9E3H: Cryo EM structure of pertussis toxin

Cryo EM structure of pertussis toxin in complex with neutralizing Fab PERT-61. Determined by electron microscopy at 2.9 Å resolution. Released 29 Oct 2025.

Method: Electron microscopy
Resolution: 2.9 Å
Organisms: Bordetella pertussis, Homo sapiens
Chains: 10
Atoms: 10,311
Mol. weight: 180.76 kDa
Released: 29 Oct 2025

Explore 9E3H in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9E3H contains 37 α-helices and 99 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, 14 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	32-37	6
α-helix	39-41	3
β-strand	48	1	3
β-strand	50-54	5	1
α-helix	57-77	21
β-strand	84-92	9	1
β-strand	97-99	3	1
α-helix	100-111	12
α-helix	118-127	10
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
α-helix	177-179	3
α-helix	181-183	3
β-strand	191-193	3	4
β-strand	198-199	2	4
α-helix	200-206	7
β-strand	225-227	3	4
α-helix	228-232	5

Chain B: 7 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	18	1	7
α-helix	19-21	3
α-helix	23-24	2
β-strand	27-29	3	8
α-helix	30-31	2
α-helix	32-36	5
α-helix	39-48	10
β-strand	54-56	3	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	8
β-strand	91-93	3	5
β-strand	100-114	15	5
β-strand	119-125	7	5
β-strand	128-135	8	5
α-helix	146-158	13
β-strand	163-173	11	5
β-strand	183-190	8	5

Chain C: 4 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	91-92	2	5
α-helix	96-98	3
β-strand	101-114	14	5
β-strand	119-125	7	5
β-strand	128-134	7	5
α-helix	143-145	3
α-helix	146-158	13
β-strand	163-173	11	5
β-strand	183-191	9	5
α-helix	194-196	3

Chain D: 2 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	6-20	15	5
β-strand	27-36	10	5
α-helix	44-46	3
β-strand	48-55	8	5
α-helix	63-74	12
β-strand	78-89	12	5
β-strand	92-102	11	5

Chain E: 3 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	5	1
β-strand	6-20	15	5
β-strand	27-36	10	5
α-helix	44-46	3
β-strand	48-55	8	5
α-helix	63-73	11
β-strand	78-89	12	5
β-strand	92-102	11	5

Chain F: 4 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	4-17	14	5
β-strand	20	1	6
β-strand	23	1	6
β-strand	25-31	7	5
α-helix	36-37	2
β-strand	38-43	6	5
α-helix	52-66	15
β-strand	70-75	6	5
α-helix	76-77	2
β-strand	84-91	8	5
α-helix	92-93	2

Chain H: 2 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	9
β-strand	11-12	2	10
β-strand	18-24	7	9
β-strand	37-43	7	11
β-strand	50-56	7	11
β-strand	61-63	3	11
α-helix	68-70	3
β-strand	71-76	6	9
β-strand	81-86	6	9
β-strand	96-102	7	11
α-helix	103-105	3
β-strand	108	1	5
β-strand	115-118	4	11
β-strand	122-123	2	11
β-strand	125-126	2	10

Chain J: 2 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	12-13	2
β-strand	20-22	3	21
β-strand	37-42	6	22
β-strand	50-56	7	22
β-strand	62-63	2	22
β-strand	71-76	6	21
β-strand	79-86	8	21
β-strand	98-102	5	22
α-helix	103-105	3
β-strand	117-118	2	22

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)
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 (AlphaFold model)
Islet-activating protein S2	B	protein	226	Bordetella pertussis	A0A0E8DFW5
Pert-61 hc	H, J	protein	128	Homo sapiens
Pert-61 lc	K, L	protein	113	Homo sapiens

Sequence of entity 1 (A), FASTA

>9E3H_1 Pertussis toxin subunit 1 (chains A)
MRCTRAIRQTARTGWLTWLAILAVTAPVTSPAWADDPPATVYRYDSRPPEDVFQNGFTAW
GNNDNVLEHLTGRSCQVGSSNSAFVSTSSSRRYTEVYLEHRMQEAVEAERAGRGTGHFIG
YIYEVRADNNFYGAASSYFEYVDTYGDNAGRILAGALATYQSEYLAHRRIPPENIRRVTR
VYHNGITGETTTTEYSNARYVSQQTRANPNPYTSRRSVASIVGTLVRMAPVVGACMARQA
ESSEAMAAWSERAGEAMVLVYYESIAYSF

Sequence of entity 2 (C), FASTA

>9E3H_2 Pertussis toxin subunit 3 (chains C)
MLINNKKLLHHILPILVLALLGMRTAQAVAPGIVIPPKALFTQQGGAYGRCPNGTRALTV
AELRGNAELQTYLRQITPGWSIYGLYDGTYLGQAYGGIIKDAPPGAGFIYRETFCITTIY
KTGQPAADHYYSKVTATRLLASTNSRLCAVFVRDGQSVIGACASPYEGRYRDMYDALRRL
LYMIYMSGLAVRVHVSKEEQYYDYEDATFQTYALTGISLCNPAASIC

Sequence of entity 3 (D, E), FASTA

>9E3H_3 Pertussis toxin subunit 4 (chains D, E)
MLRRFPTRTTAPGQGGARRSRVRALAWLLASGAMTHLSPALADVPYVLVKTNMVVTSVAM
KPYEVTPTRMLVCGIAAKLGAAASSPDAHVPFCFGKDLKRPGSSPMEVMLRAVFMQQRPL
RMFLGPKQLTFEGKPALELIRMVECSGKQDCP

Sequence of entity 4 (F), FASTA

>9E3H_4 Pertussis toxin subunit 5 (chains F)
MQRQAGLPLKANPMHTIASILLSVLGIYSPADVAGLPTHLYKNFTVQELALKLKGKNQEF
CLTAFMSGRSLVRACLSDAGHEHDTWFDTMLGFAISAYALKSRIALTVEDSPYPGTPGDL
LELQICPLNGYCE

Sequence of entity 5 (B), FASTA

>9E3H_5 Islet-activating protein S2 (chains B)
MPIDRKTLCHLLSVLPLALLGSHVARASTPGIVIPPQEQITQHGSPYGRCANKTRALTVA
ELRGSGDLQEYLRHVTRGWSIFALYDGTYLGGEYGGVIKDGTPGGAFDLKTTFCIMTTRN
TGQPATDHYYSNVTATRLLSSTNSRLCAVFVRSGQPVIGACTSPYDGKYWSMYSRLRKML
YLIYVAGISVRVHVSKEEQYYDYEDATFETYALTGISICNPGSSLC

Sequence of entity 6 (H, J), FASTA

>9E3H_6 PERT-61 HC (chains H, J)
QITLKESGPTLVKPTQTLTLTCTFSGFSLSPDIGGVGVGWIRQPPGKALEWLALIYWDDD
KRYSPSLQSRLTITKDTSKNRVVLTMINMDPVDTATYYCAHRRPPAYDSSDGDAFDIWGQ
GTMVTVSS

Sequence of entity 7 (K, L), FASTA

>9E3H_7 PERT-61 LC (chains K, L)
DIVMTQSPDSLAVSLGERATINCKSSQSVFSSSNKKNNLAWYQQKPGQPPKLLIYWASTR
ESGVPVRFSGSGSGTDFTLTISSLQAEDVTVYYCQQYYTTPYTFGQGTKLEIK

Primary citation

Cryo EM structure of pertussis toxin in complex with neutralizing Fab PERT-61. 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:

9E3K 3.2 Å, Cryo EM structure of pertussis toxin in complex with neutralizing Fab PERT-199
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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