SMTL ID : 6ucu.1

Cryo-EM structure of the mitochondrial TOM complex from yeast (dimer)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-2-2-2-2-mer

Ligands

60 x LMT: DODECYL-BETA-D-MALTOSIDE(Non-covalent)(Non-functional Binders)

LMT.1: 12 residues within 4Å: Chain A: I.303, A.305, Y.307, G.316, T.317 Chain B: L.109, L.113 Chain D: F.48, L.57, P.59 Ligands: LMT.18, LMT.19 Ligand excluded by PLIP LMT.2: 10 residues within 4Å: Chain A: T.301, I.303, L.318, D.319, S.320, F.347 Chain D: L.37, F.41 Ligands: LMT.3, LMT.12 Ligand excluded by PLIP LMT.3: 11 residues within 4Å: Chain A: L.318, G.322, H.346, F.347 Chain B: N.97, T.101, L.102, T.105 Ligands: LMT.2, LMT.12, LMT.19 Ligand excluded by PLIP LMT.4: 9 residues within 4Å: Chain A: Y.232, T.234, G.247, Q.248, L.249, L.255 Ligands: LMT.10, LMT.13, LMT.24 Ligand excluded by PLIP LMT.5: 6 residues within 4Å: Chain A: T.182, F.193, A.197, Y.217 Chain C: Q.18 Ligands: LMT.22 Ligand excluded by PLIP LMT.6: 7 residues within 4Å: Chain A: Y.171, V.178, V.180, A.199 Ligands: LMT.7, LMT.22, LMT.23 Ligand excluded by PLIP LMT.7: 7 residues within 4Å: Chain A: N.149, Q.169, Y.171, V.178, V.180 Ligands: LMT.6, LMT.8 Ligand excluded by PLIP LMT.8: 8 residues within 4Å: Chain A: W.145, N.149, S.151, L.167, E.168, Q.169 Ligands: LMT.7, LMT.9 Ligand excluded by PLIP LMT.9: 7 residues within 4Å: Chain A: L.125, Y.143, W.145, S.151, V.153 Ligands: LMT.8, LMT.27 Ligand excluded by PLIP LMT.10: 6 residues within 4Å: Chain A: L.209, T.234, Y.236, W.243 Ligands: LMT.4, LMT.11 Ligand excluded by PLIP LMT.11: 7 residues within 4Å: Chain A: W.243, F.245, L.259 Chain D: V.46, Q.50 Ligands: LMT.10, LMT.25 Ligand excluded by PLIP LMT.12: 3 residues within 4Å: Chain B: L.98 Ligands: LMT.2, LMT.3 Ligand excluded by PLIP LMT.13: 4 residues within 4Å: Chain A: L.249, G.253 Ligands: LMT.4, LMT.24 Ligand excluded by PLIP LMT.14: 22 residues within 4Å: Chain A: L.328, R.330, F.340 Chain B: T.104, L.107, L.108, P.112, L.115, A.119, Q.122 Chain F: L.84, R.85, A.86, F.104, I.106, R.330, V.332, V.338, C.355, G.356, L.357 Ligands: LMT.31 Ligand excluded by PLIP LMT.15: 7 residues within 4Å: Chain A: L.88, F.359 Chain E: L.57, P.58 Chain G: T.103, L.107 Ligands: LMT.51 Ligand excluded by PLIP LMT.16: 12 residues within 4Å: Chain A: F.104, K.113, Y.114, N.133 Chain E: P.56 Chain G: G.96, N.97, A.99, W.100, T.103 Ligands: LMT.17, LMT.50 Ligand excluded by PLIP LMT.17: 11 residues within 4Å: Chain A: Y.114, F.116, I.131, D.132, L.135 Chain E: L.54, S.55 Ligands: LMT.16, LMT.29, LMT.30, LMT.50 Ligand excluded by PLIP LMT.18: 7 residues within 4Å: Chain B: G.110, S.114, I.117, Q.121 Ligands: LMT.1, LMT.19, LMT.21 Ligand excluded by PLIP LMT.19: 6 residues within 4Å: Chain B: A.106, G.110 Ligands: LMT.1, LMT.3, LMT.18, LMT.21 Ligand excluded by PLIP LMT.20: 8 residues within 4Å: Chain B: F.92, T.93, S.95, G.96, A.99 Ligands: LMT.33, LMT.34, LMT.57 Ligand excluded by PLIP LMT.21: 7 residues within 4Å: Chain B: A.106, L.107, V.111, S.114 Ligands: LMT.18, LMT.19, LMT.32 Ligand excluded by PLIP LMT.22: 11 residues within 4Å: Chain A: A.197, A.199, T.215, Y.217 Chain C: E.22, L.25, K.26, A.29 Ligands: LMT.5, LMT.6, LMT.23 Ligand excluded by PLIP LMT.23: 10 residues within 4Å: Chain A: F.176, A.199, F.201, L.213, T.215 Chain C: A.28, A.32, W.36 Ligands: LMT.6, LMT.22 Ligand excluded by PLIP LMT.24: 9 residues within 4Å: Chain A: L.255, A.257, L.275 Chain D: I.35, G.39, F.42 Ligands: LMT.4, LMT.13, LMT.25 Ligand excluded by PLIP LMT.25: 9 residues within 4Å: Chain D: V.43, V.46, A.47, Q.50, S.51, P.52 Ligands: LMT.11, LMT.24, LMT.26 Ligand excluded by PLIP LMT.26: 6 residues within 4Å: Chain D: A.44, A.47, F.48, S.51, P.52 Ligands: LMT.25 Ligand excluded by PLIP LMT.27: 8 residues within 4Å: Chain A: N.122, L.125, L.141 Chain E: F.35, L.39, H.43 Ligands: LMT.9, LMT.28 Ligand excluded by PLIP LMT.28: 6 residues within 4Å: Chain E: F.35, Y.38, L.39, A.42, H.43 Ligands: LMT.27 Ligand excluded by PLIP LMT.29: 5 residues within 4Å: Chain E: F.50, L.54 Ligands: LMT.17, LMT.30, LMT.50 Ligand excluded by PLIP LMT.30: 11 residues within 4Å: Chain A: F.116, I.131, L.135, V.137 Chain E: H.29, Y.30, I.33, P.34, L.37 Ligands: LMT.17, LMT.29 Ligand excluded by PLIP LMT.31: 22 residues within 4Å: Chain A: L.84, R.85, A.86, F.104, I.106, R.330, V.332, V.338, C.355, G.356, L.357 Chain F: L.328, R.330, F.340 Chain G: T.104, L.107, L.108, P.112, L.115, A.119, Q.122 Ligands: LMT.14 Ligand excluded by PLIP LMT.32: 7 residues within 4Å: Chain B: T.103, L.107 Chain F: L.88, F.359 Chain J: L.57, P.58 Ligands: LMT.21 Ligand excluded by PLIP LMT.33: 12 residues within 4Å: Chain B: G.96, N.97, A.99, W.100, T.103 Chain F: F.104, K.113, Y.114, N.133 Chain J: P.56 Ligands: LMT.20, LMT.34 Ligand excluded by PLIP LMT.34: 11 residues within 4Å: Chain F: Y.114, F.116, I.131, D.132, L.135 Chain J: L.54, S.55 Ligands: LMT.20, LMT.33, LMT.57, LMT.58 Ligand excluded by PLIP LMT.35: 12 residues within 4Å: Chain F: I.303, A.305, Y.307, G.316, T.317 Chain G: L.109, L.113 Chain I: F.48, L.57, P.59 Ligands: LMT.48, LMT.49 Ligand excluded by PLIP LMT.36: 10 residues within 4Å: Chain F: T.301, I.303, L.318, D.319, S.320, F.347 Chain I: L.37, F.41 Ligands: LMT.37, LMT.46 Ligand excluded by PLIP LMT.37: 11 residues within 4Å: Chain F: L.318, G.322, H.346, F.347 Chain G: N.97, T.101, L.102, T.105 Ligands: LMT.36, LMT.46, LMT.49 Ligand excluded by PLIP LMT.38: 9 residues within 4Å: Chain F: Y.232, T.234, G.247, Q.248, L.249, L.255 Ligands: LMT.44, LMT.47, LMT.54 Ligand excluded by PLIP LMT.39: 6 residues within 4Å: Chain F: T.182, F.193, A.197, Y.217 Chain H: Q.18 Ligands: LMT.52 Ligand excluded by PLIP LMT.40: 7 residues within 4Å: Chain F: Y.171, V.178, V.180, A.199 Ligands: LMT.41, LMT.52, LMT.53 Ligand excluded by PLIP LMT.41: 7 residues within 4Å: Chain F: N.149, Q.169, Y.171, V.178, V.180 Ligands: LMT.40, LMT.42 Ligand excluded by PLIP LMT.42: 8 residues within 4Å: Chain F: W.145, N.149, S.151, L.167, E.168, Q.169 Ligands: LMT.41, LMT.43 Ligand excluded by PLIP LMT.43: 7 residues within 4Å: Chain F: L.125, Y.143, W.145, S.151, V.153 Ligands: LMT.42, LMT.59 Ligand excluded by PLIP LMT.44: 6 residues within 4Å: Chain F: L.209, T.234, Y.236, W.243 Ligands: LMT.38, LMT.45 Ligand excluded by PLIP LMT.45: 7 residues within 4Å: Chain F: W.243, F.245, L.259 Chain I: V.46, Q.50 Ligands: LMT.44, LMT.55 Ligand excluded by PLIP LMT.46: 3 residues within 4Å: Chain G: L.98 Ligands: LMT.36, LMT.37 Ligand excluded by PLIP LMT.47: 4 residues within 4Å: Chain F: L.249, G.253 Ligands: LMT.38, LMT.54 Ligand excluded by PLIP LMT.48: 7 residues within 4Å: Chain G: G.110, S.114, I.117, Q.121 Ligands: LMT.35, LMT.49, LMT.51 Ligand excluded by PLIP LMT.49: 6 residues within 4Å: Chain G: A.106, G.110 Ligands: LMT.35, LMT.37, LMT.48, LMT.51 Ligand excluded by PLIP LMT.50: 8 residues within 4Å: Chain G: F.92, T.93, S.95, G.96, A.99 Ligands: LMT.16, LMT.17, LMT.29 Ligand excluded by PLIP LMT.51: 7 residues within 4Å: Chain G: A.106, L.107, V.111, S.114 Ligands: LMT.15, LMT.48, LMT.49 Ligand excluded by PLIP LMT.52: 11 residues within 4Å: Chain F: A.197, A.199, T.215, Y.217 Chain H: E.22, L.25, K.26, A.29 Ligands: LMT.39, LMT.40, LMT.53 Ligand excluded by PLIP LMT.53: 9 residues within 4Å: Chain F: F.176, A.199, F.201, L.213, T.215 Chain H: A.32, W.36 Ligands: LMT.40, LMT.52 Ligand excluded by PLIP LMT.54: 9 residues within 4Å: Chain F: L.255, A.257, L.275 Chain I: I.35, G.39, F.42 Ligands: LMT.38, LMT.47, LMT.55 Ligand excluded by PLIP LMT.55: 9 residues within 4Å: Chain I: V.43, V.46, A.47, Q.50, S.51, P.52 Ligands: LMT.45, LMT.54, LMT.56 Ligand excluded by PLIP LMT.56: 6 residues within 4Å: Chain I: A.44, A.47, F.48, S.51, P.52 Ligands: LMT.55 Ligand excluded by PLIP LMT.57: 5 residues within 4Å: Chain J: F.50, L.54 Ligands: LMT.20, LMT.34, LMT.58 Ligand excluded by PLIP LMT.58: 11 residues within 4Å: Chain F: F.116, I.131, L.135, V.137 Chain J: H.29, Y.30, I.33, P.34, L.37 Ligands: LMT.34, LMT.57 Ligand excluded by PLIP LMT.59: 8 residues within 4Å: Chain F: N.122, L.125, L.141 Chain J: F.35, L.39, H.43 Ligands: LMT.43, LMT.60 Ligand excluded by PLIP LMT.60: 6 residues within 4Å: Chain J: F.35, Y.38, L.39, A.42, H.43 Ligands: LMT.59 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tucker, K. et al., Cryo-EM structure of the mitochondrial protein-import channel TOM complex at near-atomic resolution. Nat.Struct.Mol.Biol. (2019)

Release Date

2019-11-06

Peptides

Mitochondrial import receptor subunit TOM40: AF
Mitochondrial import receptor subunit TOM22: BG
Mitochondrial import receptor subunit TOM5: CH
Mitochondrial import receptor subunit TOM6: DI
Mitochondrial import receptor subunit TOM7: EJ

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

F
I

B
B

G
J

C
C

H
K

D
D

I
L

E
E

J
M

Membrane

We predict this structure to be a membrane protein.
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Mitochondrial import receptor subunit TOM40

Mitochondrial import receptor subunit TOM22

Mitochondrial import receptor subunit TOM5

Mitochondrial import receptor subunit TOM6

Mitochondrial import receptor subunit TOM7

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