9MR7: Genetiocally detoxified pertussis toxin

Name: PDB 9MR7: Genetiocally detoxified pertussis toxin in complex with hu1B7 Fab and hu11E6 Fab
Published: 2025-04-16
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: toxin

Genetiocally detoxified pertussis toxin in complex with hu1B7 Fab and hu11E6 Fab. Determined by electron microscopy at 3.56 Å resolution. Released 16 Apr 2025.

Method: Electron microscopy
Resolution: 3.56 Å
Organisms: Bordetella pertussis, Mus musculus
Chains: 12
Atoms: 12,463
Mol. weight: 248.37 kDa
Released: 16 Apr 2025

Explore 9MR7 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9MR7 contains 44 α-helices and 132 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: 12 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	6-11	6	1
α-helix	15-21	7
β-strand	23-24	2	2
α-helix	32-37	6
α-helix	39-41	3
β-strand	52-54	3	1
α-helix	57-77	21
β-strand	84-92	9	1
β-strand	98-99	2	1
α-helix	101-111	11
α-helix	113-115	3
α-helix	118-127	10
β-strand	129-131	3	1
β-strand	135-136	2	2
α-helix	138-140	3
β-strand	141-149	9	1
β-strand	156-162	7	1
α-helix	177-178	2
α-helix	181-183	3
β-strand	191-193	3	3
β-strand	198-199	2	3
α-helix	200-204	5
β-strand	226-227	2	3
α-helix	228-230	3

Chain B: 7 helices, 18 β-strands

Element	Residues	Length	Sheet
α-helix	10-12	3
β-strand	13	1	4
β-strand	18	1	5
β-strand	27-29	3	4
α-helix	30-31	2
α-helix	32-36	5
α-helix	39-45	7
β-strand	54-57	4	5
β-strand	60-63	4	5
α-helix	65-67	3
β-strand	70-73	4	5
β-strand	85	1	5
β-strand	87-89	3	4
β-strand	91-93	3	6
β-strand	101-102	2	7
β-strand	106	1	8
β-strand	107-114	8	7
β-strand	119-125	7	7
β-strand	128-135	8	7
α-helix	143-145	3
α-helix	146-159	14
β-strand	163	1	8
β-strand	164-168	5	7
β-strand	171-173	3	6
β-strand	183-191	9	7

Chain C: 8 helices, 18 β-strands

Element	Residues	Length	Sheet
α-helix	6-9	4
α-helix	10-12	3
β-strand	13	1	9
α-helix	17-18	2
β-strand	19	1	10
β-strand	22	1	10
α-helix	23-24	2
β-strand	27-29	3	9
α-helix	32-35	4
α-helix	39-45	7
β-strand	54-56	3	11
β-strand	60-63	4	11
β-strand	71-73	3	11
β-strand	84	1	10
β-strand	85	1	11
β-strand	87-89	3	9
β-strand	91-93	3	7
β-strand	101-106	6	7
β-strand	108	1	7
β-strand	112-114	3	7
β-strand	119-125	7	7
β-strand	128-135	8	7
α-helix	143-145	3
α-helix	146-158	13
β-strand	163-173	11	7
β-strand	183-191	9	7

Chain D: 1 helix, 5 β-strands

Element	Residues	Length	Sheet
β-strand	6-20	15	7
β-strand	27-36	10	7
β-strand	48-55	8	7
α-helix	63-74	12
β-strand	78-89	12	7
β-strand	92-102	11	7

Chain E: 2 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	6-13	8	7
β-strand	16-20	5	7
β-strand	27-36	10	7
α-helix	44-46	3
β-strand	48-55	8	7
α-helix	63-74	12
β-strand	78-89	12	7
β-strand	92-102	11	7

Chain F: 3 helices, 5 β-strands

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

Chain G: 2 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	12
β-strand	10-13	4	13
β-strand	19-25	7	12
β-strand	35-38	4	13
β-strand	45-48	4	13
β-strand	62-67	6	12
β-strand	70-75	6	12
α-helix	80-82	3
β-strand	85-87	3	13
β-strand	89-90	2	14
α-helix	96	1
β-strand	97-98	2	14
β-strand	102-106	5	13

Chain H: 2 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	15
β-strand	10-11	2	16
β-strand	18-25	8	15
α-helix	29-31	3
β-strand	34-39	6	16
β-strand	45-51	7	16
β-strand	57-59	3	16
β-strand	67-72	6	15
β-strand	77-82	6	15
α-helix	84-86	3
β-strand	88-94	7	16
β-strand	108-110	3	16

4 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Pertussis toxin subunit 1	A	protein	235	Bordetella pertussis	P04977 (AlphaFold model)
Pertussis toxin subunit 2	B	protein	199	Bordetella pertussis	P04978 (AlphaFold model)
Pertussis toxin subunit 3	C	protein	199	Bordetella pertussis	P04979 (AlphaFold model)
Pertussis toxin subunit 4	D, E	protein	110	Bordetella pertussis	P0A3R5 (AlphaFold model)
Pertussis toxin subunit 5	F	protein	99	Bordetella pertussis	P04981
hu1B7 Fab light chain	G	protein	213	Mus musculus
hu1B7 Fab heavy chain	H	protein	223	Mus musculus
hu11E6 Fab light chain	I, K	protein	214	Mus musculus
hu11E6 Fab heavy chain	J, L	protein	228	Mus musculus

Sequence of entity 1 (A), FASTA

>9MR7_1 Pertussis toxin subunit 1 (chains A)
DDPPATVYKYDSRPPEDVFQNGFTAWGNNDNVLDHLTGRSCQVGSSNSAFVSTSSSRRYT
EVYLEHRMQEAVEAERAGRGTGHFIGYIYEVRADNNFYGAASSYFEYVDTYGDNAGRILA
GALATYQSGYLAHRRIPPENIRRVTRVYHNGITGETTTTEYSNARYVSQQTRANPNPYTS
RRSVASIVGTLVRMAPVIGACMARQAESSEAMAAWSERAGEAMVLVYYESIAYSF

Sequence of entity 2 (B), FASTA

>9MR7_2 Pertussis toxin subunit 2 (chains B)
STPGIVIPPQEQITQHGGPYGRCANKTRALTVAELRGSGDLQEYLRHVTRGWSIFALYDG
TYLGGEYGGVIKDGTPGGAFDLKTTFCIMTTRNTGQPATDHYYSNVTATRLLSSTNSRLC
AVFVRSGQPVIGACTSPYDGKYWSMYSRLRKMLYLIYVAGISVRVHVSKEEQYYDYEDAT
FETYALTGISICNPGSSLC

Sequence of entity 3 (C), FASTA

>9MR7_3 Pertussis toxin subunit 3 (chains C)
VAPGIVIPPKALFTQQGGAYGRCPNGTRALTVAELRGNAELQTYLRQITPGWSIYGLYDG
TYLGQAYGGIIKDAPPGAGFIYRETFCITTIYKTGQPAADHYYSKVTATRLLASTNSRLC
AVFVRDGQSVIGACASPYEGRYRDMYDALRRLLYMIYMSGLAVRVHVSKEEQYYDYEDAT
FQTYALTGISLCNPAASIC

Sequence of entity 4 (D, E), FASTA

>9MR7_4 Pertussis toxin subunit 4 (chains D, E)
DVPYVLVKTNMVVTSVAMKPYEVTPTRMLVCGIAAKLGAAASSPDAHVPFCFGKDLKRPG
SSPMEVMLRAVFMQQRPLRMFLGPKQLTFEGKPALELIRMVECSGKQDCP

Sequence of entity 5 (F), FASTA

>9MR7_5 Pertussis toxin subunit 5 (chains F)
GLPTHLYKNFTVQELALKLKGKNQEFCLTAFMSGRSLVRACLSDAGHEHDTWFDTMLGFA
ISAYALKSRIALTVEDSPYPGTPGDLLELQICPLNGYCE

Sequence of entity 6 (G), FASTA

>9MR7_6 hu1B7 Fab light chain (chains G)
QIVLTQSPATLSVSPGERVTLTCSASSSVSFMYWYQQKPGRAPKPLIYLTSNLPSGVPAR
FSGSGSGTSYTLTINSLEAEDAATYYCQQWSSHPPTFGSGTKLEIKRTVAAPSVFIFPPS
DEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTL
SKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Sequence of entity 7 (H), FASTA

>9MR7_7 hu1B7 Fab heavy chain (chains H)
QVQLVQSGAEVKKPGASVKVSCKASGYKFTSYWMHWVRQAPGQGLEWIGNIFPGSGSTNY
AQKFQGRVTLTVDTSTSTAYMELSSLRSEDTAVYYCTRWLSGAYFDYWGQGTTVTVSSAS
TKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGL
YSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSCDK

Sequence of entity 8 (I, K), FASTA

>9MR7_8 hu11E6 Fab light chain (chains I, K)
DIVMTQSPSSLSASVGDRVTISCRASQDIDNYLSWFQQKPGGTVKLLIYYTSRLHSGVPS
RFSGSGSGTDYTLTISSLQPEDIATYFCQQGNTFPWTFGGGTKLEIKRTVAAPSVFIFPP
SDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLT
LSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Sequence of entity 9 (J, L), FASTA

>9MR7_9 hu11E6 Fab heavy chain (chains J, L)
EVQVVESGGGLVQPGRSLRLSCTTSGFTFTDYYVSWVRQAPGKALEWLGFIRNKVNGYTT
EFSSSVKGRFTISRDNSKSILYLQMNSLKIEDTAVYYCARVSYYGRGWYFDYWGQGTTLT
VSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVL
QSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDK

Primary citation

Structural basis for neutralizing antibody binding to pertussis toxin. Goldsmith, J.A., Nguyen, A.W., Wilen, R.E. et al. Proc Natl Acad Sci U S A (2025) 122:e2419457122-e2419457122. DOI 10.1073/pnas.2419457122 · 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
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

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