8W5J: Yeast TOM core complex
Cryo-EM structure of the yeast TOM core complex (from TOM-TIM23 complex). Determined by electron microscopy at 4.4 Å resolution. Released 28 Feb 2024.
- Method
- Electron microscopy
- Resolution
- 4.4 Å
- Organism
- Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
- Chains
- 10
- Atoms
- 7,356
- Mol. weight
- 156.94 kDa
- Ligands
- 46E
- Released
- 28 Feb 2024
Explore 8W5J in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
8W5J contains 25 α-helices and 42 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: 7 helices, 21 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 50-54 | 5 | |
| α-helix | 57-62 | 6 | |
| α-helix | 63-65 | 3 | |
| α-helix | 68 | 1 | |
| α-helix | 69-74 | 6 | |
| β-strand | 83-93 | 11 | 1 |
| β-strand | 97-106 | 10 | 1 |
| β-strand | 114-121 | 8 | 1 |
| β-strand | 125-132 | 8 | 1 |
| β-strand | 136-143 | 8 | 1 |
| β-strand | 149-157 | 9 | 1 |
| β-strand | 164-172 | 9 | 1 |
| β-strand | 176-183 | 8 | 1 |
| β-strand | 187 | 1 | 2 |
| β-strand | 193 | 1 | 2 |
| β-strand | 195-206 | 12 | 1 |
| β-strand | 209-219 | 11 | 1 |
| α-helix | 225-226 | 2 | |
| β-strand | 227-237 | 11 | 1 |
| β-strand | 243-249 | 7 | 1 |
| β-strand | 255-264 | 10 | 1 |
| β-strand | 267-275 | 9 | 1 |
| β-strand | 299-308 | 10 | 1 |
| β-strand | 312-319 | 8 | 1 |
| β-strand | 323-330 | 8 | 1 |
| β-strand | 336-345 | 10 | 1 |
| β-strand | 350-362 | 13 | 1 |
| α-helix | 365-372 | 8 | |
Chains B and J: 1 helix, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 87-134 | 48 | |
Chains C and K: 1 helix, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 14-48 | 35 | |
Chain D: 2 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 31-50 | 20 | |
| α-helix | 53-57 | 5 | |
Chain E: 2 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 20-43 | 24 | |
| α-helix | 50-54 | 5 | |
Chain I: 5 helices, 21 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 50-55 | 6 | |
| α-helix | 63-65 | 3 | |
| α-helix | 68-74 | 7 | |
| β-strand | 84-93 | 10 | 3 |
| β-strand | 97-106 | 10 | 3 |
| β-strand | 114-121 | 8 | 3 |
| β-strand | 125-132 | 8 | 3 |
| β-strand | 138-144 | 7 | 3 |
| β-strand | 150-156 | 7 | 3 |
| β-strand | 164-172 | 9 | 3 |
| β-strand | 176-183 | 8 | 3 |
| β-strand | 187 | 1 | 4 |
| β-strand | 193 | 1 | 4 |
| β-strand | 196-206 | 11 | 3 |
| β-strand | 209-218 | 10 | 3 |
| α-helix | 225-226 | 2 | |
| β-strand | 227-237 | 11 | 3 |
| β-strand | 243-249 | 7 | 3 |
| β-strand | 255-262 | 8 | 3 |
| β-strand | 267-275 | 9 | 3 |
| β-strand | 299-308 | 10 | 3 |
| β-strand | 312-319 | 8 | 3 |
| β-strand | 323-331 | 9 | 3 |
| β-strand | 336-345 | 10 | 3 |
| β-strand | 350-362 | 13 | 3 |
| α-helix | 365-372 | 8 | |
Chain L: 2 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 31-50 | 20 | |
| α-helix | 52-57 | 6 | |
Chain M: 3 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 20-30 | 11 | |
| α-helix | 32-43 | 12 | |
| α-helix | 50-54 | 5 | |
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| Mitochondrial import receptor subunit TOM40 | A, I | protein | 387 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | P23644 (AlphaFold model) |
| Mitochondrial import receptor subunit TOM22 | B, J | protein | 152 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | P49334 (AlphaFold model) |
| Mitochondrial import receptor subunit TOM5 | C, K | protein | 50 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | P80967 (AlphaFold model) |
| Mitochondrial import receptor subunit TOM6 | D, L | protein | 61 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | P33448 (AlphaFold model) |
| Mitochondrial import receptor subunit TOM7 | E, M | protein | 60 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | P53507 |
Sequence of entity 1 (A, I), FASTA
>8W5J_1 Mitochondrial import receptor subunit TOM40 (chains A, I)
MSAPTPLAEASQIPTIPALSPLTAKQSKGNFFSSNPISSFVVDTYKQLHSHRQSLELVNP
GTVENLNKEVSRDVFLSQYFFTGLRADLNKAFSMNPAFQTSHTFSIGSQALPKYAFSALF
ANDNLFAQGNIDNDLSVSGRLNYGWDKKNISKVNLQISDGQPTMCQLEQDYQASDFSVNV
KTLNPSFSEKGEFTGVAVASFLQSVTPQLALGLETLYSRTDGSAPGDAGVSYLTRYVSKK
QDWIFSGQLQANGALIASLWRKVAQNVEAGIETTLQAGMVPITDPLMGTPIGIQPTVEGS
TTIGAKYEYRQSVYRGTLDSNGKVACFLERKVLPTLSVLFCGEIDHFKNDTKIGCGLQFE
TAGNQELLMLQQGLDADGNPLQALPQL
Sequence of entity 2 (B, J), FASTA
>8W5J_2 Mitochondrial import receptor subunit TOM22 (chains B, J)
MVELTEIKDDVVQLDEPQFSRNQAIVEEKASATNNDVVDDEDDSDSDFEDEFDENETLLD
RIVALKDIVPPGKRQTISNFFGFTSSFVRNAFTKSGNLAWTLTTTALLLGVPLSLSILAE
QQLIEMEKTFDLQSDANNILAQGEKDAAATAN
Sequence of entity 3 (C, K), FASTA
>8W5J_3 Mitochondrial import receptor subunit TOM5 (chains C, K)
MFGLPQQEVSEEEKRAHQEQTEKTLKQAAYVAAFLWVSPMIWHLVKKQWK
Sequence of entity 4 (D, L), FASTA
>8W5J_4 Mitochondrial import receptor subunit TOM6 (chains D, L)
MDGMFAMPGAAAGAASPQQPKSRFQAFKESPLYTIALNGAFFVAGVAFIQSPLMDMLAPQ
L
Sequence of entity 5 (E, M), FASTA
>8W5J_5 Mitochondrial import receptor subunit TOM7 (chains E, M)
MSFLPSFILSDESKERISKILTLTHNVAHYGWIPFVLYLGWAHTSNRPNFLNLLSPLPSV
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| 46E | (2R)-3-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-(tetradecanoyloxy)propyl… | C33 H66 N O8 P | 1 |
Primary citation
The architecture of substrate-engaged TOM-TIM23 supercomplex reveals preprotein proximity sites for mitochondrial protein translocation. Wang, Q., Zhuang, J., Huang, R. et al. Cell Discov (2024) 10:19-19. DOI 10.1038/s41421-023-00643-y · PubMed
Other PDB entries of the same protein (UniProt P23644 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 9J99 2.94 Å, Substrate-engaged TOM complex from yeast
- 7E4H 3.01 Å, Cryo-EM structure of the yeast mitochondrial SAM-Tom40 complex at 3.0 angstrom
- 7E4I 3.05 Å, Cryo-EM structure of the yeast mitochondrial SAM-Tom40/Tom5/Tom6 complex at 3.0 angstrom
- 6UCU 3.06 Å, Cryo-EM structure of the mitochondrial TOM complex from yeast (dimer)
- 7VKU 3.2 Å, Cryo-EM structure of SAM-Tom40 intermediate complex
- 8XKY 3.42 Å, Structure of the TOM40 complex annealed
- 8W5K 3.6 Å, Cryo-EM structure of the yeast TOM core complex crosslinked by BS3 (from TOM-TIM23…
- 8XKW 3.64 Å, Structure of the TOM40 complex unannealed
- 8XKX 3.7 Å, Structure of the TOM40 complex with pre-protein
- 6JNF 3.81 Å, Cryo-EM structure of the translocator of the outer mitochondrial membrane
- 6UCV 4.1 Å, Cryo-EM structure of the mitochondrial TOM complex from yeast (tetramer)
- 8HCO 4.1 Å, Substrate-engaged TOM complex from yeast
Browse structure collections
About this viewer
MolViewer shows 8W5J directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.