8HCO: Substrate-engaged TOM complex from yeast
Substrate-engaged TOM complex from yeast. Determined by electron microscopy at 4.1 Å resolution. Released 13 Sept 2023.
- Method
- Electron microscopy
- Resolution
- 4.1 Å
- Organisms
- Saccharomyces cerevisiae S288C, Aequorea victoria
- Chains
- 11
- Atoms
- 9,330
- Mol. weight
- 217.82 kDa
- Released
- 13 Sept 2023
Explore 8HCO in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
8HCO contains 28 α-helices and 62 β-strands across 11 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, 23 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 50-55 | 6 | |
| α-helix | 57-62 | 6 | |
| α-helix | 68-71 | 4 | |
| β-strand | 85-93 | 9 | 1 |
| β-strand | 98-105 | 8 | 1 |
| β-strand | 114-121 | 8 | 1 |
| β-strand | 125-131 | 7 | 1 |
| α-helix | 133-135 | 3 | |
| β-strand | 137-144 | 8 | 1 |
| β-strand | 150-157 | 8 | 1 |
| α-helix | 162-163 | 2 | |
| β-strand | 164-172 | 9 | 1 |
| β-strand | 176-187 | 12 | 1 |
| β-strand | 193-204 | 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 | 255-262 | 8 | 1 |
| β-strand | 267-276 | 10 | 1 |
| β-strand | 279 | 1 | 2 |
| β-strand | 295 | 1 | 2 |
| β-strand | 298-308 | 11 | 1 |
| β-strand | 312-319 | 8 | 1 |
| β-strand | 323-331 | 9 | 1 |
| β-strand | 336-345 | 10 | 1 |
| β-strand | 350-362 | 13 | 1 |
| α-helix | 365-371 | 7 | |
| β-strand | 374 | 1 | 3 |
| α-helix | 379 | 1 | |
| β-strand | 380 | 1 | 3 |
| α-helix | 381 | 1 | |
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 | 14-47 | 34 | |
Chains D and L: 2 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 31-49 | 19 | |
| α-helix | 52-57 | 6 | |
Chain E: 2 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 28-41 | 14 | |
| α-helix | 50-54 | 5 | |
Chain G: 1 helix, 14 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 290-300 | 11 | 4 |
| β-strand | 304-314 | 11 | 4 |
| β-strand | 319-326 | 8 | 4 |
| α-helix | 335-339 | 5 | |
| β-strand | 351 | 1 | 4 |
| β-strand | 370-378 | 9 | 4 |
| β-strand | 383-392 | 10 | 4 |
| β-strand | 397-406 | 10 | 4 |
| β-strand | 419 | 1 | 5 |
| β-strand | 427-433 | 7 | 4 |
| β-strand | 438-448 | 11 | 4 |
| β-strand | 449 | 1 | 5 |
| β-strand | 454-465 | 12 | 4 |
| β-strand | 477-486 | 10 | 4 |
| β-strand | 495-505 | 11 | 4 |
Chain I: 6 helices, 25 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 57-60 | 4 | |
| α-helix | 68-72 | 5 | |
| β-strand | 85-91 | 7 | 6 |
| β-strand | 99-105 | 7 | 6 |
| β-strand | 114-121 | 8 | 6 |
| β-strand | 125-132 | 8 | 6 |
| β-strand | 136-144 | 9 | 6 |
| β-strand | 150-156 | 7 | 6 |
| β-strand | 164-172 | 9 | 6 |
| β-strand | 176-183 | 8 | 6 |
| β-strand | 195-203 | 9 | 6 |
| β-strand | 209-219 | 11 | 6 |
| α-helix | 225-226 | 2 | |
| β-strand | 227-237 | 11 | 6 |
| β-strand | 243-249 | 7 | 6 |
| β-strand | 255-261 | 7 | 6 |
| β-strand | 267-273 | 7 | 6 |
| β-strand | 276 | 1 | 7 |
| β-strand | 279-281 | 3 | 8 |
| β-strand | 293-295 | 3 | 8 |
| β-strand | 298 | 1 | 7 |
| β-strand | 301-308 | 8 | 6 |
| β-strand | 312-318 | 7 | 6 |
| β-strand | 323-330 | 8 | 6 |
| β-strand | 337-345 | 9 | 6 |
| β-strand | 350-362 | 13 | 6 |
| α-helix | 365-371 | 7 | |
| β-strand | 374 | 1 | 9 |
| α-helix | 379 | 1 | |
| β-strand | 380 | 1 | 9 |
| α-helix | 381 | 1 | |
Chain M: 2 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 32-42 | 11 | |
| 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 S288C | P23644 (AlphaFold model) |
| Mitochondrial import receptor subunit TOM22 | B, J | protein | 152 | Saccharomyces cerevisiae S288C | P49334 (AlphaFold model) |
| Mitochondrial import receptor subunit TOM5 | C, K | protein | 50 | Saccharomyces cerevisiae S288C | P80967 (AlphaFold model) |
| Mitochondrial import receptor subunit TOM6 | D, L | protein | 61 | Saccharomyces cerevisiae S288C | P33448 (AlphaFold model) |
| Mitochondrial import receptor subunit TOM7 | E, M | protein | 60 | Saccharomyces cerevisiae S288C | P53507 |
| sfGFP | G | protein | 553 | Aequorea victoria | P00175, P0ABQ4, P42212 |
Sequence of entity 1 (A, I), FASTA
>8HCO_1 Mitochondrial import receptor subunit TOM40 (chains A, I)
MSAPTPLAEASQIPTIPALSPLTAKQSKGNFFSSNPISSFVVDTYKQLHSHRQSLELVNP
GTVENLNKEVSRDVFLSQYFFTGLRADLNKAFSMNPAFQTSHTFSIGSQALPKYAFSALF
ANDNLFAQGNIDNDLSVSGRLNYGWDKKNISKVNLQISDGQPTMCQLEQDYQASDFSVNV
KTLNPSFSEKGEFTGVAVASFLQSVTPQLALGLETLYSRTDGSAPGDAGVSYLTRYVSKK
QDWIFSGQLQANGALIASLWRKVAQNVEAGIETTLQAGMVPITDPLMGTPIGIQPTVEGS
TTIGAKYEYRQSVYRGTLDSNGKVACFLERKVLPTLSVLFCGEIDHFKNDTKIGCGLQFE
TAGNQELLMLQQGLDADGNPLQALPQL
Sequence of entity 2 (B, J), FASTA
>8HCO_2 Mitochondrial import receptor subunit TOM22 (chains B, J)
MVELTEIKDDVVQLDEPQFSRNQAIVEEKASATNNDVVDDEDDSDSDFEDEFDENETLLD
RIVALKDIVPPGKRQTISNFFGFTSSFVRNAFTKSGNLAWTLTTTALLLGVPLSLSILAE
QQLIEMEKTFDLQSDANNILAQGEKDAAATAN
Sequence of entity 3 (C, K), FASTA
>8HCO_3 Mitochondrial import receptor subunit TOM5 (chains C, K)
MFGLPQQEVSEEEKRAHQEQTEKTLKQAAYVAAFLWVSPMIWHLVKKQWK
Sequence of entity 4 (D, L), FASTA
>8HCO_4 Mitochondrial import receptor subunit TOM6 (chains D, L)
MDGMFAMPGAAAGAASPQQPKSRFQAFKESPLYTIALNGAFFVAGVAFIQSPLMDMLAPQ
L
Sequence of entity 5 (E, M), FASTA
>8HCO_5 Mitochondrial import receptor subunit TOM7 (chains E, M)
MSFLPSFILSDESKERISKILTLTHNVAHYGWIPFVLYLGWAHTSNRPNFLNLLSPLPSV
Sequence of entity 6 (G), FASTA
>8HCO_6 sfGFP (chains G)
YGSTVPKSKSFEQDSSSVAYLNWHNGQIDNEPKLDMNKQKISPAEVAKHNKPDDCWVVIN
GYVYDLTRFLPNHPGMISLIAALAVDRVIGMENAMPWNLPADLAWFKRNTLNKPVIMGRH
TWESIGRPLPGRKNIILSSQPGTDDRVTWVKSVDEAIAASGDVPEIMVIGGGRVYEQFLP
KAQKLYLTHIDAEVEGDTHFPDYEPDDWESVFSEFHDADAQNSHSYSFEILERRGQDVIK
FNAGKDVTAIFEPLHAPNVIDKYIAPEKKLGPLQGSGSGSKGEELFTGVVPILVELDGDV
NGHKFSVRGEGEGDATNGKLTLKFICTTGKLPVPWPTLVTTFXVQCFSRYPDHMKRHDFF
KSAMPEGYVQERTISFKDDGTYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYN
FNSHNVYITADKQKNGIKANFKIRHNVEDGSVQLADHYQQNTPIGDGPVLLPDNHYLSTQ
SVLSKDPNEKRDHMVLLEFVTAAGITHGSAGLEVLFQGPANGGSAWSHPQFEKGGGSGGG
SGGGSWSHPQFEK
Primary citation
Molecular pathway of mitochondrial preprotein import through the TOM-TIM23 supercomplex. Zhou, X., Yang, Y., Wang, G. et al. Nat Struct Mol Biol (2023) 30:1996-2008. DOI 10.1038/s41594-023-01103-7 · 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)
- 8W5J 4.4 Å, Cryo-EM structure of the yeast TOM core complex (from TOM-TIM23 complex)
Browse structure collections
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