format, chain P [auth F] MOL2 format, chain Q [auth G] MOL2 format, chain R [auth G] MOL2 format, chain S [auth G] MOL2 format, chain T [auth H] MOL2 format, chain U [auth H] mmCIF format, chain I [auth D] mmCIF format, chain J [auth D] mmCIF format, chain K [auth D] mmCIF format, chain M [auth E] mmCIF format, chain N [auth E] mmCIF format, chain P [auth F] mmCIF format, chain Q [auth G] mmCIF format, chain R [auth G] mmCIF format, chain S [auth G] mmCIF format, chain T [auth H] mmCIF format, chain U [auth H]	I [auth D] J [auth D] K [auth D] M [auth E] N [auth E] I [auth D], J [auth D], K [auth D], M [auth E], N [auth E], P [auth F], Q [auth G], R [auth G], S [auth G], T [auth H], U [auth H]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain I [auth D] Focus chain J [auth D] Focus chain K [auth D] Focus chain M [auth E] Focus chain N [auth E] Focus chain P [auth F] Focus chain Q [auth G] Focus chain R [auth G] Focus chain S [auth G] Focus chain T [auth H] Focus chain U [auth H] Interactions & Density Focus chain I [auth D] Focus chain J [auth D] Focus chain K [auth D] Focus chain M [auth E] Focus chain N [auth E] Focus chain P [auth F] Focus chain Q [auth G] Focus chain R [auth G] Focus chain S [auth G] Focus chain T [auth H] Focus chain U [auth H]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A]	G [auth A], H [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Interactions & Density Focus chain G [auth A] Focus chain H [auth A]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
HIC Query on HIC	A	L-PEPTIDE LINKING	C₇ H₁₁ N₃ O₂		HIS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.60 ?
R-Value Free: 0.222 (Depositor), 0.230 (DCC)
R-Value Work: 0.185 (Depositor), 0.194 (DCC)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( ? )	Angle ( ? )
a = 60.308	α = 90
b = 91.091	β = 106.403
c = 72.291	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data scaling
PHASER	phasing
Coot	model building
MxCuBE	data collection
XDS	data reduction

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2025-02-12

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	R03AI112854
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	R01AI137056

Revision History (Full details and data files)

Version 1.0: 2025-02-12
Type: Initial release

Prepare Data

Validate Data

Deposit Data

Help and Resources

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Cholera holotoxin variant (chimera with E. coli heat-labile enterotoxin, 1 C-terminal substitution)

Cholera toxin variants

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Entity ID: 2