6RO0: Genetically detoxified pertussis toxin gdpt

Name: PDB 6RO0: Crystal structure of genetically detoxified pertussis toxin gdpt.
Published: 2020-06-03
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: toxin

Crystal structure of genetically detoxified pertussis toxin gdpt. Determined by X-ray diffraction at 2.13 Å resolution. Released 3 Jun 2020.

Method: X-ray diffraction
Resolution: 2.13 Å
Organism: Bordetella pertussis
Chains: 12
Atoms: 15,084
Mol. weight: 255.67 kDa
Released: 3 Jun 2020

Explore 6RO0 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6RO0 contains 79 α-helices and 124 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: 11 helices, 17 β-strands

Element	Residues	Length	Sheet
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	41-42	2	4
β-strand	45-46	2	4
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	113-115	3
α-helix	118-126	9
β-strand	129-133	5	1
β-strand	135-136	2	2
α-helix	138-140	3
β-strand	141-150	10	1
β-strand	155-162	8	1
β-strand	174	1	1
α-helix	177-178	2
α-helix	181-183	3
β-strand	191-193	3	5
β-strand	198-199	2	5
α-helix	200-206	7
β-strand	225-227	3	5
α-helix	228-230	3

Chain B: 10 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	6-9	4
α-helix	10-12	3
β-strand	13	1	6
β-strand	18	1	7
α-helix	19-21	3
α-helix	23-24	2
β-strand	27-29	3	6
α-helix	30-31	2
α-helix	32-36	5
α-helix	39-48	10
β-strand	54-57	4	7
β-strand	60-63	4	7
α-helix	65-67	3
β-strand	70-73	4	7
β-strand	85	1	7
β-strand	87-89	3	6
β-strand	91-93	3	8
β-strand	101-114	14	8
β-strand	119-125	7	8
β-strand	128-135	8	8
α-helix	143-145	3
α-helix	146-159	14
β-strand	163-173	11	8
β-strand	183-191	9	8

Chain C: 11 helices, 17 β-strands

Element	Residues	Length	Sheet
α-helix	4-9	6
α-helix	10-12	3
β-strand	13	1	9
β-strand	18-19	2	10
β-strand	22	1	10
α-helix	23-24	2
β-strand	27-29	3	9
α-helix	30-31	2
α-helix	32-36	5
α-helix	39-48	10
α-helix	49-50	2
β-strand	54-56	3	10
β-strand	60-63	4	10
β-strand	70-73	4	10
α-helix	78-81	4
β-strand	84-85	2	10
β-strand	87-89	3	9
β-strand	91-93	3	8
β-strand	100-114	15	8
β-strand	119-125	7	8
β-strand	128-135	8	8
α-helix	143-145	3
α-helix	146-159	14
β-strand	163-173	11	8
β-strand	183-191	9	8
β-strand	193	1	11
α-helix	194-196	3
β-strand	198	1	11

Chains D, E, J and K: 2 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	6-20	15	8
β-strand	27-36	10	8
α-helix	44-46	3
β-strand	48-55	8	8
α-helix	63-74	12
β-strand	78-89	12	8
β-strand	92-102	11	8

Chains F and L: 4 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	4-20	17	8
β-strand	23-31	9	8
β-strand	38-43	6	8
α-helix	52-65	14
β-strand	69-75	7	8
α-helix	76-77	2
α-helix	83	1
β-strand	84-91	8	8
α-helix	92-93	2

Chain G: 11 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	6-11	6	12
α-helix	15-21	7
β-strand	23-24	2	13
β-strand	29	1	14
α-helix	32-37	6
α-helix	39-41	3
β-strand	48	1	14
β-strand	50-54	5	12
α-helix	57-76	20
β-strand	84-92	9	12
β-strand	97-99	3	12
α-helix	100-111	12
α-helix	113-115	3
α-helix	118-126	9
β-strand	129-133	5	12
β-strand	135-136	2	13
β-strand	141-150	10	12
β-strand	155-162	8	12
β-strand	174	1	12
α-helix	177-178	2
α-helix	181-183	3
β-strand	191-193	3	15
β-strand	198-199	2	15
α-helix	200-206	7
β-strand	225-227	3	15
α-helix	228-230	3

Chain H: 10 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	5-9	5
α-helix	10-12	3
β-strand	13	1	16
β-strand	18	1	17
α-helix	19-21	3
α-helix	23-24	2
β-strand	27-29	3	16
α-helix	30-31	2
α-helix	32-36	5
α-helix	39-48	10
β-strand	54-57	4	17
β-strand	60-63	4	17
α-helix	65-67	3
β-strand	70-73	4	17
β-strand	85	1	17
β-strand	87-89	3	16
β-strand	91-93	3	18
β-strand	101-114	14	18
β-strand	117-125	9	18
β-strand	128-135	8	18
α-helix	143-145	3
α-helix	146-159	14
β-strand	163-173	11	18
β-strand	183-191	9	18

Chain I: 10 helices, 17 β-strands

Element	Residues	Length	Sheet
α-helix	5-9	5
α-helix	10-12	3
β-strand	13	1	19
β-strand	18-19	2	20
β-strand	22	1	20
α-helix	23-24	2
β-strand	27-29	3	19
α-helix	30-31	2
α-helix	32-36	5
α-helix	39-48	10
β-strand	54-57	4	20
β-strand	60-63	4	20
β-strand	71-73	3	20
α-helix	78-81	4
β-strand	84-85	2	20
β-strand	87-89	3	19
β-strand	91-93	3	18
β-strand	100-114	15	18
β-strand	119-125	7	18
β-strand	128-135	8	18
α-helix	143-145	3
α-helix	146-159	14
β-strand	163-173	11	18
β-strand	183-191	9	18
β-strand	193	1	21
α-helix	194-196	3
β-strand	198	1	21

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Pertussis toxin subunit 1	A, G	protein	269	Bordetella pertussis	P04977 (AlphaFold model)
Islet-activating protein S2	B, H	protein	226	Bordetella pertussis	P04978 (AlphaFold model)
Islet-activating protein S3	C, I	protein	227	Bordetella pertussis	P04979 (AlphaFold model)
Islet-activating protein S4	D, E, J, K	protein	152	Bordetella pertussis	P0A3R5 (AlphaFold model)
Pertussis toxin subunit 5	F, L	protein	133	Bordetella pertussis	P04981

Sequence of entity 1 (A, G), FASTA

>6RO0_1 Pertussis toxin subunit 1 (chains A, G)
MRCTRAIRQTARTGWLTWLAILAVTAPVTSPAWADDPPATVYKYDSRPPEDVFQNGFTAW
GNNDNVLEHLTGRSCQVGSSNSAFVSTSSSRRYTEVYLEHRMQEAVEAERAGRGTGHFIG
YIYEVRADNNFYGAASSYFEYVDTYGDNAGRILAGALATYQSGYLAHRRIPPENIRRVTR
VYHNGITGETTTTEYSNARYVSQQTRANPNPYTSRRSVASIVGTLVRMAPVVGACMARQA
ESSEAMAAWSERAGEAMVLVYYESIAYSF

Sequence of entity 2 (B, H), FASTA

>6RO0_2 Islet-activating protein S2 (chains B, H)
MPIDRKTLCHLLSVLPLALLGSHVARASTPGIVIPPQEQITQHGSPYGRCANKTRALTVA
ELRGSGDLQEYLRHVTRGWSIFALYDGTYLGGEYGGVIKDGTPGGAFDLKTTFCIMTTRN
TGQPATDHYYSNVTATRLLSSTNSRLCAVFVRSGQPVIGACTSPYDGKYWSMYSRLRKML
YLIYVAGISVRVHVSKEEQYYDYEDATFETYALTGISICNPGSSLC

Sequence of entity 3 (C, I), FASTA

>6RO0_3 Islet-activating protein S3 (chains C, I)
MLINNKKLLHHILPILVLALLGMRTAQAVAPGIVIPPKALFTQQGGAYGRCPNGTRALTV
AELRGNAELQTYLRQITPGWSIYGLYDGTYLGQAYGGIIKDAPPGAGFIYRETFCITTIY
KTGQPAADHYYSKVTATRLLASTNSRLCAVFVRDGQSVIGACASPYEGRYRDMYDALRRL
LYMIYMSGLAVRVHVSKEEQYYDYEDATFQTYALTGISLCNPAASIC

Sequence of entity 4 (D, E, J, K), FASTA

>6RO0_4 Islet-activating protein S4 (chains D, E, J, K)
MLRRFPTRTTAPGQGGARRSRVRALAWLLASGAMTHLSPALADVPYVLVKTNMVVTSVAM
KPYEVTPTRMLVCGIAAKLGAAASSPDAHVPFCFGKDLKRPGSSPMEVMLRAVFMQQRPL
RMFLGPKQLTFEGKPALELIRMVECSGKQDCP

Sequence of entity 5 (F, L), FASTA

>6RO0_5 Pertussis toxin subunit 5 (chains F, L)
MQRQAGLPLKANPMHTIASILLSVLGIYSPADVAGLPTHLYKNFTVQELALKLKGKNQEF
CLTAFMSGRSLVRACLSDAGHEHDTWFDTMLGFAISAYALKSRIALTVEDSPYPGTPGDL
LELQICPLNGYCE

Primary citation

Genetically detoxified pertussis toxin displays near identical structure to its wild-type and exhibits robust immunogenicity. Ausar, S.F., Zhu, S., Duprez, J. et al. Commun Biol (2020) 3:427-427. DOI 10.1038/s42003-020-01153-3 · 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+
7SKK 1.65 Å, pertussis toxin in complex with ADPR and Nicotinamide
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

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