8QRE: Cholera holotoxin

Name: PDB 8QRE: Cholera holotoxin (wildtype)
Published: 2024-05-15
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: toxin

Cholera holotoxin (wildtype). Determined by X-ray diffraction at 2.3 Å resolution. Released 15 May 2024.

Method: X-ray diffraction
Resolution: 2.3 Å
Organism: Vibrio cholerae O1
Chains: 12
Atoms: 13,002
Mol. weight: 174.34 kDa
Ligands: GLA, GAL
Released: 15 May 2024

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

Secondary structure: helices and β-sheets

8QRE contains 78 α-helices and 82 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: 19 helices, 11 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	34-36	3
α-helix	41-46	6
β-strand	59-62	4	3
β-strand	63	1	1
α-helix	66-76	11
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	134-135	2	1
α-helix	139	1
β-strand	140-141	2	1
α-helix	142	1
α-helix	147-150	4
α-helix	155-157	3
α-helix	158-160	3
α-helix	172-175	4
α-helix	179-181	3
α-helix	183-184	2
α-helix	198-225	28
α-helix	232-235	4

Chain B: 19 helices, 11 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	34-36	3
α-helix	41-46	6
β-strand	59-62	4	7
β-strand	63	1	5
α-helix	66-76	11
β-strand	82-89	8	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	134-135	2	5
α-helix	139	1
β-strand	140-141	2	5
α-helix	142	1
α-helix	147-150	4
α-helix	155-157	3
α-helix	158-160	3
α-helix	172-175	4
α-helix	179-181	3
α-helix	183-184	2
α-helix	199-225	27
α-helix	232-235	4

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

Element	Residues	Length	Sheet
α-helix	5-9	5
β-strand	15-23	9	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	1
β-strand	81-88	8	8
β-strand	94-102	9	8

Chains E, G, H and L: 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	38-41	4	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 I: 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	94-101	8	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

>8QRE_1 Cholera enterotoxin subunit A (chains A, B)
NDDKLYRADSRPPDEIKQSGGLMPRGQSEYFDRGTQMNINLYDHARGTQTGFVRHDDGYV
STSISLRSAHLVGQTILSGHSTYYIYVIATAPNMFNVNDVLGAYSPHPDEQEVSALGGIP
YSQIYGWYRVHFGVLDEQLHRNRGYRDRYYSNLDIAPAADGYGLAGFPPEHRAWREEPWI
HHAPPGCGNAPRSSMSNTCDEKTQSLGVKFLDEYQSKVKRQIFSGYQSDIDTHNRIKDEL

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

>8QRE_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
GLA	alpha-D-galactopyranose	C6 H12 O6	1
GAL	beta-D-galactopyranose	C6 H12 O6	10

Water and common crystallization additives (PEG, ACT, GOL, NA) are not listed.

Primary citation

Using Vibrio natriegens for High-Yield Production of Challenging Expression Targets and for Protein Perdeuteration. Mojica, N., Kersten, F., Montserrat-Canals, M. et al. Biochemistry (2024) 63:587-598. DOI 10.1021/acs.biochem.3c00612 · PubMed

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

8OXS 1.6 Å, Cholera holotoxin variant (chimera with E. coli heat-labile enterotoxin, 4 C-terminal…
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
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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