8XVA: Human TOM complex with whole Tom20
Human TOM complex with whole Tom20. Determined by electron microscopy at 5.92 Å resolution. Released 7 Aug 2024.
- Method
- Electron microscopy
- Resolution
- 5.92 Å
- Organism
- Homo sapiens
- Chains
- 11
- Atoms
- 5,415
- Mol. weight
- 163.86 kDa
- Released
- 7 Aug 2024
Explore 8XVA in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
8XVA contains 30 α-helices and 42 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.
Chains A and F: 2 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 27-36 | 10 | |
| α-helix | 41-61 | 21 | |
Chains B and I: 2 helices, 21 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 77-79 | 3 | |
| α-helix | 85-91 | 7 | |
| β-strand | 100-107 | 8 | 1 |
| β-strand | 113-121 | 9 | 1 |
| β-strand | 128-136 | 9 | 1 |
| β-strand | 140-142 | 3 | 2 |
| β-strand | 145-146 | 2 | 2 |
| β-strand | 149-154 | 6 | 1 |
| β-strand | 160-169 | 10 | 1 |
| β-strand | 172-180 | 9 | 1 |
| β-strand | 187-195 | 9 | 1 |
| β-strand | 199-209 | 11 | 1 |
| β-strand | 214-223 | 10 | 1 |
| β-strand | 229-240 | 12 | 1 |
| β-strand | 243-256 | 14 | 1 |
| β-strand | 259-266 | 8 | 1 |
| β-strand | 269-276 | 8 | 1 |
| β-strand | 282-291 | 10 | 1 |
| β-strand | 296-307 | 12 | 1 |
| β-strand | 312-319 | 8 | 1 |
| β-strand | 323-331 | 9 | 1 |
| β-strand | 337-346 | 10 | 1 |
| β-strand | 351-360 | 10 | 1 |
Chain C: 3 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 59-91 | 33 | |
| α-helix | 92-96 | 5 | |
| α-helix | 97-117 | 21 | |
Chains D and E: 1 helix, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 16-47 | 32 | |
Chains G and J: 4 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 6-38 | 33 | |
| α-helix | 41 | 1 | |
| α-helix | 46-48 | 3 | |
| α-helix | 49-54 | 6 | |
Chain H: 1 helix, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 59-121 | 63 | |
Chain K: 8 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 2-26 | 25 | |
| α-helix | 36-59 | 24 | |
| α-helix | 65-78 | 14 | |
| α-helix | 85-95 | 11 | |
| α-helix | 99-100 | 2 | |
| α-helix | 105-112 | 8 | |
| α-helix | 115-117 | 3 | |
| α-helix | 119-144 | 26 | |
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 TOM40 homolog | B, I | protein | 361 | Homo sapiens | O96008 (AlphaFold model) |
| Mitochondrial import receptor subunit TOM22 homolog | C, H | protein | 142 | Homo sapiens | Q9NS69 (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 |
| Mitochondrial import receptor subunit TOM20 homolog | K | protein | 145 | Homo sapiens | Q15388 |
Sequence of entity 1 (A, F), FASTA
>8XVA_1 Mitochondrial import receptor subunit TOM6 homolog (chains A, F)
MASSTVPVSAAGSANETPEIPDNVGDWLRGVYRFATDRNDFRRNLILNLGLFAAGVWLAR
NLSDIDLMAPQPGV
Sequence of entity 2 (B, I), FASTA
>8XVA_2 Mitochondrial import receptor subunit TOM40 homolog (chains B, I)
MGNVLAASSPPAGPPPPPAPALVGLPPPPPSPPGFTLPPLGGSLGAGTSTSRSSERTPGA
ATASASGAAEDGACGCLPNPGTFEECHRKCKELFPIQMEGVKLTVNKGLSNHFQVNHTVA
LSTIGESNYHFGVTYVGTKQLSPTEAFPVLVGDMDNSGSLNAQVIHQLGPGLRSKMAIQT
QQSKFVNWQVDGEYRGSDFTAAVTLGNPDVLVGSGILVAHYLQSITPCLALGGELVYHRR
PGEEGTVMSLAGKYTLNNWLATVTLGQAGMHATYYHKASDQLQVGVEFEASTRMQDTSVS
FGYQLDLPKANLLFKGSVDSNWIVGATLEKKLPPLPLTLALGAFLNHRKNKFQCGFGLTI
G
Sequence of entity 3 (C, H), FASTA
>8XVA_3 Mitochondrial import receptor subunit TOM22 homolog (chains C, H)
MAAAVAAAGAGEPQSPDELLPKGDAEKPEEELEEDDDEELDETLSERLWGLTEMFPERVR
SAAGATFDLSLFVAQKMYRFSRAALWIGTTSFMILVLPVVFETEKLQMEQQQQLQQRQIL
LGPNTGLSGGMPGALPSLPGKI
Sequence of entity 4 (D, E), FASTA
>8XVA_4 Mitochondrial import receptor subunit TOM5 homolog (chains D, E)
MFRIEGLAPKLDPEEMKRKMREDVISSIRNFLIYVALLRVTPFILKKLDSI
Sequence of entity 5 (G, J), FASTA
>8XVA_5 Mitochondrial import receptor subunit TOM7 homolog (chains G, J)
MVKLSKEAKQRLQQLFKGSQFAIRWGFIPLVIYLGFKRGADPGMPEPTVLSLLWG
Sequence of entity 6 (K), FASTA
>8XVA_6 Mitochondrial import receptor subunit TOM20 homolog (chains K)
MVGRNSAIAAGVCGALFIGYCIYFDRKRRSDPNFKNRLRERRKKQKLAKERAGLSKLPDL
KDAEAVQKFFLEEIQLGEELLAQGEYEKGVDHLTNAIAVCGQPQQLLQVLQQTLPPPVFQ
MLLTKLPTISQRIVSAQSLAEDDVE
Primary citation
Structure of the intact Tom20 receptor in the human translocase of the outer membrane complex. Su, J., Tian, X., Wang, Z. et al. PNAS Nexus (2024) 3:pgae269-pgae269. DOI 10.1093/pnasnexus/pgae269 · PubMed
Other PDB entries of the same protein (UniProt Q96B49 (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)
- 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
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