7VD2: Human TOM complex without cross-linking
Human TOM complex without cross-linking. Determined by electron microscopy at 2.53 Å resolution. Released 13 Jul 2022.
- Method
- Electron microscopy
- Resolution
- 2.53 Å
- Organism
- Homo sapiens
- Chains
- 10
- Atoms
- 9,117
- Mol. weight
- 171.37 kDa
- Ligands
- UND, PC1
- Released
- 13 Jul 2022
Explore 7VD2 in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
7VD2 contains 27 α-helices and 38 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: 2 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 27-36 | 10 | |
| α-helix | 41-59 | 19 | |
Chain B: 5 helices, 19 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 77-79 | 3 | |
| α-helix | 83-85 | 3 | |
| α-helix | 88-91 | 4 | |
| α-helix | 95-97 | 3 | |
| β-strand | 100-108 | 9 | 1 |
| β-strand | 113-121 | 9 | 1 |
| β-strand | 128-139 | 12 | 1 |
| β-strand | 147-155 | 9 | 1 |
| β-strand | 160-169 | 10 | 1 |
| β-strand | 172-180 | 9 | 1 |
| β-strand | 185-195 | 11 | 1 |
| β-strand | 199-209 | 11 | 1 |
| β-strand | 214-224 | 11 | 1 |
| β-strand | 229-240 | 12 | 1 |
| β-strand | 243-255 | 13 | 1 |
| β-strand | 259-266 | 8 | 1 |
| β-strand | 269-277 | 9 | 1 |
| β-strand | 282-291 | 10 | 1 |
| β-strand | 296-307 | 12 | 1 |
| α-helix | 308-310 | 3 | |
| β-strand | 312-319 | 8 | 1 |
| β-strand | 323-331 | 9 | 1 |
| β-strand | 338-346 | 9 | 1 |
| β-strand | 351-359 | 9 | 1 |
Chain C: 2 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 63-95 | 33 | |
| α-helix | 97-117 | 21 | |
Chain D: 1 helix, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 14-47 | 34 | |
Chain E: 1 helix, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 17-47 | 31 | |
Chain F: 2 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 26-35 | 10 | |
| α-helix | 41-60 | 20 | |
Chain G: 3 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 6-38 | 33 | |
| α-helix | 45-47 | 3 | |
| α-helix | 49-52 | 4 | |
Chain H: 2 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 64-95 | 32 | |
| α-helix | 97-117 | 21 | |
2 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 TOM6 homolog | A, F | protein | 74 | Homo sapiens | Q96B49 (AlphaFold model) |
| Mitochondrial import receptor subunit TOM5 homolog | D, E | protein | 51 | Homo sapiens | Q8N4H5 (AlphaFold model) |
| Mitochondrial import receptor subunit TOM7 homolog | G, J | protein | 55 | Homo sapiens | Q9P0U1 (AlphaFold model) |
| Mitochondrial import receptor subunit TOM22 homolog | C, H | protein | 142 | Homo sapiens | Q9NS69 (AlphaFold model) |
| Mitochondrial import receptor subunit TOM40 homolog | B, I | protein | 361 | Homo sapiens | O96008 |
Sequence of entity 1 (A, F), FASTA
>7VD2_1 Mitochondrial import receptor subunit TOM6 homolog (chains A, F)
MASSTVPVSAAGSANETPEIPDNVGDWLRGVYRFATDRNDFRRNLILNLGLFAAGVWLAR
NLSDIDLMAPQPGV
Sequence of entity 2 (D, E), FASTA
>7VD2_2 Mitochondrial import receptor subunit TOM5 homolog (chains D, E)
MFRIEGLAPKLDPEEMKRKMREDVISSIRNFLIYVALLRVTPFILKKLDSI
Sequence of entity 3 (G, J), FASTA
>7VD2_3 Mitochondrial import receptor subunit TOM7 homolog (chains G, J)
MVKLSKEAKQRLQQLFKGSQFAIRWGFIPLVIYLGFKRGADPGMPEPTVLSLLWG
Sequence of entity 4 (C, H), FASTA
>7VD2_4 Mitochondrial import receptor subunit TOM22 homolog (chains C, H)
MAAAVAAAGAGEPQSPDELLPKGDAEKPEEELEEDDDEELDETLSERLWGLTEMFPERVR
SAAGATFDLSLFVAQKMYRFSRAALWIGTTSFMILVLPVVFETEKLQMEQQQQLQQRQIL
LGPNTGLSGGMPGALPSLPGKI
Sequence of entity 5 (B, I), FASTA
>7VD2_5 Mitochondrial import receptor subunit TOM40 homolog (chains B, I)
MGNVLAASSPPAGPPPPPAPALVGLPPPPPSPPGFTLPPLGGSLGAGTSTSRSSERTPGA
ATASASGAAEDGACGCLPNPGTFEECHRKCKELFPIQMEGVKLTVNKGLSNHFQVNHTVA
LSTIGESNYHFGVTYVGTKQLSPTEAFPVLVGDMDNSGSLNAQVIHQLGPGLRSKMAIQT
QQSKFVNWQVDGEYRGSDFTAAVTLGNPDVLVGSGILVAHYLQSITPCLALGGELVYHRR
PGEEGTVMSLAGKYTLNNWLATVTLGQAGMHATYYHKASDQLQVGVEFEASTRMQDTSVS
FGYQLDLPKANLLFKGSVDSNWIVGATLEKKLPPLPLTLALGAFLNHRKNKFQCGFGLTI
G
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| UND | Undecane | C11 H24 | 16 |
| PC1 | 1,2-diacyl-sn-glycero-3-phosphocholine | C44 H88 N O8 P | 27 |
Primary citation
Structural basis of Tom20 and Tom22 cytosolic domains as the human TOM complex receptors. Su, J., Liu, D., Yang, F. et al. Proc Natl Acad Sci U S A (2022) 119:e2200158119-e2200158119. DOI 10.1073/pnas.2200158119 · PubMed
Other PDB entries of the same protein (UniProt Q96B49 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 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)
- 8XDN 2.93 Å, TOM complex with small molecule
- 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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