9E3L: Cryo EM structure of pertussis toxin
Cryo EM structure of pertussis toxin in complex with neutralizing Fab PERT-169 and PERT-203. Determined by electron microscopy at 3.4 Å resolution. Released 29 Oct 2025.
- Method
- Electron microscopy
- Resolution
- 3.4 Å
- Organisms
- Bordetella pertussis, Homo sapiens
- Chains
- 12
- Atoms
- 11,931
- Mol. weight
- 271.08 kDa
- Released
- 29 Oct 2025
Explore 9E3L in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
9E3L contains 31 α-helices and 113 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: 9 helices, 14 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 6-11 | 6 | 1 |
| α-helix | 15-18 | 4 | |
| β-strand | 24 | 1 | 2 |
| β-strand | 29 | 1 | 3 |
| α-helix | 32-37 | 6 | |
| β-strand | 48 | 1 | 3 |
| β-strand | 50-54 | 5 | 1 |
| α-helix | 58-76 | 19 | |
| β-strand | 83-92 | 10 | 1 |
| β-strand | 97-99 | 3 | 1 |
| α-helix | 100-110 | 11 | |
| α-helix | 118-127 | 10 | |
| β-strand | 129-133 | 5 | 1 |
| β-strand | 135 | 1 | 2 |
| β-strand | 141-150 | 10 | 1 |
| β-strand | 155-162 | 8 | 1 |
| α-helix | 177-178 | 2 | |
| α-helix | 181-183 | 3 | |
| β-strand | 191-193 | 3 | 4 |
| β-strand | 198-199 | 2 | 4 |
| α-helix | 200-205 | 6 | |
| β-strand | 226-227 | 2 | 4 |
| α-helix | 228-232 | 5 | |
Chain B: 1 helix, 6 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 92 | 1 | 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 | 182-191 | 10 | 5 |
Chain C: 5 helices, 14 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 10-12 | 3 | |
| β-strand | 19 | 1 | 6 |
| β-strand | 22 | 1 | 6 |
| β-strand | 27-29 | 3 | 7 |
| α-helix | 32-36 | 5 | |
| α-helix | 40-48 | 9 | |
| β-strand | 54-56 | 3 | 8 |
| β-strand | 61-63 | 3 | 8 |
| β-strand | 70-72 | 3 | 8 |
| β-strand | 84 | 1 | 6 |
| β-strand | 87-89 | 3 | 7 |
| β-strand | 92-93 | 2 | 9 |
| β-strand | 100-114 | 15 | 9 |
| β-strand | 119-125 | 7 | 9 |
| β-strand | 128-135 | 8 | 9 |
| α-helix | 146-158 | 13 | |
| β-strand | 163-172 | 10 | 9 |
| β-strand | 184-191 | 8 | 9 |
| α-helix | 194-196 | 3 | |
Chain D: 1 helix, 8 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 6-11 | 6 | 5 |
| β-strand | 13-20 | 8 | 9 |
| β-strand | 27-34 | 8 | 9 |
| β-strand | 48-55 | 8 | 9 |
| α-helix | 63-74 | 12 | |
| β-strand | 78-82 | 5 | 5 |
| β-strand | 86-89 | 4 | 9 |
| β-strand | 92-96 | 5 | 9 |
| β-strand | 99-102 | 4 | 5 |
Chain E: 2 helices, 7 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 | 78-82 | 5 | 9 |
| β-strand | 87-89 | 3 | 10 |
| β-strand | 92-94 | 3 | 10 |
| β-strand | 95-102 | 8 | 9 |
Chain F: 3 helices, 6 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 5-7 | 3 | 9 |
| β-strand | 11-18 | 8 | 5 |
| β-strand | 25-31 | 7 | 5 |
| α-helix | 36-37 | 2 | |
| β-strand | 38-42 | 5 | 5 |
| α-helix | 52-65 | 14 | |
| β-strand | 71-75 | 5 | 9 |
| α-helix | 76-77 | 2 | |
| β-strand | 85-91 | 7 | 9 |
Chain G: 0 helices, 7 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 18-20 | 3 | 11 |
| β-strand | 38 | 1 | 12 |
| β-strand | 68 | 1 | 11 |
| β-strand | 73 | 1 | 13 |
| β-strand | 78 | 1 | 13 |
| β-strand | 81-83 | 3 | 11 |
| β-strand | 95 | 1 | 12 |
Chain H: 1 helix, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 38 | 1 | 14 |
| α-helix | 60 | 1 | |
| β-strand | 70-72 | 3 | 15 |
| β-strand | 75-77 | 3 | 15 |
| β-strand | 95 | 1 | 14 |
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 | 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-203 hc | G | protein | 233 | Homo sapiens | |
| Pert-203 lc | H | protein | 219 | Homo sapiens | |
| Pert-169 hc | I, K | protein | 230 | Homo sapiens | |
| Pert-169 lc | J, L | protein | 216 | Homo sapiens | |
Sequence of entity 1 (A), FASTA
>9E3L_1 Pertussis toxin subunit 1 (chains A)
MRCTRAIRQTARTGWLTWLAILAVTAPVTSPAWADDPPATVYRYDSRPPEDVFQNGFTAW
GNNDNVLEHLTGRSCQVGSSNSAFVSTSSSRRYTEVYLEHRMQEAVEAERAGRGTGHFIG
YIYEVRADNNFYGAASSYFEYVDTYGDNAGRILAGALATYQSEYLAHRRIPPENIRRVTR
VYHNGITGETTTTEYSNARYVSQQTRANPNPYTSRRSVASIVGTLVRMAPVVGACMARQA
ESSEAMAAWSERAGEAMVLVYYESIAYSF
Sequence of entity 2 (B), FASTA
>9E3L_2 Islet-activating protein S2 (chains B)
MPIDRKTLCHLLSVLPLALLGSHVARASTPGIVIPPQEQITQHGSPYGRCANKTRALTVA
ELRGSGDLQEYLRHVTRGWSIFALYDGTYLGGEYGGVIKDGTPGGAFDLKTTFCIMTTRN
TGQPATDHYYSNVTATRLLSSTNSRLCAVFVRSGQPVIGACTSPYDGKYWSMYSRLRKML
YLIYVAGISVRVHVSKEEQYYDYEDATFETYALTGISICNPGSSLC
Sequence of entity 3 (C), FASTA
>9E3L_3 Pertussis toxin subunit 3 (chains C)
MLINNKKLLHHILPILVLALLGMRTAQAVAPGIVIPPKALFTQQGGAYGRCPNGTRALTV
AELRGNAELQTYLRQITPGWSIYGLYDGTYLGQAYGGIIKDAPPGAGFIYRETFCITTIY
KTGQPAADHYYSKVTATRLLASTNSRLCAVFVRDGQSVIGACASPYEGRYRDMYDALRRL
LYMIYMSGLAVRVHVSKEEQYYDYEDATFQTYALTGISLCNPAASIC
Sequence of entity 4 (D, E), FASTA
>9E3L_4 Pertussis toxin subunit 4 (chains D, E)
MLRRFPTRTTAPGQGGARRSRVRALAWLLASGAMTHLSPALADVPYVLVKTNMVVTSVAM
KPYEVTPTRMLVCGIAAKLGAAASSPDAHVPFCFGKDLKRPGSSPMEVMLRAVFMQQRPL
RMFLGPKQLTFEGKPALELIRMVECSGKQDCP
Sequence of entity 5 (F), FASTA
>9E3L_5 Pertussis toxin subunit 5 (chains F)
MQRQAGLPLKANPMHTIASILLSVLGIYSPADVAGLPTHLYKNFTVQELALKLKGKNQEF
CLTAFMSGRSLVRACLSDAGHEHDTWFDTMLGFAISAYALKSRIALTVEDSPYPGTPGDL
LELQICPLNGYCE
Sequence of entity 6 (G), FASTA
>9E3L_6 PERT-203 HC (chains G)
QVQLQESGPGLVKPSGTLSLTCAVSGGSISSNDWWSWVRQSPGKGLEWIGESYHSGGTNY
NPSLTSRVTISVDQSKNHFSLRLSSVTAADTAVYFCARRTIGNYDISTGYYTPAVFFDSW
GQGILVIVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGV
HTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSC
Sequence of entity 7 (H), FASTA
>9E3L_7 PERT-203 LC (chains H)
DIVMTQSPLSLPVTPGEPASISCRSSQSLLHSNTYNYLDWYLQKPGQSPQLLIYLGSHRA
SGVPDRFSGSGSGTDFTLKISRVEAEDVGVYYCMQSLQTPWTFGQGTKVEIKRTVAAPSV
FIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSL
SSTLTLSKADYEKHKVYACEVTHQGLRSPVTKSFNRGEC
Sequence of entity 8 (I, K), FASTA
>9E3L_8 PERT-169 HC (chains I, K)
QVQLVQAGGEVKKPGTSVNVSCKASVYTFTNYYLHWVRQAPGQGLEWMGVMNPSGGKTIY
AQKFQGRVTTTRDTSTSTVYMELRSLRSEDTAVYYCARGLYYGDSSGYFGAGEFDHWGQG
TLVIVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTF
PAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSC
Sequence of entity 9 (J, L), FASTA
>9E3L_9 PERT-169 LC (chains J, L)
QAVVTQEPSLTVSPGGTVTLTCGSSTGAVTSGHYPFWLQQKPGQAPRTLIYDTSNKHSWT
PARFSASLLGGKAALTLSGAQPEDEAEYYCLLSYSGARRVFGGGTKLTVLGQPKAAPSVT
LFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASS
YLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPTECS
Primary citation
Cryo EM structure of pertussis toxin in complex with neutralizing Fab PERT-169 and PERT-203. 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
- 9E3J 3.6 Å, Cryo EM structure of pertussis toxin in complex with neutralizing Fab PERT-171
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