9GCO: Thioredoxin
Xenorhabdus bovienii Thioredoxin complex with Rhs toxin TreX and immunity protein TriX. Determined by X-ray diffraction at 2.0 Å resolution. Released 4 Dec 2024.
- Method
- X-ray diffraction
- Resolution
- 2.0 Å
- Organism
- Xenorhabdus bovienii SS-2004
- Chains
- 6
- Atoms
- 6,155
- Mol. weight
- 89.61 kDa
- Ligands
- CA
- Released
- 4 Dec 2024
Explore 9GCO in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
9GCO contains 35 α-helices and 68 β-strands across 6 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.
Chains A and D: 4 helices, 8 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 13-14 | 2 | 1 |
| α-helix | 17-19 | 3 | |
| β-strand | 20-21 | 2 | 2 |
| β-strand | 24-25 | 2 | 2 |
| β-strand | 30-36 | 7 | 1 |
| α-helix | 41-56 | 16 | |
| β-strand | 62-67 | 6 | 1 |
| α-helix | 73-77 | 5 | |
| β-strand | 82-83 | 2 | 3 |
| β-strand | 85-90 | 6 | 1 |
| β-strand | 93-99 | 7 | 1 |
| α-helix | 104-114 | 11 | |
Chain B: 8 helices, 14 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 12-18 | 7 | 3 |
| α-helix | 22-28 | 7 | |
| β-strand | 30 | 1 | 4 |
| β-strand | 36 | 1 | 5 |
| α-helix | 39-44 | 6 | |
| β-strand | 47 | 1 | 6 |
| β-strand | 50 | 1 | 6 |
| β-strand | 51 | 1 | 5 |
| β-strand | 53-57 | 5 | 3 |
| α-helix | 60-63 | 4 | |
| α-helix | 64-67 | 4 | |
| β-strand | 75-82 | 8 | 3 |
| β-strand | 86-87 | 2 | 3 |
| α-helix | 88-92 | 5 | |
| α-helix | 93-95 | 3 | |
| α-helix | 99-101 | 3 | |
| β-strand | 103-107 | 5 | 3 |
| β-strand | 110 | 1 | 4 |
| α-helix | 112-114 | 3 | |
| β-strand | 115-121 | 7 | 3 |
| β-strand | 127 | 1 | 3 |
| β-strand | 131-133 | 3 | 3 |
Chain C: 5 helices, 12 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 4-13 | 10 | 7 |
| β-strand | 16-27 | 12 | 7 |
| β-strand | 31-37 | 7 | 7 |
| β-strand | 42-48 | 7 | 7 |
| α-helix | 51-61 | 11 | |
| β-strand | 66-67 | 2 | 7 |
| β-strand | 69 | 1 | 8 |
| α-helix | 70-72 | 3 | |
| β-strand | 76-77 | 2 | 9 |
| α-helix | 80-86 | 7 | |
| β-strand | 90-93 | 4 | 9 |
| β-strand | 95 | 1 | 10 |
| β-strand | 98 | 1 | 10 |
| α-helix | 102-104 | 3 | |
| β-strand | 105-107 | 3 | 9 |
| β-strand | 111 | 1 | 8 |
| α-helix | 120-133 | 14 | |
Chain E: 9 helices, 14 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 12-18 | 7 | 13 |
| α-helix | 22-28 | 7 | |
| β-strand | 30 | 1 | 14 |
| β-strand | 36 | 1 | 15 |
| α-helix | 39-44 | 6 | |
| β-strand | 47 | 1 | 16 |
| β-strand | 50 | 1 | 16 |
| β-strand | 51 | 1 | 15 |
| β-strand | 53-57 | 5 | 13 |
| α-helix | 60-63 | 4 | |
| α-helix | 64-67 | 4 | |
| β-strand | 75-82 | 8 | 13 |
| β-strand | 86-87 | 2 | 13 |
| α-helix | 88-92 | 5 | |
| α-helix | 93-95 | 3 | |
| α-helix | 99-101 | 3 | |
| β-strand | 103-107 | 5 | 13 |
| β-strand | 110 | 1 | 14 |
| α-helix | 112-114 | 3 | |
| β-strand | 115-121 | 7 | 13 |
| β-strand | 127 | 1 | 13 |
| β-strand | 131-133 | 3 | 13 |
| α-helix | 135-138 | 4 | |
Chain F: 5 helices, 12 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 4-13 | 10 | 17 |
| β-strand | 16-27 | 12 | 17 |
| β-strand | 31-38 | 8 | 17 |
| β-strand | 41-48 | 8 | 17 |
| α-helix | 51-61 | 11 | |
| β-strand | 66-67 | 2 | 17 |
| β-strand | 69 | 1 | 18 |
| α-helix | 70-72 | 3 | |
| β-strand | 76-77 | 2 | 19 |
| α-helix | 80-85 | 6 | |
| β-strand | 90-93 | 4 | 19 |
| β-strand | 95 | 1 | 20 |
| β-strand | 98 | 1 | 20 |
| α-helix | 102-104 | 3 | |
| β-strand | 105-107 | 3 | 19 |
| β-strand | 111 | 1 | 18 |
| α-helix | 120-133 | 14 | |
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| Thioredoxin | A, D | protein | 115 | Xenorhabdus bovienii SS-2004 | D3V6L5 (AlphaFold model) |
| Toxin TreX | B, E | protein | 140 | Xenorhabdus bovienii SS-2004 | D3UXR3 |
| Immunity Protein TriX | C, F | protein | 142 | Xenorhabdus bovienii SS-2004 | D3UXR2 (AlphaFold model) |
Sequence of entity 1 (A, D), FASTA
>9GCO_1 Thioredoxin (chains A, D)
GASNEKIISDRIIHLADADFDAKKLNVKGAVLIEFWAEWCGPCKMIAPILDEVSEEYAGK
LTVAKLNVDDHEQTPKAHGIRGIPTLMLFKDGEKVATQVGALSKTQLKAFLDSHI
Sequence of entity 2 (B, E), FASTA
>9GCO_2 Toxin TreX (chains B, E)
MAGGIGNKGDYIITYRGDTRSFTEIFDKGFETLGPSKDLYKHALDNRAPPSDFVSTTIDP
TKTISFATKYGQKSGYMYTMKTNHGIDVNKALGARSPFAAEAEIAMPGGVRAEDILGARA
VNADGEMWDYTILNPKRYGK
Sequence of entity 3 (C, F), FASTA
>9GCO_3 Immunity Protein TriX (chains C, F)
MTDVDKRKIKIILNGEMEEAELHMITSPNRHCCLKIFHNNNQLAESNDTDYFSCFADLRN
QLKNIIFLCKGAKINVYPSAMSRDMSDGIVAYETTLGQPGLPENQVHIFDFEDKYVDITP
EEQRKFHSQWFESLVDHHHHHH
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| CA | Calcium ion | Ca | 7 |
Water and common crystallization additives (PEG) are not listed.
Primary citation
Thioredoxin 1 moonlights as a chaperone for an interbacterial ADP-ribosyltransferase toxin. Dumont, B., Terradot, L., Cascales, E. et al. Nat Commun (2024) 15:10388-10388. DOI 10.1038/s41467-024-54892-w · PubMed
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