6RO0: Genetically detoxified pertussis toxin gdpt
Crystal structure of genetically detoxified pertussis toxin gdpt. Determined by X-ray diffraction at 2.13 Å resolution. Released 3 Jun 2020.
- Method
- X-ray diffraction
- Resolution
- 2.13 Å
- Organism
- Bordetella pertussis
- Chains
- 12
- Atoms
- 15,084
- Mol. weight
- 255.67 kDa
- Released
- 3 Jun 2020
Explore 6RO0 in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
6RO0 contains 79 α-helices and 124 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: 11 helices, 17 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 | 32-36 | 5 | |
| β-strand | 41-42 | 2 | 4 |
| β-strand | 45-46 | 2 | 4 |
| β-strand | 48 | 1 | 3 |
| 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 | 100-111 | 12 | |
| α-helix | 113-115 | 3 | |
| α-helix | 118-126 | 9 | |
| β-strand | 129-133 | 5 | 1 |
| 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 | 174 | 1 | 1 |
| α-helix | 177-178 | 2 | |
| α-helix | 181-183 | 3 | |
| β-strand | 191-193 | 3 | 5 |
| β-strand | 198-199 | 2 | 5 |
| α-helix | 200-206 | 7 | |
| β-strand | 225-227 | 3 | 5 |
| α-helix | 228-230 | 3 | |
Chain B: 10 helices, 14 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 6-9 | 4 | |
| α-helix | 10-12 | 3 | |
| β-strand | 13 | 1 | 6 |
| β-strand | 18 | 1 | 7 |
| α-helix | 19-21 | 3 | |
| α-helix | 23-24 | 2 | |
| β-strand | 27-29 | 3 | 6 |
| α-helix | 30-31 | 2 | |
| α-helix | 32-36 | 5 | |
| α-helix | 39-48 | 10 | |
| β-strand | 54-57 | 4 | 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 | 6 |
| β-strand | 91-93 | 3 | 8 |
| β-strand | 101-114 | 14 | 8 |
| β-strand | 119-125 | 7 | 8 |
| β-strand | 128-135 | 8 | 8 |
| α-helix | 143-145 | 3 | |
| α-helix | 146-159 | 14 | |
| β-strand | 163-173 | 11 | 8 |
| β-strand | 183-191 | 9 | 8 |
Chain C: 11 helices, 17 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 4-9 | 6 | |
| α-helix | 10-12 | 3 | |
| β-strand | 13 | 1 | 9 |
| β-strand | 18-19 | 2 | 10 |
| β-strand | 22 | 1 | 10 |
| α-helix | 23-24 | 2 | |
| β-strand | 27-29 | 3 | 9 |
| α-helix | 30-31 | 2 | |
| α-helix | 32-36 | 5 | |
| α-helix | 39-48 | 10 | |
| α-helix | 49-50 | 2 | |
| β-strand | 54-56 | 3 | 10 |
| β-strand | 60-63 | 4 | 10 |
| β-strand | 70-73 | 4 | 10 |
| α-helix | 78-81 | 4 | |
| β-strand | 84-85 | 2 | 10 |
| β-strand | 87-89 | 3 | 9 |
| β-strand | 91-93 | 3 | 8 |
| β-strand | 100-114 | 15 | 8 |
| β-strand | 119-125 | 7 | 8 |
| β-strand | 128-135 | 8 | 8 |
| α-helix | 143-145 | 3 | |
| α-helix | 146-159 | 14 | |
| β-strand | 163-173 | 11 | 8 |
| β-strand | 183-191 | 9 | 8 |
| β-strand | 193 | 1 | 11 |
| α-helix | 194-196 | 3 | |
| β-strand | 198 | 1 | 11 |
Chains D, E, J and K: 2 helices, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 6-20 | 15 | 8 |
| β-strand | 27-36 | 10 | 8 |
| α-helix | 44-46 | 3 | |
| β-strand | 48-55 | 8 | 8 |
| α-helix | 63-74 | 12 | |
| β-strand | 78-89 | 12 | 8 |
| β-strand | 92-102 | 11 | 8 |
Chains F and L: 4 helices, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 4-20 | 17 | 8 |
| β-strand | 23-31 | 9 | 8 |
| β-strand | 38-43 | 6 | 8 |
| α-helix | 52-65 | 14 | |
| β-strand | 69-75 | 7 | 8 |
| α-helix | 76-77 | 2 | |
| α-helix | 83 | 1 | |
| β-strand | 84-91 | 8 | 8 |
| α-helix | 92-93 | 2 | |
Chain G: 11 helices, 15 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 6-11 | 6 | 12 |
| α-helix | 15-21 | 7 | |
| β-strand | 23-24 | 2 | 13 |
| β-strand | 29 | 1 | 14 |
| α-helix | 32-37 | 6 | |
| α-helix | 39-41 | 3 | |
| β-strand | 48 | 1 | 14 |
| β-strand | 50-54 | 5 | 12 |
| α-helix | 57-76 | 20 | |
| β-strand | 84-92 | 9 | 12 |
| β-strand | 97-99 | 3 | 12 |
| α-helix | 100-111 | 12 | |
| α-helix | 113-115 | 3 | |
| α-helix | 118-126 | 9 | |
| β-strand | 129-133 | 5 | 12 |
| β-strand | 135-136 | 2 | 13 |
| β-strand | 141-150 | 10 | 12 |
| β-strand | 155-162 | 8 | 12 |
| β-strand | 174 | 1 | 12 |
| α-helix | 177-178 | 2 | |
| α-helix | 181-183 | 3 | |
| β-strand | 191-193 | 3 | 15 |
| β-strand | 198-199 | 2 | 15 |
| α-helix | 200-206 | 7 | |
| β-strand | 225-227 | 3 | 15 |
| α-helix | 228-230 | 3 | |
Chain H: 10 helices, 14 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 5-9 | 5 | |
| α-helix | 10-12 | 3 | |
| β-strand | 13 | 1 | 16 |
| β-strand | 18 | 1 | 17 |
| α-helix | 19-21 | 3 | |
| α-helix | 23-24 | 2 | |
| β-strand | 27-29 | 3 | 16 |
| α-helix | 30-31 | 2 | |
| α-helix | 32-36 | 5 | |
| α-helix | 39-48 | 10 | |
| β-strand | 54-57 | 4 | 17 |
| β-strand | 60-63 | 4 | 17 |
| α-helix | 65-67 | 3 | |
| β-strand | 70-73 | 4 | 17 |
| β-strand | 85 | 1 | 17 |
| β-strand | 87-89 | 3 | 16 |
| β-strand | 91-93 | 3 | 18 |
| β-strand | 101-114 | 14 | 18 |
| β-strand | 117-125 | 9 | 18 |
| β-strand | 128-135 | 8 | 18 |
| α-helix | 143-145 | 3 | |
| α-helix | 146-159 | 14 | |
| β-strand | 163-173 | 11 | 18 |
| β-strand | 183-191 | 9 | 18 |
Chain I: 10 helices, 17 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 5-9 | 5 | |
| α-helix | 10-12 | 3 | |
| β-strand | 13 | 1 | 19 |
| β-strand | 18-19 | 2 | 20 |
| β-strand | 22 | 1 | 20 |
| α-helix | 23-24 | 2 | |
| β-strand | 27-29 | 3 | 19 |
| α-helix | 30-31 | 2 | |
| α-helix | 32-36 | 5 | |
| α-helix | 39-48 | 10 | |
| β-strand | 54-57 | 4 | 20 |
| β-strand | 60-63 | 4 | 20 |
| β-strand | 71-73 | 3 | 20 |
| α-helix | 78-81 | 4 | |
| β-strand | 84-85 | 2 | 20 |
| β-strand | 87-89 | 3 | 19 |
| β-strand | 91-93 | 3 | 18 |
| β-strand | 100-114 | 15 | 18 |
| β-strand | 119-125 | 7 | 18 |
| β-strand | 128-135 | 8 | 18 |
| α-helix | 143-145 | 3 | |
| α-helix | 146-159 | 14 | |
| β-strand | 163-173 | 11 | 18 |
| β-strand | 183-191 | 9 | 18 |
| β-strand | 193 | 1 | 21 |
| α-helix | 194-196 | 3 | |
| β-strand | 198 | 1 | 21 |
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| Pertussis toxin subunit 1 | A, G | protein | 269 | Bordetella pertussis | P04977 (AlphaFold model) |
| Islet-activating protein S2 | B, H | protein | 226 | Bordetella pertussis | P04978 (AlphaFold model) |
| Islet-activating protein S3 | C, I | protein | 227 | Bordetella pertussis | P04979 (AlphaFold model) |
| Islet-activating protein S4 | D, E, J, K | protein | 152 | Bordetella pertussis | P0A3R5 (AlphaFold model) |
| Pertussis toxin subunit 5 | F, L | protein | 133 | Bordetella pertussis | P04981 |
Sequence of entity 1 (A, G), FASTA
>6RO0_1 Pertussis toxin subunit 1 (chains A, G)
MRCTRAIRQTARTGWLTWLAILAVTAPVTSPAWADDPPATVYKYDSRPPEDVFQNGFTAW
GNNDNVLEHLTGRSCQVGSSNSAFVSTSSSRRYTEVYLEHRMQEAVEAERAGRGTGHFIG
YIYEVRADNNFYGAASSYFEYVDTYGDNAGRILAGALATYQSGYLAHRRIPPENIRRVTR
VYHNGITGETTTTEYSNARYVSQQTRANPNPYTSRRSVASIVGTLVRMAPVVGACMARQA
ESSEAMAAWSERAGEAMVLVYYESIAYSF
Sequence of entity 2 (B, H), FASTA
>6RO0_2 Islet-activating protein S2 (chains B, H)
MPIDRKTLCHLLSVLPLALLGSHVARASTPGIVIPPQEQITQHGSPYGRCANKTRALTVA
ELRGSGDLQEYLRHVTRGWSIFALYDGTYLGGEYGGVIKDGTPGGAFDLKTTFCIMTTRN
TGQPATDHYYSNVTATRLLSSTNSRLCAVFVRSGQPVIGACTSPYDGKYWSMYSRLRKML
YLIYVAGISVRVHVSKEEQYYDYEDATFETYALTGISICNPGSSLC
Sequence of entity 3 (C, I), FASTA
>6RO0_3 Islet-activating protein S3 (chains C, I)
MLINNKKLLHHILPILVLALLGMRTAQAVAPGIVIPPKALFTQQGGAYGRCPNGTRALTV
AELRGNAELQTYLRQITPGWSIYGLYDGTYLGQAYGGIIKDAPPGAGFIYRETFCITTIY
KTGQPAADHYYSKVTATRLLASTNSRLCAVFVRDGQSVIGACASPYEGRYRDMYDALRRL
LYMIYMSGLAVRVHVSKEEQYYDYEDATFQTYALTGISLCNPAASIC
Sequence of entity 4 (D, E, J, K), FASTA
>6RO0_4 Islet-activating protein S4 (chains D, E, J, K)
MLRRFPTRTTAPGQGGARRSRVRALAWLLASGAMTHLSPALADVPYVLVKTNMVVTSVAM
KPYEVTPTRMLVCGIAAKLGAAASSPDAHVPFCFGKDLKRPGSSPMEVMLRAVFMQQRPL
RMFLGPKQLTFEGKPALELIRMVECSGKQDCP
Sequence of entity 5 (F, L), FASTA
>6RO0_5 Pertussis toxin subunit 5 (chains F, L)
MQRQAGLPLKANPMHTIASILLSVLGIYSPADVAGLPTHLYKNFTVQELALKLKGKNQEF
CLTAFMSGRSLVRACLSDAGHEHDTWFDTMLGFAISAYALKSRIALTVEDSPYPGTPGDL
LELQICPLNGYCE
Primary citation
Genetically detoxified pertussis toxin displays near identical structure to its wild-type and exhibits robust immunogenicity. Ausar, S.F., Zhu, S., Duprez, J. et al. Commun Biol (2020) 3:427-427. DOI 10.1038/s42003-020-01153-3 · 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
- 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
- 9MR7 3.56 Å, Genetiocally detoxified pertussis toxin in complex with hu1B7 Fab and hu11E6 Fab
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