SMTL ID : 9eih.1

Import stalled PINK1 TOM complex

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 3.10 Å

Oligo State

hetero-2-2-4-4-4-4-4-2-mer

Ligands

17 x PC1: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE(Non-covalent)

PC1.1: 11 residues within 4Å: Chain C: V.38, L.40, V.65, L.262, R.263, L.288, L.290 Chain F: Y.194, S.197, F.199 Chain I: R.39 Ligand excluded by PLIP PC1.2: 10 residues within 4Å: Chain D: L.262, R.263 Chain G: Y.194, F.199, A.201, Y.221 Chain J: I.28, V.35, R.39 Ligands: PC1.6 Ligand excluded by PLIP PC1.3: 10 residues within 4Å: Chain E: F.301, S.320, W.322, R.348 Chain O: F.80 Chain S: R.38, R.43, N.44, L.47, L.51 Ligand excluded by PLIP PC1.4: 12 residues within 4Å: Chain F: T.297, S.320, N.321, W.322, R.348 Chain M: R.38, R.43, N.44, L.47, L.51 Chain Q: S.91, F.92 Ligand excluded by PLIP PC1.5: 15 residues within 4Å: Chain G: T.297, V.318, S.320, N.321, W.322, R.348 Chain N: R.38, R.43, N.44, L.47 Chain R: F.80, A.84, I.87, S.91, V.96 Ligand excluded by PLIP PC1.6: 12 residues within 4Å: Chain G: S.174, K.184, F.185, V.190, V.203, P.208, D.209, V.210 Chain L: F.16, Q.20 Chain Z: R.119 Ligands: PC1.2 Ligand excluded by PLIP PC1.7: 24 residues within 4Å: Chain G: V.101, A.326, T.327, L.328, K.330, L.339, L.341, F.356, L.358 Chain H: V.101, K.330, L.332, L.341, A.343, L.358 Chain P: M.93, I.94, P.98, E.102, K.105 Chain R: M.93, L.97, P.98, F.101 Ligand excluded by PLIP PC1.8: 9 residues within 4Å: Chain A: E.64 Chain F: F.185, W.188, P.208, D.209, V.210 Chain K: F.16, Q.20 Chain Y: R.119 Ligand excluded by PLIP PC1.9: 13 residues within 4Å: Chain G: F.131, M.154, D.155, N.156, S.157, G.158 Chain L: R.24, W.25, F.36, V.49 Chain P: Y.78, R.82 Ligands: PC1.14 Ligand excluded by PLIP PC1.10: 14 residues within 4Å: Chain F: L.231, L.250, A.251, G.252, K.253, Y.254, L.256, N.257, W.259, A.261, V.263, L.265, Y.274 Chain M: R.60 Ligand excluded by PLIP PC1.11: 11 residues within 4Å: Chain G: L.231, L.250, G.252, Y.254, N.257, W.259, A.261, V.263, Y.274 Chain N: F.52, R.60 Ligand excluded by PLIP PC1.12: 17 residues within 4Å: Chain F: H.117, S.127, Y.129, F.131, N.156 Chain K: V.49, L.52, L.53, W.54 Chain O: R.82, L.85, W.86, T.89, F.101 Chain Y: R.66, F.69 Ligands: PC1.13 Ligand excluded by PLIP PC1.13: 13 residues within 4Å: Chain F: F.131, M.154, N.156, S.157 Chain K: R.24, W.25, I.28, P.29, I.32, Y.33 Chain O: Y.78, R.82 Ligands: PC1.12 Ligand excluded by PLIP PC1.14: 16 residues within 4Å: Chain G: L.103, H.117, S.127, Y.129, F.131, N.156 Chain L: V.49, L.52, L.53, W.54 Chain P: R.82, L.85, W.86, T.89, F.92 Ligands: PC1.9 Ligand excluded by PLIP PC1.15: 16 residues within 4Å: Chain E: V.101, L.332, A.343, L.358 Chain F: N.311, L.328, K.330, L.332, L.341, A.343 Chain O: M.93, P.98, K.105 Chain Q: M.93, P.98, K.105 Ligand excluded by PLIP PC1.16: 13 residues within 4Å: Chain E: E.126, S.127, Y.129, N.156 Chain F: N.350 Chain Q: R.82, L.85, W.86, T.89 Chain U: V.49, L.52, L.53, W.54 Ligand excluded by PLIP PC1.17: 10 residues within 4Å: Chain H: T.297, S.320, N.321, W.322, R.348 Chain T: R.38, R.43, N.44, L.47, L.51 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Callegari, S. et al., Structure of human PINK1 at a mitochondrial TOM-VDAC array. Science (2025)

Release Date

2025-03-12

Peptides

Mitochondrial import receptor subunit TOM20 homolog: AB
Non-selective voltage-gated ion channel VDAC2: CD
Mitochondrial import receptor subunit TOM40 homolog: EFGH
Mitochondrial import receptor subunit TOM5 homolog: IJWX
Mitochondrial import receptor subunit TOM7 homolog: KLUV
Mitochondrial import receptor subunit TOM6 homolog: MNST
Mitochondrial import receptor subunit TOM22 homolog: OPQR
Serine/threonine-protein kinase PINK1, mitochondrial: YZ

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

C
E

D
F

E
G

F
H

G
I

H
J

I
K

J
L

W
Y

X
Z

K
M

L
N

U
W

V
X

M
O

N
P

S
U

T
V

O
Q

P
R

Q
S

R
T

Y
A

Z
B

Membrane

We predict this structure to be a membrane protein.
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Mitochondrial import receptor subunit TOM20 homolog

Non-selective voltage-gated ion channel VDAC2

Mitochondrial import receptor subunit TOM40 homolog

Mitochondrial import receptor subunit TOM5 homolog

Mitochondrial import receptor subunit TOM7 homolog

Mitochondrial import receptor subunit TOM6 homolog

Mitochondrial import receptor subunit TOM22 homolog

Serine/threonine-protein kinase PINK1, mitochondrial

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