7SKK: Pertussis toxin

pertussis toxin in complex with ADPR and Nicotinamide. Determined by X-ray diffraction at 1.65 Å resolution. Released 13 Apr 2022.

Method: X-ray diffraction
Resolution: 1.65 Å
Organism: Bordetella pertussis
Chains: 4
Atoms: 6,673
Mol. weight: 86.11 kDa
Ligands: AR6, NCA
Released: 13 Apr 2022

Explore 7SKK in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7SKK contains 29 α-helices and 49 β-strands across 4 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: 8 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	2-4	3
β-strand	6-11	6	1
α-helix	15-21	7
β-strand	23-24	2	2
β-strand	29	1	3
α-helix	32-36	5
β-strand	48	1	3
β-strand	50-54	5	1
α-helix	57-76	20
β-strand	84-92	9	1
β-strand	97-99	3	1
α-helix	100-111	12
α-helix	122-124	3
β-strand	129-133	5	1
β-strand	135-136	2	2
α-helix	138-140	3
β-strand	141-149	9	1
β-strand	156-162	7	1
β-strand	174	1	1
α-helix	177-178	2

Chain B: 6 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	2-4	3
β-strand	6-11	6	4
α-helix	15-21	7
β-strand	23-24	2	5
β-strand	29	1	6
α-helix	32-36	5
β-strand	48	1	6
β-strand	50-54	5	4
α-helix	57-76	20
β-strand	84-92	9	4
β-strand	97-99	3	4
α-helix	100-111	12
β-strand	129-133	5	4
β-strand	135-136	2	5
α-helix	138-140	3
β-strand	141-149	9	4
β-strand	156-162	7	4

Chain C: 8 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	6-11	6	7
α-helix	15-21	7
β-strand	23-24	2	8
β-strand	29	1	9
α-helix	32-36	5
β-strand	48	1	9
β-strand	50-54	5	7
α-helix	57-76	20
β-strand	84-92	9	7
β-strand	97-99	3	7
α-helix	100-107	8
α-helix	115-120	6
α-helix	123-126	4
β-strand	129-133	5	7
β-strand	135-136	2	8
α-helix	138-140	3
β-strand	141-149	9	7
β-strand	156-162	7	7
β-strand	174	1	7
α-helix	177-178	2

Chain D: 7 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	2-4	3
β-strand	6-11	6	10
α-helix	15-21	7
β-strand	23-24	2	11
β-strand	29	1	12
α-helix	32-36	5
β-strand	48	1	12
β-strand	50-54	5	10
α-helix	57-76	20
β-strand	83-92	10	10
β-strand	97-99	3	10
α-helix	100-111	12
β-strand	117	1	13
β-strand	120	1	13
β-strand	129-133	5	10
β-strand	135-136	2	11
α-helix	138-140	3
β-strand	141-150	10	10
β-strand	156-162	7	10
β-strand	174	1	10
α-helix	177-178	2

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Pertussis toxin subunit 1	A, B, C, D	protein	184	Bordetella pertussis	P04977 (AlphaFold model)

Sequence of entity 1 (A, B, C, D), FASTA

>7SKK_1 Pertussis toxin subunit 1 (chains A, B, C, D)
GPGDPPATVYRYDSRPPEDVFQNGFTAWGNNDNVLEHLTGRSSQVGSSNSAFVSTSSSRR
YTEVYLEHRMQEAVEAERAGRGTGHFIGYIYEVRADNNFYGAASSYFEYVDTYGDNAGRI
LAGALATYQSEYLAHRRIPPENIRRVTRVYHNGITGETTTTEYSNARYVSQQTRANPNPY
TSRR

Ligands and cofactors

ID	Name	Formula	Copies
AR6	[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-dihydroxy-oxolan-2-yl]methyl[hydroxy-[…	C15 H23 N5 O14 P2	4
NCA	Nicotinamide	C6 H6 N2 O	4

Water and common crystallization additives (SO4) are not listed.

Primary citation

Crystal structures of pertussis toxin with NAD + and analogs provide structural insights into the mechanism of its cytosolic ADP-ribosylation activity. Sakari, M., Tran, M.T., Rossjohn, J. et al. J Biol Chem (2022) 298:101892-101892. DOI 10.1016/j.jbc.2022.101892 · PubMed

Other PDB entries of the same protein (UniProt P04977 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7SNE 1.0 Å, Pertussis toxin S1 subunit bound to BaAD
7SKI 1.1 Å, Pertussis toxin in complex with PJ34
7U6Z 1.3 Å, Pertussis toxin E129D NAD
7SKY 1.37 Å, Pertussis toxin S1 bound to NAD+
6RO0 2.13 Å, Crystal structure of genetically detoxified pertussis toxin gdpt.
1BCP 2.7 Å, Binary complex of pertussis toxin and ATP
1PRT 2.9 Å, The crystal structure of pertussis toxin
1PTO 3.5 Å, The structure of a pertussis toxin-sugar complex as a model for receptor binding
9MR7 3.56 Å, Genetiocally detoxified pertussis toxin in complex with hu1B7 Fab and hu11E6 Fab

Browse structure collections

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