8OXS: Cholera holotoxin variant

Name: PDB 8OXS: Cholera holotoxin variant (chimera with E. coli heat-labile enterotoxin, 4 C-terminal substitutions)
Published: 2024-08-14
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: toxin

Cholera holotoxin variant (chimera with E. coli heat-labile enterotoxin, 4 C-terminal substitutions). Determined by X-ray diffraction at 1.6 Å resolution. Released 14 Aug 2024.

Method: X-ray diffraction
Resolution: 1.6 Å
Organism: Vibrio cholerae O1
Chains: 12
Atoms: 13,700
Mol. weight: 174.83 kDa
Ligands: GAL, GLA
Released: 14 Aug 2024

Explore 8OXS in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8OXS contains 80 α-helices and 80 β-strands across 12 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 18 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	4-9	6	1
α-helix	13-19	7
β-strand	21-22	2	2
α-helix	23-24	2
α-helix	41-46	6
β-strand	59-62	4	3
β-strand	63	1	1
α-helix	66-77	12
β-strand	82-89	8	1
β-strand	94-96	3	3
α-helix	97-101	5
α-helix	102-104	3
α-helix	108-110	3
β-strand	113-116	4	3
β-strand	119-120	2	2
α-helix	121-123	3
β-strand	124-131	8	1
β-strand	134-141	8	1
α-helix	142	1
α-helix	147-151	5
α-helix	155-157	3
α-helix	158-160	3
α-helix	162-164	3
α-helix	172-175	4
α-helix	179-182	4
α-helix	183-184	2
α-helix	198-223	26
α-helix	224-226	3

Chain B: 19 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	4-9	6	5
α-helix	13-19	7
β-strand	21-22	2	6
α-helix	23-24	2
α-helix	41-45	5
β-strand	59-62	4	7
β-strand	63	1	5
α-helix	66-77	12
β-strand	83-89	7	5
β-strand	94-96	3	7
α-helix	97-101	5
α-helix	102-104	3
α-helix	108-110	3
β-strand	113-116	4	7
β-strand	119-120	2	6
α-helix	121-123	3
β-strand	124-131	8	5
β-strand	134-141	8	5
α-helix	142	1
α-helix	147-151	5
α-helix	155-157	3
α-helix	158-160	3
α-helix	162-164	3
α-helix	172-175	4
α-helix	179-182	4
α-helix	183-184	2
α-helix	198-223	26
α-helix	224-226	3
α-helix	232-235	4

Chain C: 4 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	5-9	5
β-strand	15-22	8	8
β-strand	26-30	5	8
β-strand	38-41	4	8
β-strand	47-50	4	8
α-helix	51-53	3
α-helix	59-78	20
α-helix	80-81	2
β-strand	82-88	7	8
β-strand	94-102	9	8

Chains D, J and K: 4 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	5-9	5
β-strand	15-22	8	4
β-strand	26-30	5	4
β-strand	37-41	5	4
β-strand	47-50	4	4
α-helix	51-53	3
α-helix	59-78	20
α-helix	80-81	2
β-strand	82-88	7	4
β-strand	94-102	9	4

Chains E and I: 5 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	5-9	5
β-strand	15-22	8	4
β-strand	26-30	5	4
β-strand	37-41	5	4
β-strand	47-50	4	4
α-helix	51-53	3
α-helix	59-61	3
α-helix	62-78	17
α-helix	80-81	2
β-strand	82-88	7	4
β-strand	94-102	9	4

Chains F and H: 4 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	5-10	6
β-strand	15-22	8	4
β-strand	26-30	5	4
β-strand	37-41	5	4
β-strand	47-50	4	4
α-helix	51-53	3
α-helix	59-78	20
α-helix	80-81	2
β-strand	82-88	7	4
β-strand	94-102	9	4

Chain G: 5 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	5-9	5
β-strand	15-22	8	4
β-strand	26-30	5	4
β-strand	37-41	5	4
β-strand	47-50	4	4
α-helix	51-53	3
α-helix	59-61	3
α-helix	62-77	16
α-helix	80-81	2
β-strand	82-88	7	4
β-strand	94-102	9	4

Chain L: 4 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	5-9	5
β-strand	15-22	8	8
β-strand	26-30	5	8
β-strand	37-41	5	8
β-strand	47-50	4	8
α-helix	51-53	3
α-helix	59-77	19
α-helix	80-81	2
β-strand	82-88	7	8
β-strand	94-102	9	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Cholera enterotoxin subunit A	A, B	protein	240	Vibrio cholerae O1	P01555 (AlphaFold model)
Cholera enterotoxin subunit B	C, D, E, F, G, H, I, J, K, L	protein	103	Vibrio cholerae O1	P01556 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>8OXS_1 Cholera enterotoxin subunit A (chains A, B)
NDDKLYRADSRPPDEIKQSGGLMPRGQSEYFDRGTQMNINLYDHARGTQTGFVRHDDGYV
STSISLRSAHLVGQTILSGHSTYYIYVIATAPNMFNVNDVLGAYSPHPDEQEVSALGGIP
YSQIYGWYRVHFGVLDEQLHRNRGYRDRYYSNLDIAPAADGYGLAGFPPEHRAWREEPWI
HHAPPGCGNAPRSSMSNTCDEKTQSLGVKFLDEYQSKVKRQIFSGYQSEVDIYNRIKDEL

Sequence of entity 2 (C, D, E, F, G, H, I, J, K, L), FASTA

>8OXS_2 Cholera enterotoxin subunit B (chains C, D, E, F, G, H, I, J, K, L)
TPQNITDLCAEYHNTQIHTLNDKIFSYTESLAGKREMAIITFKNGATFQVEVPGSQHIDS
QKKAIERMKDTLRIAYLTEAKVEKLCVWNNKTPHAIAAISMAN

Ligands and cofactors

ID	Name	Formula	Copies
GAL	beta-D-galactopyranose	C6 H12 O6	10
GLA	alpha-D-galactopyranose	C6 H12 O6	7

Water and common crystallization additives (EPE, NA) are not listed.

Primary citation

Cholera toxin variants. Heim, J.B., Serrano, A., Kersten, F. et al. To be published.

Other PDB entries of the same protein (UniProt P01555 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8Q6I 1.6 Å, Cholera holotoxin variant (chimera with E. coli heat-labile enterotoxin, 1 C-terminal…
1S5D 1.75 Å, Cholera holotoxin with an A-subunit Y30S mutation, Crystal form 2
2A5D 1.8 Å, Structural basis for the activation of cholera toxin by human ARF6-GTP
1S5E 1.9 Å, Cholera holotoxin, Crystal form 1
2A5F 2.02 Å, Cholera toxin A1 subunit bound to its substrate, NAD+, and its human protein activator,…
1S5B 2.13 Å, Cholera holotoxin with an A-subunit Y30S mutation Form 3
8QRE 2.3 Å, Cholera holotoxin (wildtype)
1XTC 2.4 Å, Cholera toxin
1S5C 2.5 Å, Cholera holotoxin with an A-subunit Y30S mutation, Crystal form 1
1S5F 2.6 Å, Cholera holotoxin, Crystal form 2
2A5G 2.66 Å, Cholera toxin A1 subunit bound to ARF6(Q67L)

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