6JNF: Translocator of the outer mitochondrial membrane
Cryo-EM structure of the translocator of the outer mitochondrial membrane. Determined by electron microscopy at 3.81 Å resolution. Released 16 Oct 2019.
- Method
- Electron microscopy
- Resolution
- 3.81 Å
- Organism
- Saccharomyces cerevisiae S288c
- Chains
- 10
- Atoms
- 7,271
- Mol. weight
- 160.3 kDa
- Ligands
- 46E
- Released
- 16 Oct 2019
Explore 6JNF in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
6JNF contains 22 α-helices and 64 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.
Chains A and F: 2 helices, 32 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 68-71 | 4 | |
| β-strand | 84-91 | 8 | 1 |
| β-strand | 97-106 | 10 | 1 |
| β-strand | 115-117 | 3 | 2 |
| β-strand | 119-121 | 3 | 1 |
| β-strand | 126-127 | 2 | 3 |
| β-strand | 130-132 | 3 | 2 |
| β-strand | 137-142 | 6 | 3 |
| β-strand | 153-157 | 5 | 3 |
| β-strand | 164 | 1 | 3 |
| β-strand | 166-167 | 2 | 4 |
| β-strand | 172 | 1 | 1 |
| β-strand | 176-177 | 2 | 1 |
| β-strand | 181-183 | 3 | 4 |
| β-strand | 195-196 | 2 | 5 |
| β-strand | 197-198 | 2 | 4 |
| β-strand | 201-203 | 3 | 1 |
| β-strand | 209-213 | 5 | 1 |
| β-strand | 215 | 1 | 6 |
| β-strand | 218-219 | 2 | 5 |
| β-strand | 227 | 1 | 5 |
| β-strand | 230 | 1 | 6 |
| β-strand | 232-236 | 5 | 1 |
| β-strand | 245-249 | 5 | 1 |
| β-strand | 255-259 | 5 | 1 |
| β-strand | 271-274 | 4 | 1 |
| β-strand | 300-303 | 4 | 1 |
| β-strand | 306-309 | 4 | 1 |
| β-strand | 312-315 | 4 | 1 |
| β-strand | 318-319 | 2 | 1 |
| β-strand | 323-330 | 8 | 1 |
| β-strand | 337-345 | 9 | 1 |
| β-strand | 351-362 | 12 | 1 |
| α-helix | 369-372 | 4 | |
Chains B and G: 3 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 19-25 | 7 | |
| α-helix | 33-42 | 10 | |
| α-helix | 51-53 | 3 | |
Chains C and H: 2 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 98-101 | 4 | |
| α-helix | 111-129 | 19 | |
Chains D and I: 2 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 19-40 | 22 | |
| α-helix | 45-48 | 4 | |
Chains E and J: 2 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 32-49 | 18 | |
| α-helix | 52-56 | 5 | |
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| Mitochondrial import receptor subunit TOM40 | A, F | protein | 387 | Saccharomyces cerevisiae S288c | P23644 (AlphaFold model) |
| Mitochondrial import receptor subunit TOM7 | B, G | protein | 60 | Saccharomyces cerevisiae S288c | P53507 (AlphaFold model) |
| Mitochondrial import receptor subunit TOM22 | C, H | protein | 166 | Saccharomyces cerevisiae S288c | P49334 (AlphaFold model) |
| Mitochondrial import receptor subunit TOM5 | D, I | protein | 50 | Saccharomyces cerevisiae S288c | P80967 (AlphaFold model) |
| Mitochondrial import receptor subunit TOM6 | E, J | protein | 61 | Saccharomyces cerevisiae S288c | P33448 |
Sequence of entity 1 (A, F), FASTA
>6JNF_1 Mitochondrial import receptor subunit TOM40 (chains A, F)
MSAPTPLAEASQIPTIPALSPLTAKQSKGNFFSSNPISSFVVDTYKQLHSHRQSLELVNP
GTVENLNKEVSRDVFLSQYFFTGLRADLNKAFSMNPAFQTSHTFSIGSQALPKYAFSALF
ANDNLFAQGNIDNDLSVSGRLNYGWDKKNISKVNLQISDGQPTMCQLEQDYQASDFSVNV
KTLNPSFSEKGEFTGVAVASFLQSVTPQLALGLETLYSRTDGSAPGDAGVSYLTRYVSKK
QDWIFSGQLQANGALIASLWRKVAQNVEAGIETTLQAGMVPITDPLMGTPIGIQPTVEGS
TTIGAKYEYRQSVYRGTLDSNGKVACFLERKVLPTLSVLFCGEIDHFKNDTKIGCGLQFE
TAGNQELLMLQQGLDADGNPLQALPQL
Sequence of entity 2 (B, G), FASTA
>6JNF_2 Mitochondrial import receptor subunit TOM7 (chains B, G)
MSFLPSFILSDESKERISKILTLTHNVAHYGWIPFVLYLGWAHTSNRPNFLNLLSPLPSV
Sequence of entity 3 (C, H), FASTA
>6JNF_3 Mitochondrial import receptor subunit TOM22 (chains C, H)
MVELTEIKDDVVQLDEPQFSRNQAIVEEKASATNNDVVDDEDDSDSDFEDEFDENETLLD
RIVALKDIVPPGKRQTISNFFGFTSSFVRNAFTKSGNLAWTLTTTALLLGVPLSLSILAE
QQLIEMEKTFDLQSDANNILAQGEKDAAATANGSPGHHHHHHHHHH
Sequence of entity 4 (D, I), FASTA
>6JNF_4 Mitochondrial import receptor subunit TOM5 (chains D, I)
MFGLPQQEVSEEEKRAHQEQTEKTLKQAAYVAAFLWVSPMIWHLVKKQWK
Sequence of entity 5 (E, J), FASTA
>6JNF_5 Mitochondrial import receptor subunit TOM6 (chains E, J)
MDGMFAMPGAAAGAASPQQPKSRFQAFKESPLYTIALNGAFFVAGVAFIQSPLMDMLAPQ
L
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
Structure of the mitochondrial import gate reveals distinct preprotein paths. Araiso, Y., Tsutsumi, A., Qiu, J. et al. Nature (2019) 575:395-401. DOI 10.1038/s41586-019-1680-7 · 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
- 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
- 8W5J 4.4 Å, Cryo-EM structure of the yeast TOM core complex (from TOM-TIM23 complex)
Browse structure collections
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