PDB-8q6i: Cholera holotoxin variant (chimera with E. coli heat-labile enter...

ID or keywords:

Entry

Database: PDB / ID: 8q6i

Title

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

Components

(Cholera enterotoxin subunit ...) x 2

Keywords

TOXIN / Cholera toxin / Vibrio cholerae / Bacterial toxin / E. coli heat-labile enterotoxin / Chimera / Holotoxin

Function / homology

Function and homology information

symbiont-mediated activation of host G protein-coupled receptor signal transduction / host cell surface binding / galactose binding / positive regulation of tyrosine phosphorylation of STAT protein / glycosyltransferase activity / Transferases; Glycosyltransferases; Pentosyltransferases / catalytic complex / nucleotidyltransferase activity / toxin activity / periplasmic space ...
Similarity search - Function

Biological species

Vibrio cholerae O1 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.603 Å

Authors

Mojica, N. / Cordara, G. / Kersten, F. / Heim, J.B. / Krengel, U.

Funding support

United States, 2items

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

Citation

Journal: To be published
Title: Cholera toxin variants
Authors: Kersten, F. / Serrano, A. / Mojica, N. / Cordara, G. / Heim, J.B. / Tatulian, S.A. / Krengel, U. / Teter, K.

History

Deposition	Aug 11, 2023	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Feb 12, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	8q6i.cif.gz	188.7 KB	Display	PDBx/mmCIF format
PDB format	pdb8q6i.ent.gz		Display	PDB format
PDBx/mmJSON format	8q6i.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	8q6i_validation.pdf.gz	487.1 KB	Display	wwPDB validaton report
Full document	8q6i_full_validation.pdf.gz	497.8 KB	Display
Data in XML	8q6i_validation.xml.gz	39.3 KB	Display
Data in CIF	8q6i_validation.cif.gz	52.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/q6/8q6i ftp://data.pdbj.org/pub/pdb/validation_reports/q6/8q6i	HTTPS FTP

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Related structure data

Related structure data	8oxsC C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#69 - Sep 2005 Cholera Toxin similarity (8)

Deposited unit

A: Cholera enterotoxin subunit A

D: Cholera enterotoxin subunit B

E: Cholera enterotoxin subunit B

F: Cholera enterotoxin subunit B

G: Cholera enterotoxin subunit B

H: Cholera enterotoxin subunit B

hetero molecules

86.6 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	60.308, 91.091, 72.291
Angle α, β, γ (deg.)	90.000, 106.403, 90.000
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Beg auth comp-ID: THR / Beg label comp-ID: THR / End auth comp-ID: ASN / End label comp-ID: ASN / Auth seq-ID: 1 - 103 / Label seq-ID: 1 - 103

NCS ensembles :

ID	Details
1	Local NCS retraints between domains: 1 2
2	Local NCS retraints between domains: 3 4
3	Local NCS retraints between domains: 5 6
4	Local NCS retraints between domains: 7 8
5	Local NCS retraints between domains: 9 10
6	Local NCS retraints between domains: 11 12
7	Local NCS retraints between domains: 13 14
8	Local NCS retraints between domains: 15 16
9	Local NCS retraints between domains: 17 18
10	Local NCS retraints between domains: 19 20

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Cholera enterotoxin subunit ... , 2 types, 6 molecules ADEFGH

#1: Protein	Cholera enterotoxin subunit A / Cholera enterotoxin / A chain Mass: 27256.016 Da / Num. of mol.: 1 / Mutation: D229E Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio cholerae O1 (bacteria) / Gene: ctxA, toxA, VC_1457 / Production host: Vibrio natriegens (bacteria) / References: UniProt: P01555
#2: Protein	Cholera enterotoxin subunit B / Cholera enterotoxin B chain / Cholera enterotoxin gamma chain / Choleragenoid Mass: 11623.267 Da / Num. of mol.: 5 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio cholerae O1 (bacteria) / Gene: ctxB, toxB, VC_1456 / Production host: Vibrio natriegens (bacteria) / References: UniProt: P01556

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Non-polymers , 4 types, 423 molecules

#3: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C₃H₈O₃
#5: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₄H₁₀O₃
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 408 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	N
Has protein modification	Y

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.25 Å³/Da / Density % sol: 45.35 % / Description: irregular prism
Crystal grow	Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 8 Details: Crystallization mix: 20% PEG6000 0.2 M lithium chloride 0.1 M Tris pH 8.0 Protein storage buffer: 0.05 M Tris/HCl pH 7.5 0.2 M NaCl

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Data collection

Diffraction	Mean temperature: 100 K / Ambient temp details: cryostream / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.87313 Å
Detector	Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jun 25, 2022
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.87313 Å / Relative weight: 1
Reflection	Resolution: 1.6→48.84 Å / Num. obs: 95507 / % possible obs: 96.71 % / Redundancy: 7.1 % / B_iso Wilson estimate: 29.3 Å² / CC_1/2: 0.999 / R_merge(I) obs: 0.085 / R_pim(I) all: 0.034 / R_rim(I) all: 0.092 / Net I/σ(I): 10.8
Reflection shell	Resolution: 1.6→1.66 Å / Redundancy: 7.4 % / R_merge(I) obs: 2.808 / Mean I/σ(I) obs: 0.7 / Num. unique obs: 8864 / CC_1/2: 0.436 / R_pim(I) all: 1.108 / R_rim(I) all: 3.022 / % possible all: 92.1

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0430	refinement
XDS	VERSION Jun 30, 2023	data scaling
PHASER	2.8.3	phasing
Coot	0.9.8.95	model building
MxCuBE	3	data collection
XDS	VERSION Jun 30, 2023	data reduction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.603→48.84 Å / Cor.coef. F_o:F_c: 0.972 / Cor.coef. F_o:F_c free: 0.958 / SU B: 2.959 / SU ML: 0.094 / Cross valid method: FREE R-VALUE / ESU R: 0.101 / ESU R Free: 0.101
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2215	4607	4.852 %
R_work	0.185	90353	-
all	0.187	-	-
obs	-	94960	96.709 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 28.494 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.734 Å²	-0 Å²	-0.793 Å²
2-	-	2.226 Å²	0 Å²
3-	-	-	-0.874 Å²

Refinement step

Cycle: LAST / Resolution: 1.603→48.84 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5885	0	82	408	6375

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.007	0.012	6632
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	6222
X-RAY DIFFRACTION	r_angle_refined_deg	1.487	1.818	9018
X-RAY DIFFRACTION	r_angle_other_deg	0.524	1.787	14413
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.248	5	846
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	2.811	2	35
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.53	10	1184
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	14.691	10	306
X-RAY DIFFRACTION	r_chiral_restr	0.078	0.2	982
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	7952
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	1517
X-RAY DIFFRACTION	r_nbd_refined	0.218	0.2	1382
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.193	0.2	5541
X-RAY DIFFRACTION	r_nbtor_refined	0.175	0.2	3217
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.078	0.2	3463
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.214	0.2	439
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.073	0.2	2
X-RAY DIFFRACTION	r_metal_ion_refined	0.087	0.2	3
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.134	0.2	18
X-RAY DIFFRACTION	r_nbd_other	0.18	0.2	82
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.085	0.2	20
X-RAY DIFFRACTION	r_mcbond_it	2.471	2.861	3252
X-RAY DIFFRACTION	r_mcbond_other	2.462	2.861	3252
X-RAY DIFFRACTION	r_mcangle_it	3.507	5.124	4142
X-RAY DIFFRACTION	r_mcangle_other	3.513	5.124	4143
X-RAY DIFFRACTION	r_scbond_it	2.943	3.18	3380
X-RAY DIFFRACTION	r_scbond_other	2.942	3.181	3381
X-RAY DIFFRACTION	r_scangle_it	4.399	5.707	4876
X-RAY DIFFRACTION	r_scangle_other	4.399	5.708	4877
X-RAY DIFFRACTION	r_lrange_it	5.87	29.631	7615
X-RAY DIFFRACTION	r_lrange_other	5.87	29.632	7616
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.094	0.05	3505
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.087	0.05	3537
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.089	0.05	3511
X-RAY DIFFRACTION	r_ncsr_local_group_4	0.095	0.05	3530
X-RAY DIFFRACTION	r_ncsr_local_group_5	0.066	0.05	3509
X-RAY DIFFRACTION	r_ncsr_local_group_6	0.061	0.05	3502
X-RAY DIFFRACTION	r_ncsr_local_group_7	0.055	0.05	3517
X-RAY DIFFRACTION	r_ncsr_local_group_8	0.074	0.05	3399
X-RAY DIFFRACTION	r_ncsr_local_group_9	0.067	0.05	3413
X-RAY DIFFRACTION	r_ncsr_local_group_10	0.07	0.05	3349

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Refine-ID	Type	Rms dev position (Å)	Weight position
1	1	D	X-RAY DIFFRACTION	Local ncs	0.09421	0.0501
1	2	E	X-RAY DIFFRACTION	Local ncs	0.09421	0.0501
2	3	D	X-RAY DIFFRACTION	Local ncs	0.08744	0.0501
2	4	F	X-RAY DIFFRACTION	Local ncs	0.08744	0.0501
3	5	D	X-RAY DIFFRACTION	Local ncs	0.08916	0.0501
3	6	G	X-RAY DIFFRACTION	Local ncs	0.08916	0.0501
4	7	D	X-RAY DIFFRACTION	Local ncs	0.09492	0.0501
4	8	H	X-RAY DIFFRACTION	Local ncs	0.09492	0.0501
5	9	E	X-RAY DIFFRACTION	Local ncs	0.0665	0.0501
5	10	F	X-RAY DIFFRACTION	Local ncs	0.0665	0.0501
6	11	E	X-RAY DIFFRACTION	Local ncs	0.06112	0.05011
6	12	G	X-RAY DIFFRACTION	Local ncs	0.06112	0.05011
7	13	E	X-RAY DIFFRACTION	Local ncs	0.0548	0.05011
7	14	H	X-RAY DIFFRACTION	Local ncs	0.0548	0.05011
8	15	F	X-RAY DIFFRACTION	Local ncs	0.07389	0.0501
8	16	G	X-RAY DIFFRACTION	Local ncs	0.07389	0.0501
9	17	F	X-RAY DIFFRACTION	Local ncs	0.06696	0.0501
9	18	H	X-RAY DIFFRACTION	Local ncs	0.06696	0.0501
10	19	G	X-RAY DIFFRACTION	Local ncs	0.07025	0.0501
10	20	H	X-RAY DIFFRACTION	Local ncs	0.07025	0.0501

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
1.603-1.644	0.44	327	0.435	5965	X-RAY DIFFRACTION	86.5951
1.644-1.689	0.394	353	0.377	6442	X-RAY DIFFRACTION	96.1511
1.689-1.738	0.332	329	0.341	6249	X-RAY DIFFRACTION	96.5649
1.738-1.792	0.302	300	0.29	6153	X-RAY DIFFRACTION	96.6886
1.792-1.85	0.289	315	0.251	5928	X-RAY DIFFRACTION	96.7757
1.85-1.915	0.244	324	0.225	5748	X-RAY DIFFRACTION	97.2142
1.915-1.988	0.222	291	0.209	5570	X-RAY DIFFRACTION	97.3588
1.988-2.069	0.263	261	0.212	5360	X-RAY DIFFRACTION	96.349
2.069-2.16	0.249	260	0.205	5186	X-RAY DIFFRACTION	97.8968
2.16-2.266	0.215	217	0.186	4963	X-RAY DIFFRACTION	97.5334
2.266-2.388	0.23	244	0.176	4729	X-RAY DIFFRACTION	98.2806
2.388-2.532	0.216	213	0.173	4513	X-RAY DIFFRACTION	98.1516
2.532-2.707	0.215	199	0.168	4233	X-RAY DIFFRACTION	98.3577
2.707-2.923	0.227	214	0.17	3917	X-RAY DIFFRACTION	98.5213
2.923-3.201	0.224	192	0.168	3639	X-RAY DIFFRACTION	98.7371
3.201-3.576	0.201	174	0.168	3277	X-RAY DIFFRACTION	98.4313
3.576-4.126	0.198	147	0.156	2913	X-RAY DIFFRACTION	98.3607
4.126-5.044	0.154	107	0.132	2527	X-RAY DIFFRACTION	99.1717
5.044-7.096	0.183	96	0.183	1923	X-RAY DIFFRACTION	99.2138
7.096-48.84	0.198	44	0.177	1119	X-RAY DIFFRACTION	98.3926

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Cholera enterotoxin subunit ... , 2 types, 6 molecules ADEFGH

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Non-polymers , 4 types, 423 molecules

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Cholera enterotoxin subunit ... , 2 types, 6 molecules ADEFGH

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Non-polymers , 4 types, 423 molecules

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