7VBY: Tom core complex with Tom20 and Tom22 subunits
Tom core complex with Tom20 and Tom22 subunits. Determined by electron microscopy at 2.54 Å resolution. Released 7 Sept 2022.
- Method
- Electron microscopy
- Resolution
- 2.54 Å
- Organism
- Homo sapiens
- Chains
- 10
- Atoms
- 8,207
- Mol. weight
- 262.25 kDa
- Ligands
- PC1, UND
- Released
- 7 Sept 2022
Explore 7VBY in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
7VBY contains 26 α-helices and 43 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 | 41-60 | 20 | |
Chain B: 4 helices, 22 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 77-79 | 3 | |
| α-helix | 88-91 | 4 | |
| α-helix | 95-97 | 3 | |
| β-strand | 100-110 | 11 | 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 | 149-155 | 7 | 1 |
| β-strand | 160-166 | 7 | 1 |
| β-strand | 174-181 | 8 | 1 |
| β-strand | 184-190 | 7 | 1 |
| β-strand | 193-194 | 2 | 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 | 269-279 | 11 | 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 | 323-332 | 10 | 1 |
| β-strand | 337-346 | 10 | 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 | 16-47 | 32 | |
Chain F: 2 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 26-36 | 11 | |
| 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 |
|---|
| Translocase of the Outer Membrane | B, I | protein | 828 | Homo sapiens | O96008 (AlphaFold model), Q15388 (AlphaFold model) |
| 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 |
| Mitochondrial import receptor subunit TOM22 homolog | C, H | protein | 142 | Homo sapiens | Q9NS69 |
Sequence of entity 1 (B, I), FASTA
>7VBY_1 Translocase of the Outer Membrane (chains B, I)
MGNVLAASSPPAGPPPPPAPALVGLPPPPPSPPGFTLPPLGGSLGAGTSTSRSSERTPGA
ATASASGAAEDGACGCLPNPGTFEECHRKCKELFPIQMEGVKLTVNKGLSNHFQVNHTVA
LSTIGESNYHFGVTYVGTKQLSPTEAFPVLVGDMDNSGSLNAQVIHQLGPGLRSKMAIQT
QQSKFVNWQVDGEYRGSDFTAAVTLGNPDVLVGSGILVAHYLQSITPCLALGGELVYHRR
PGEEGTVMSLAGKYTLNNWLATVTLGQAGMHATYYHKASDQLQVGVEFEASTRMQDTSVS
FGYQLDLPKANLLFKGSVDSNWIVGATLEKKLPPLPLTLALGAFLNHRKNKFQCGFGLTI
GMVGRNSAIAAGVCGALFIGYCIYFDRKRRSDPNFKNRLRERRKKQKLAKERAGLSKLPD
LKDAEAVQKFFLEEIQLGEELLAQGEYEKGVDHLTNAIAVCGQPQQLLQVLQQTLPPPVF
QMLLTKLPTISQRIVSAQSLAEDDVEMAAAVAAAGAGEPQSPDELLPKGDAEKPEEELEE
DDDEELDETLSERLWGLTEMFPERVRSAAGATFDLSLFVAQKMYRFSRAALWIGTTSFMI
LVLPVVFETEKLQMEQQQQLQQRQILLGPNTGLSGGMPGALPSLPGKIMFRIEGLAPKLD
PEEMKRKMREDVISSIRNFLIYVALLRVTPFILKKLDSIMASSTVPVSAAGSANETPEIP
DNVGDWLRGVYRFATDRNDFRRNLILNLGLFAAGVWLARNLSDIDLMAPQPGVMVKLSKE
AKQRLQQLFKGSQFAIRWGFIPLVIYLGFKRGADPGMPEPTVLSLLWG
Sequence of entity 2 (A, F), FASTA
>7VBY_2 Mitochondrial import receptor subunit TOM6 homolog (chains A, F)
MASSTVPVSAAGSANETPEIPDNVGDWLRGVYRFATDRNDFRRNLILNLGLFAAGVWLAR
NLSDIDLMAPQPGV
Sequence of entity 3 (D, E), FASTA
>7VBY_3 Mitochondrial import receptor subunit TOM5 homolog (chains D, E)
MFRIEGLAPKLDPEEMKRKMREDVISSIRNFLIYVALLRVTPFILKKLDSI
Sequence of entity 4 (G, J), FASTA
>7VBY_4 Mitochondrial import receptor subunit TOM7 homolog (chains G, J)
MVKLSKEAKQRLQQLFKGSQFAIRWGFIPLVIYLGFKRGADPGMPEPTVLSLLWG
Sequence of entity 5 (C, H), FASTA
>7VBY_5 Mitochondrial import receptor subunit TOM22 homolog (chains C, H)
MAAAVAAAGAGEPQSPDELLPKGDAEKPEEELEEDDDEELDETLSERLWGLTEMFPERVR
SAAGATFDLSLFVAQKMYRFSRAALWIGTTSFMILVLPVVFETEKLQMEQQQQLQQRQIL
LGPNTGLSGGMPGALPSLPGKI
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| PC1 | 1,2-diacyl-sn-glycero-3-phosphocholine | C44 H88 N O8 P | 11 |
| UND | Undecane | C11 H24 | 12 |
Primary citation
Tom core complex with Tom20 and Tom22 subunits. Liu, D.S., Sui, S.F. 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
- 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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