9E3J: Cryo EM structure of pertussis toxin
Cryo EM structure of pertussis toxin in complex with neutralizing Fab PERT-171. Determined by electron microscopy at 3.6 Å resolution. Released 29 Oct 2025.
- Method
- Electron microscopy
- Resolution
- 3.6 Å
- Organisms
- Bordetella pertussis, Homo sapiens
- Chains
- 8
- Atoms
- 8,113
- Mol. weight
- 153.21 kDa
- Released
- 29 Oct 2025
Explore 9E3J in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
9E3J contains 25 α-helices and 73 β-strands across 8 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: 9 helices, 13 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 6-11 | 6 | 1 |
| α-helix | 15-18 | 4 | |
| β-strand | 23-24 | 2 | 2 |
| α-helix | 32-36 | 5 | |
| α-helix | 39-41 | 3 | |
| β-strand | 50-52 | 3 | 3 |
| β-strand | 54 | 1 | 1 |
| α-helix | 57-77 | 21 | |
| β-strand | 84-92 | 9 | 1 |
| β-strand | 97-99 | 3 | 3 |
| α-helix | 100-110 | 11 | |
| α-helix | 113-115 | 3 | |
| α-helix | 118-127 | 10 | |
| β-strand | 130-133 | 4 | 3 |
| 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 | 191-193 | 3 | 4 |
| β-strand | 198-199 | 2 | 4 |
| α-helix | 200-206 | 7 | |
| β-strand | 226-227 | 2 | 4 |
Chain B: 7 helices, 13 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 19-21 | 3 | |
| α-helix | 23-24 | 2 | |
| β-strand | 27-29 | 3 | 5 |
| α-helix | 32-37 | 6 | |
| α-helix | 39-48 | 10 | |
| β-strand | 55-56 | 2 | 6 |
| β-strand | 60 | 1 | 7 |
| β-strand | 61-62 | 2 | 6 |
| β-strand | 73 | 1 | 7 |
| α-helix | 78-81 | 4 | |
| β-strand | 85 | 1 | 6 |
| β-strand | 87-89 | 3 | 5 |
| β-strand | 92-93 | 2 | 8 |
| β-strand | 101-114 | 14 | 9 |
| β-strand | 119-125 | 7 | 9 |
| β-strand | 128-135 | 8 | 9 |
| α-helix | 143-145 | 3 | |
| α-helix | 146-158 | 13 | |
| β-strand | 163-173 | 11 | 9 |
| β-strand | 183-191 | 9 | 9 |
Chain C: 2 helices, 6 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 93 | 1 | 10 |
| β-strand | 100-114 | 15 | 9 |
| β-strand | 119-125 | 7 | 9 |
| β-strand | 128-135 | 8 | 9 |
| α-helix | 143-145 | 3 | |
| α-helix | 146-158 | 13 | |
| β-strand | 163-172 | 10 | 9 |
| β-strand | 183-191 | 9 | 9 |
Chain D: 2 helices, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 6-20 | 15 | 9 |
| β-strand | 27-36 | 10 | 9 |
| α-helix | 44-46 | 3 | |
| β-strand | 48-55 | 8 | 9 |
| α-helix | 63-74 | 12 | |
| β-strand | 78-89 | 12 | 9 |
| β-strand | 92-102 | 11 | 9 |
Chain E: 1 helix, 6 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 11-13 | 3 | 9 |
| β-strand | 16-20 | 5 | 9 |
| β-strand | 27-36 | 10 | 9 |
| β-strand | 48-55 | 8 | 9 |
| α-helix | 63-74 | 12 | |
| β-strand | 78-81 | 4 | 9 |
| β-strand | 99-102 | 4 | 9 |
Chain F: 3 helices, 8 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 7-20 | 14 | 9 |
| β-strand | 23-31 | 9 | 9 |
| β-strand | 37-43 | 7 | 9 |
| α-helix | 52-66 | 15 | |
| β-strand | 69-72 | 4 | 9 |
| β-strand | 73-74 | 2 | 11 |
| α-helix | 83 | 1 | |
| β-strand | 84-85 | 2 | 9 |
| β-strand | 86-88 | 3 | 11 |
| β-strand | 89-91 | 3 | 9 |
| α-helix | 92-93 | 2 | |
Chain H: 0 helices, 12 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 5-7 | 3 | 12 |
| β-strand | 12 | 1 | 13 |
| β-strand | 18-23 | 6 | 12 |
| β-strand | 34-39 | 6 | 14 |
| β-strand | 46-51 | 6 | 14 |
| β-strand | 60 | 1 | 14 |
| β-strand | 68-73 | 6 | 12 |
| β-strand | 78-83 | 6 | 12 |
| β-strand | 92-99 | 8 | 14 |
| β-strand | 109-112 | 4 | 14 |
| β-strand | 116-118 | 3 | 14 |
| β-strand | 120 | 1 | 13 |
Chain L: 1 helix, 10 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 4-7 | 4 | 15 |
| β-strand | 10-12 | 3 | 16 |
| β-strand | 19-25 | 7 | 15 |
| β-strand | 33-38 | 6 | 14 |
| β-strand | 45-49 | 5 | 14 |
| β-strand | 53-54 | 2 | 14 |
| β-strand | 62-65 | 4 | 15 |
| β-strand | 70-75 | 6 | 15 |
| α-helix | 80-82 | 3 | |
| β-strand | 85-90 | 6 | 14 |
| β-strand | 103-105 | 3 | 16 |
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-171 hc | H | protein | 122 | Homo sapiens | |
| Pert-171 lc | L | protein | 107 | Homo sapiens | |
Sequence of entity 1 (A), FASTA
>9E3J_1 Pertussis toxin subunit 1 (chains A)
MRCTRAIRQTARTGWLTWLAILAVTAPVTSPAWADDPPATVYRYDSRPPEDVFQNGFTAW
GNNDNVLEHLTGRSCQVGSSNSAFVSTSSSRRYTEVYLEHRMQEAVEAERAGRGTGHFIG
YIYEVRADNNFYGAASSYFEYVDTYGDNAGRILAGALATYQSEYLAHRRIPPENIRRVTR
VYHNGITGETTTTEYSNARYVSQQTRANPNPYTSRRSVASIVGTLVRMAPVVGACMARQA
ESSEAMAAWSERAGEAMVLVYYESIAYSF
Sequence of entity 2 (B), FASTA
>9E3J_2 Islet-activating protein S2 (chains B)
MPIDRKTLCHLLSVLPLALLGSHVARASTPGIVIPPQEQITQHGSPYGRCANKTRALTVA
ELRGSGDLQEYLRHVTRGWSIFALYDGTYLGGEYGGVIKDGTPGGAFDLKTTFCIMTTRN
TGQPATDHYYSNVTATRLLSSTNSRLCAVFVRSGQPVIGACTSPYDGKYWSMYSRLRKML
YLIYVAGISVRVHVSKEEQYYDYEDATFETYALTGISICNPGSSLC
Sequence of entity 3 (C), FASTA
>9E3J_3 Pertussis toxin subunit 3 (chains C)
MLINNKKLLHHILPILVLALLGMRTAQAVAPGIVIPPKALFTQQGGAYGRCPNGTRALTV
AELRGNAELQTYLRQITPGWSIYGLYDGTYLGQAYGGIIKDAPPGAGFIYRETFCITTIY
KTGQPAADHYYSKVTATRLLASTNSRLCAVFVRDGQSVIGACASPYEGRYRDMYDALRRL
LYMIYMSGLAVRVHVSKEEQYYDYEDATFQTYALTGISLCNPAASIC
Sequence of entity 4 (D, E), FASTA
>9E3J_4 Pertussis toxin subunit 4 (chains D, E)
MLRRFPTRTTAPGQGGARRSRVRALAWLLASGAMTHLSPALADVPYVLVKTNMVVTSVAM
KPYEVTPTRMLVCGIAAKLGAAASSPDAHVPFCFGKDLKRPGSSPMEVMLRAVFMQQRPL
RMFLGPKQLTFEGKPALELIRMVECSGKQDCP
Sequence of entity 5 (F), FASTA
>9E3J_5 Pertussis toxin subunit 5 (chains F)
MQRQAGLPLKANPMHTIASILLSVLGIYSPADVAGLPTHLYKNFTVQELALKLKGKNQEF
CLTAFMSGRSLVRACLSDAGHEHDTWFDTMLGFAISAYALKSRIALTVEDSPYPGTPGDL
LELQICPLNGYCE
Sequence of entity 6 (H), FASTA
>9E3J_6 PERT-171 HC (chains H)
CQVLVESGGGVVRPGRSLRLSCAASGFTFTSYTMHWVRQAPGKGLEWVAIIWYDGTNEDY
ADSVKGRFTISRDNSKNTLYLDMNSLRAEDTAMYYCARDWDNYGYSYYFDYWGQGTLVTV
SS
Sequence of entity 7 (L), FASTA
>9E3J_7 PERT-171 LC (chains L)
DIQMTQSPSTLSASIGDRVTITCRASQSIYSWLAWYQHKPGNAPKLLIYKASSLESGVPS
RFSGSGSGTEFTLTISSLQPDDFASYYCQQYNSYPWTFGQGTKVEIK
Primary citation
Cryo EM structure of pertussis toxin in complex with neutralizing Fab PERT-171. 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
- 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…
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