9E3K: Cryo EM structure of pertussis toxin

Cryo EM structure of pertussis toxin in complex with neutralizing Fab PERT-199. Determined by electron microscopy at 3.2 Å resolution. Released 29 Oct 2025.

Method: Electron microscopy
Resolution: 3.2 Å
Organisms: Bordetella pertussis, Homo sapiens
Chains: 10
Atoms: 10,021
Mol. weight: 178.78 kDa
Released: 29 Oct 2025

Explore 9E3K in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9E3K contains 37 α-helices and 95 β-strands across 10 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, 13 β-strands

Element	Residues	Length	Sheet
β-strand	6-11	6	1
α-helix	15-21	7
β-strand	29	1	2
α-helix	32-37	6
β-strand	48	1	2
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	101-111	11
α-helix	113-115	3
α-helix	118-127	10
β-strand	129-133	5	1
α-helix	138-140	3
β-strand	141-150	10	1
β-strand	155-160	6	1
β-strand	174	1	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	225-227	3	3
α-helix	228-232	5

Chain B: 2 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	101-114	14	4
β-strand	119-125	7	4
β-strand	128-135	8	4
α-helix	143-145	3
α-helix	146-159	14
β-strand	163-172	10	4
β-strand	183-191	9	4

Chain C: 10 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	10-12	3
β-strand	13	1	5
β-strand	18-19	2	6
β-strand	22	1	6
α-helix	23-24	2
β-strand	27-29	3	5
α-helix	30-31	2
α-helix	32-37	6
α-helix	39-46	8
β-strand	55-56	2	6
β-strand	61-62	2	6
α-helix	65-67	3
β-strand	71-72	2	6
β-strand	84-85	2	6
β-strand	87-89	3	5
β-strand	91-93	3	4
α-helix	96-98	3
β-strand	101-114	14	4
β-strand	119-125	7	4
β-strand	128-135	8	4
α-helix	143-145	3
α-helix	146-158	13
β-strand	163-173	11	4
β-strand	183-191	9	4
α-helix	194-196	3

Chain D: 2 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	8-20	13	4
β-strand	27-36	10	4
α-helix	44-46	3
β-strand	48-55	8	4
α-helix	63-74	12
β-strand	78-89	12	4
β-strand	92-102	11	4

Chain E: 1 helix, 6 β-strands

Element	Residues	Length	Sheet
β-strand	6-7	2	4
β-strand	11-20	10	4
β-strand	27-36	10	4
β-strand	48-55	8	4
α-helix	63-73	11
β-strand	78-89	12	4
β-strand	92-102	11	4

Chain F: 4 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	4-6	3	4
β-strand	10-17	8	4
β-strand	25	1	7
β-strand	26-31	6	4
α-helix	36-37	2
β-strand	38-40	3	4
β-strand	43	1	7
α-helix	52-66	15
β-strand	69-75	7	4
α-helix	76-77	2
β-strand	84-91	8	4
α-helix	92-93	2

Chain H: 1 helix, 11 β-strands

Element	Residues	Length	Sheet
β-strand	4	1	8
β-strand	7	1	9
β-strand	19-23	5	9
β-strand	24	1	8
β-strand	34-40	7	10
β-strand	44-51	8	10
β-strand	58-60	3	10
β-strand	69-73	5	9
β-strand	78-82	5	9
α-helix	88-90	3
β-strand	92-97	6	10
β-strand	124-126	3	10

Chain J: 2 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	4	1	15
β-strand	7	1	16
β-strand	10-11	2	17
β-strand	18-23	6	16
β-strand	24	1	15
α-helix	29-31	3
β-strand	33-40	8	17
β-strand	44-51	8	17
β-strand	58-60	3	17
β-strand	68-73	6	16
β-strand	78-83	6	16
α-helix	88-90	3
β-strand	92-99	8	17
β-strand	120	1	17
β-strand	124-127	4	17

2 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	269	Bordetella pertussis	T1SR96 (AlphaFold model)
Islet-activating protein S2	B	protein	226	Bordetella pertussis	A0A0E8DFW5 (AlphaFold model)
Pertussis toxin subunit 3	C	protein	227	Bordetella pertussis	P04979 (AlphaFold model)
Pertussis toxin subunit 4	D, E	protein	152	Bordetella pertussis	P0A3R5 (AlphaFold model)
Pertussis toxin subunit 5	F	protein	133	Bordetella pertussis	P04981
Pert-199 hc	H, J	protein	130	Homo sapiens
Pert-199 lc	K, L	protein	108	Homo sapiens

Sequence of entity 1 (A), FASTA

>9E3K_1 Pertussis toxin subunit 1 (chains A)
MRCTRAIRQTARTGWLTWLAILAVTAPVTSPAWADDPPATVYRYDSRPPEDVFQNGFTAW
GNNDNVLEHLTGRSCQVGSSNSAFVSTSSSRRYTEVYLEHRMQEAVEAERAGRGTGHFIG
YIYEVRADNNFYGAASSYFEYVDTYGDNAGRILAGALATYQSEYLAHRRIPPENIRRVTR
VYHNGITGETTTTEYSNARYVSQQTRANPNPYTSRRSVASIVGTLVRMAPVVGACMARQA
ESSEAMAAWSERAGEAMVLVYYESIAYSF

Sequence of entity 2 (B), FASTA

>9E3K_2 Islet-activating protein S2 (chains B)
MPIDRKTLCHLLSVLPLALLGSHVARASTPGIVIPPQEQITQHGSPYGRCANKTRALTVA
ELRGSGDLQEYLRHVTRGWSIFALYDGTYLGGEYGGVIKDGTPGGAFDLKTTFCIMTTRN
TGQPATDHYYSNVTATRLLSSTNSRLCAVFVRSGQPVIGACTSPYDGKYWSMYSRLRKML
YLIYVAGISVRVHVSKEEQYYDYEDATFETYALTGISICNPGSSLC

Sequence of entity 3 (C), FASTA

>9E3K_3 Pertussis toxin subunit 3 (chains C)
MLINNKKLLHHILPILVLALLGMRTAQAVAPGIVIPPKALFTQQGGAYGRCPNGTRALTV
AELRGNAELQTYLRQITPGWSIYGLYDGTYLGQAYGGIIKDAPPGAGFIYRETFCITTIY
KTGQPAADHYYSKVTATRLLASTNSRLCAVFVRDGQSVIGACASPYEGRYRDMYDALRRL
LYMIYMSGLAVRVHVSKEEQYYDYEDATFQTYALTGISLCNPAASIC

Sequence of entity 4 (D, E), FASTA

>9E3K_4 Pertussis toxin subunit 4 (chains D, E)
MLRRFPTRTTAPGQGGARRSRVRALAWLLASGAMTHLSPALADVPYVLVKTNMVVTSVAM
KPYEVTPTRMLVCGIAAKLGAAASSPDAHVPFCFGKDLKRPGSSPMEVMLRAVFMQQRPL
RMFLGPKQLTFEGKPALELIRMVECSGKQDCP

Sequence of entity 5 (F), FASTA

>9E3K_5 Pertussis toxin subunit 5 (chains F)
MQRQAGLPLKANPMHTIASILLSVLGIYSPADVAGLPTHLYKNFTVQELALKLKGKNQEF
CLTAFMSGRSLVRACLSDAGHEHDTWFDTMLGFAISAYALKSRIALTVEDSPYPGTPGDL
LELQICPLNGYCE

Sequence of entity 6 (H, J), FASTA

>9E3K_6 PERT-199 HC (chains H, J)
QAQLVESGGGVVQPGGSLRLSCAASKFTISNDALHWVRQTPGKGLEWVAVISHDGSNKYY
AASVRGRFTVSRDNSQNTLYLQMSSLRAEDTAVYYCAREPYCRSTSCYLYGAAYYGLDVW
GQGTTVTVSS

Sequence of entity 7 (K, L), FASTA

>9E3K_7 PERT-199 LC (chains K, L)
DIVLTQSPGTLSLSPGERATLSCRASRSLSSVYLAWYQQKPGQAPRLLIYGASSRATGIP
DRFSGSGSGTDFTLTISSLKPEDSAVYFCQQYADSPLTFGGGTKVEIK

Primary citation

Cryo EM structure of pertussis toxin in complex with neutralizing Fab PERT-199. Binshtein, E., Crowe, J.E. To be published.

Other PDB entries of the same protein (UniProt T1SR96 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9E3H 2.9 Å, Cryo EM structure of pertussis toxin in complex with neutralizing Fab PERT-61
9E3L 3.4 Å, Cryo EM structure of pertussis toxin in complex with neutralizing Fab PERT-169 and…
9E3J 3.6 Å, Cryo EM structure of pertussis toxin in complex with neutralizing Fab PERT-171

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