SMTL ID : 9eij.1

Import stalled PINK1 TOM complex, extended TOM20 helix class

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 3.30 Å

Oligo State

hetero-1-2-2-3-2-2-2-1-mer

Ligands

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

PC1.1: 8 residues within 4Å: Chain B: Y.78 Chain C: L.262, R.263 Chain D: Y.194, G.196, S.197, F.199, V.203 9 PLIP interactions: 5 interactions with chain D, 3 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: D:F.199, D:V.203, C:L.262, B:Y.78 Hydrogen bonds: D:Y.194, D:S.197, D:S.197 Salt bridges: C:R.263, C:R.263 PC1.2: 14 residues within 4Å: Chain D: T.297, Y.303, S.320, N.321, W.322, R.348 Chain I: R.38, R.43, N.44, L.47 Chain K: F.80, A.84, S.91, V.96 6 PLIP interactions: 1 interactions with chain I, 3 interactions with chain K, 2 interactions with chain D Salt bridges: I:R.43, D:R.348 Hydrophobic interactions: K:F.80, K:F.80, K:V.96, D:W.322 PC1.3: 12 residues within 4Å: Chain E: T.297, S.320, N.321, W.322, R.348 Chain J: F.80 Chain L: R.38, R.43, N.44, L.47, N.48, L.51 6 PLIP interactions: 1 interactions with chain J, 3 interactions with chain L, 2 interactions with chain E Hydrophobic interactions: J:F.80, E:W.322 Salt bridges: L:R.38, L:R.43, L:R.43, E:R.348 PC1.4: 10 residues within 4Å: Chain D: K.184, F.185, W.188, P.208, D.209, V.210 Chain H: F.16, Q.20, I.23 Chain O: R.119 12 PLIP interactions: 4 interactions with chain H, 1 interactions with chain A, 6 interactions with chain D, 1 interactions with chain O Hydrophobic interactions: H:F.16, H:F.16, H:I.23, D:F.185, D:W.188, D:W.188, D:V.210 Hydrogen bonds: H:Q.20, D:D.209, D:V.210, O:R.119 Salt bridges: A:E.64 PC1.5: 8 residues within 4Å: Chain D: F.131, D.155, N.156 Chain H: R.24, W.25 Chain J: Y.78, R.82 Ligands: PC1.8 8 PLIP interactions: 4 interactions with chain H, 2 interactions with chain D, 2 interactions with chain J Hydrophobic interactions: H:W.25, H:W.25, H:W.25, D:F.131, D:F.131 Salt bridges: H:R.24, J:R.82, J:R.82 PC1.6: 7 residues within 4Å: Chain D: Y.254, L.256, N.257, W.259, V.263 Chain I: F.52, R.60 9 PLIP interactions: 3 interactions with chain I, 6 interactions with chain D Hydrophobic interactions: I:F.52, D:Y.254, D:Y.254, D:Y.254, D:V.263 Salt bridges: I:R.60, I:R.60 Hydrogen bonds: D:N.257, D:W.259 PC1.7: 21 residues within 4Å: Chain D: V.101, A.326, T.327, L.328, K.330, L.332, L.339, L.341, G.342, F.356, L.358 Chain E: K.330, L.332, L.339, L.358 Chain J: M.93, I.94, P.98, E.102, K.105 Chain K: P.98 13 PLIP interactions: 2 interactions with chain J, 7 interactions with chain D, 3 interactions with chain E, 1 interactions with chain K Hydrophobic interactions: J:I.94, D:V.101, D:L.328, D:L.328, D:L.339, D:F.356, D:L.358, E:K.330, E:L.358, K:P.98 Salt bridges: J:K.105, D:K.330, E:K.330 PC1.8: 14 residues within 4Å: Chain D: L.103, E.126, S.127, Y.129, N.156 Chain H: L.53, W.54 Chain J: R.82, L.85, W.86, T.89, F.92, L.97 Ligands: PC1.5 12 PLIP interactions: 8 interactions with chain J, 4 interactions with chain D Hydrophobic interactions: J:L.85, J:T.89, J:F.92, J:F.92, J:L.97, D:L.103, D:Y.129 Salt bridges: J:R.82, J:R.82, D:E.126 pi-Cation interactions: J:W.86 Hydrogen bonds: D:N.156 PC1.9: 12 residues within 4Å: Chain D: N.350 Chain E: E.126, S.127, Y.129, N.156 Chain K: R.82, L.85, W.86, T.89, F.101 Chain M: L.53, W.54 9 PLIP interactions: 3 interactions with chain E, 5 interactions with chain K, 1 interactions with chain M Hydrophobic interactions: E:Y.129, K:T.89, K:F.101, M:W.54 Hydrogen bonds: E:N.156 Salt bridges: E:E.126, K:R.82 pi-Cation interactions: K:W.86, K:W.86

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: A
Non-selective voltage-gated ion channel VDAC2: BC
Mitochondrial import receptor subunit TOM40 homolog: DE
Mitochondrial import receptor subunit TOM5 homolog: FGN
Mitochondrial import receptor subunit TOM7 homolog: HM
Mitochondrial import receptor subunit TOM6 homolog: IL
Mitochondrial import receptor subunit TOM22 homolog: JK
Serine/threonine-protein kinase PINK1, mitochondrial: O

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

B
E

C
F

D
I

E
J

F
K

G
L

N
Z

H
N

M
X

I
P

L
V

J
R

K
T

O
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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