8XDN: TOM complex with small molecule
TOM complex with small molecule. Determined by electron microscopy at 2.93 Å resolution. Released 11 Jun 2025.
- Method
- Electron microscopy
- Resolution
- 2.93 Å
- Organism
- Homo sapiens
- Chains
- 10
- Atoms
- 6,894
- Mol. weight
- 148.51 kDa
- Ligands
- FUD, PC1
- Released
- 11 Jun 2025
Explore 8XDN in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
8XDN contains 21 α-helices and 46 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: 4 helices, 23 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 77-79 | 3 | |
| α-helix | 84-86 | 3 | |
| α-helix | 88-91 | 4 | |
| α-helix | 95-97 | 3 | |
| β-strand | 101-108 | 8 | 1 |
| β-strand | 113-121 | 9 | 1 |
| β-strand | 128-136 | 9 | 1 |
| β-strand | 149-155 | 7 | 1 |
| β-strand | 160-169 | 10 | 1 |
| β-strand | 172-181 | 10 | 1 |
| β-strand | 184-195 | 12 | 1 |
| β-strand | 199-209 | 11 | 1 |
| β-strand | 214-223 | 10 | 1 |
| β-strand | 229 | 1 | 2 |
| β-strand | 232-240 | 9 | 1 |
| β-strand | 243-251 | 9 | 1 |
| β-strand | 252-255 | 4 | 2 |
| β-strand | 259-263 | 5 | 2 |
| β-strand | 269-276 | 8 | 2 |
| β-strand | 282-291 | 10 | 2 |
| β-strand | 298-307 | 10 | 2 |
| β-strand | 312-319 | 8 | 2 |
| β-strand | 323-330 | 8 | 2 |
| β-strand | 337-339 | 3 | 1 |
| β-strand | 340-346 | 7 | 2 |
| β-strand | 351-355 | 5 | 2 |
| β-strand | 358-360 | 3 | 1 |
Chain B: 3 helices, 23 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 76-79 | 4 | |
| α-helix | 88-91 | 4 | |
| α-helix | 95-96 | 2 | |
| β-strand | 100-108 | 9 | 3 |
| β-strand | 114-121 | 8 | 3 |
| β-strand | 128-136 | 9 | 3 |
| β-strand | 149-155 | 7 | 3 |
| β-strand | 160-167 | 8 | 3 |
| β-strand | 172-181 | 10 | 3 |
| β-strand | 184-195 | 12 | 3 |
| β-strand | 199-209 | 11 | 3 |
| β-strand | 214-226 | 13 | 3 |
| β-strand | 229-240 | 12 | 3 |
| β-strand | 243-255 | 13 | 3 |
| β-strand | 259-263 | 5 | 3 |
| β-strand | 266 | 1 | 3 |
| β-strand | 273-276 | 4 | 3 |
| β-strand | 282-287 | 6 | 3 |
| β-strand | 290-291 | 2 | 4 |
| β-strand | 296-297 | 2 | 4 |
| β-strand | 300-307 | 8 | 3 |
| β-strand | 312-319 | 8 | 3 |
| β-strand | 323-329 | 7 | 3 |
| β-strand | 340-346 | 7 | 3 |
| β-strand | 351-355 | 5 | 3 |
| β-strand | 360 | 1 | 3 |
Chain C: 3 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 73-91 | 19 | |
| α-helix | 92-96 | 5 | |
| α-helix | 97-108 | 12 | |
Chain D: 1 helix, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 73-108 | 36 | |
Chain E: 1 helix, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 42-59 | 18 | |
Chain F: 1 helix, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 42-60 | 19 | |
Chain G: 3 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 6-38 | 33 | |
| α-helix | 45-47 | 3 | |
| α-helix | 50-52 | 3 | |
Chain H: 3 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 6-38 | 33 | |
| α-helix | 45-48 | 4 | |
| α-helix | 49-52 | 4 | |
1 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| Mitochondrial import receptor subunit TOM40 homolog | A, B | protein | 361 | Homo sapiens | O96008 (AlphaFold model) |
| Mitochondrial import receptor subunit TOM22 homolog | C, D | protein | 142 | Homo sapiens | Q9NS69 (AlphaFold model) |
| Mitochondrial import receptor subunit TOM6 homolog | E, F | protein | 74 | Homo sapiens | Q96B49 (AlphaFold model) |
| Mitochondrial import receptor subunit TOM7 homolog | G, H | protein | 55 | Homo sapiens | Q9P0U1 (AlphaFold model) |
| Mitochondrial import receptor subunit TOM5 homolog | I, J | protein | 51 | Homo sapiens | Q8N4H5 |
Sequence of entity 1 (A, B), FASTA
>8XDN_1 Mitochondrial import receptor subunit TOM40 homolog (chains A, B)
MGNVLAASSPPAGPPPPPAPALVGLPPPPPSPPGFTLPPLGGSLGAGTSTSRSSERTPGA
ATASASGAAEDGACGCLPNPGTFEECHRKCKELFPIQMEGVKLTVNKGLSNHFQVNHTVA
LSTIGESNYHFGVTYVGTKQLSPTEAFPVLVGDMDNSGSLNAQVIHQLGPGLRSKMAIQT
QQSKFVNWQVDGEYRGSDFTAAVTLGNPDVLVGSGILVAHYLQSITPCLALGGELVYHRR
PGEEGTVMSLAGKYTLNNWLATVTLGQAGMHATYYHKASDQLQVGVEFEASTRMQDTSVS
FGYQLDLPKANLLFKGSVDSNWIVGATLEKKLPPLPLTLALGAFLNHRKNKFQCGFGLTI
G
Sequence of entity 2 (C, D), FASTA
>8XDN_2 Mitochondrial import receptor subunit TOM22 homolog (chains C, D)
MAAAVAAAGAGEPQSPDELLPKGDAEKPEEELEEDDDEELDETLSERLWGLTEMFPERVR
SAAGATFDLSLFVAQKMYRFSRAALWIGTTSFMILVLPVVFETEKLQMEQQQQLQQRQIL
LGPNTGLSGGMPGALPSLPGKI
Sequence of entity 3 (E, F), FASTA
>8XDN_3 Mitochondrial import receptor subunit TOM6 homolog (chains E, F)
MASSTVPVSAAGSANETPEIPDNVGDWLRGVYRFATDRNDFRRNLILNLGLFAAGVWLAR
NLSDIDLMAPQPGV
Sequence of entity 4 (G, H), FASTA
>8XDN_4 Mitochondrial import receptor subunit TOM7 homolog (chains G, H)
MVKLSKEAKQRLQQLFKGSQFAIRWGFIPLVIYLGFKRGADPGMPEPTVLSLLWG
Sequence of entity 5 (I, J), FASTA
>8XDN_5 Mitochondrial import receptor subunit TOM5 homolog (chains I, J)
MFRIEGLAPKLDPEEMKRKMREDVISSIRNFLIYVALLRVTPFILKKLDSI
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| FUD | D-fructose | C6 H12 O6 | 1 |
| PC1 | 1,2-diacyl-sn-glycero-3-phosphocholine | C44 H88 N O8 P | 1 |
Primary citation
TOM complex with small molecule. Wang, W.H., Yang, M.J. To be published.
Other PDB entries of the same protein (UniProt O96008 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 7VD2 2.53 Å, Human TOM complex without cross-linking
- 7VBY 2.54 Å, Tom core complex with Tom20 and Tom22 subunits.
- 9EII 2.75 Å, Import stalled PINK1 TOM complex, symmetry expanded
- 9JXV 2.89 Å, human translocase of the outer mitochondrial membrane (TOM complex)
- 9WV3 2.98 Å, Human TOM complex with substrate Tim22-GGC1-sfGFP
- 7CP9 3.0 Å, Cryo-EM structure of human mitochondrial translocase TOM complex at 3.0 angstrom.
- 9EIH 3.1 Å, Import stalled PINK1 TOM complex
- 9WV2 3.15 Å, Human TOM complex with substrate GGC1-sfGFP
- 9EIJ 3.3 Å, Import stalled PINK1 TOM complex, extended TOM20 helix class
- 7CK6 3.4 Å, Protein translocase of mitochondria
- 7VC4 3.74 Å, Tom complex with Tom22 and Tom20 subunits
- 7VDD 3.74 Å, Human TOM complex with cross-linking
Browse structure collections
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