SMTL ID : 9eii.1

Import stalled PINK1 TOM complex, symmetry expanded

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 2.75 Å

Oligo State

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

Ligands

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

PC1.1: 24 residues within 4Å: Chain C: V.38, L.40, S.57, V.65, L.262, R.263, L.288, L.290 Chain D: Y.194, G.196, S.197, F.199, A.201, L.217, A.219, Y.221, Y.237 Chain F: R.21, I.28, F.31, L.32, V.35, A.36 Chain G: M.1 11 PLIP interactions: 4 interactions with chain C, 5 interactions with chain F, 2 interactions with chain D Hydrophobic interactions: C:L.40, C:V.65, C:L.290, C:L.290, F:F.31, F:L.32, F:L.32, F:V.35, F:A.36, D:A.201, D:L.217 PC1.2: 15 residues within 4Å: Chain D: T.297, F.301, Y.303, V.318, S.320, N.321, W.322, R.348 Chain H: R.38, R.43, N.44, L.47, L.51, A.54, W.57 8 PLIP interactions: 5 interactions with chain D, 3 interactions with chain H Hydrophobic interactions: D:F.301, D:F.301, D:Y.303, D:V.318, H:A.54, H:W.57 Hydrogen bonds: D:R.348 Salt bridges: H:R.43 PC1.3: 25 residues within 4Å: Chain D: T.327, L.328, K.330, L.332, P.333, L.339, L.341, A.343, L.358 Chain E: V.101, A.326, L.328, K.330, L.332, L.341, G.342, A.343, L.358 Chain I: M.93, K.105 Chain J: M.93, L.97, P.98, F.101, E.109 17 PLIP interactions: 7 interactions with chain J, 5 interactions with chain E, 1 interactions with chain I, 4 interactions with chain D Hydrophobic interactions: J:L.97, J:P.98, J:P.98, J:F.101, E:V.101, E:L.328, E:K.330, E:L.341, D:L.328, D:A.343, D:L.358 Salt bridges: J:K.105, J:K.105, J:E.109, E:K.330, I:K.105, D:K.330 PC1.4: 12 residues within 4Å: Chain D: L.250, Y.254, L.256, N.257, W.259, A.261, V.263, M.270, Y.274 Chain H: L.49, F.52, R.60 14 PLIP interactions: 5 interactions with chain H, 9 interactions with chain D Hydrophobic interactions: H:L.49, H:L.49, H:F.52, D:L.250, D:Y.254, D:Y.254, D:Y.254, D:V.263, D:Y.274, D:Y.274 Salt bridges: H:R.60, H:R.60 Hydrogen bonds: D:N.257, D:W.259 PC1.5: 13 residues within 4Å: Chain E: T.297, F.301, V.318, D.319, S.320, N.321, W.322, R.348 Chain K: R.38, R.43, N.44, L.51, L.58 9 PLIP interactions: 5 interactions with chain E, 4 interactions with chain K Hydrophobic interactions: E:F.301, E:F.301, E:F.301, E:V.318, K:L.51, K:L.51 Salt bridges: E:R.348, K:R.38, K:R.43 PC1.6: 12 residues within 4Å: Chain A: R.119 Chain D: H.166, M.176, K.184, F.185, W.188, P.208, D.209, V.210 Chain G: F.16, Q.20, I.23 9 PLIP interactions: 5 interactions with chain D, 3 interactions with chain G, 1 interactions with chain A Hydrophobic interactions: D:H.166, D:F.185, D:W.188, D:P.208, G:F.16, G:I.23 Hydrogen bonds: D:V.210, G:Q.20 Salt bridges: A:R.119 PC1.7: 12 residues within 4Å: Chain D: F.131, M.154, D.155, N.156, G.158 Chain G: R.24, W.25, I.32, Y.33 Chain I: Y.78, R.82 Ligands: PC1.8 9 PLIP interactions: 1 interactions with chain D, 5 interactions with chain G, 3 interactions with chain I Hydrophobic interactions: D:F.131, G:W.25, G:I.32, G:Y.33, G:Y.33 Salt bridges: G:R.24, I:R.82, I:R.82 Hydrogen bonds: I:Y.78 PC1.8: 17 residues within 4Å: Chain D: L.103, H.117, E.126, S.127, Y.129, F.131, N.156 Chain E: N.350 Chain G: V.49, L.52, L.53, W.54 Chain I: R.82, L.85, W.86, T.89 Ligands: PC1.7 12 PLIP interactions: 4 interactions with chain I, 3 interactions with chain G, 5 interactions with chain D Hydrophobic interactions: I:T.89, G:L.52, G:L.53, G:W.54, D:L.103, D:Y.129, D:F.131 Salt bridges: I:R.82, I:R.82, D:E.126 pi-Cation interactions: I: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 J: R.82, L.85, W.86, T.89, F.92 Chain L: L.53, W.54 14 PLIP interactions: 7 interactions with chain J, 3 interactions with chain L, 4 interactions with chain E Hydrophobic interactions: J:W.86, J:T.89, J:F.92, L:L.53, L:W.54, L:W.54, E:Y.129, E:Y.129 Salt bridges: J:R.82, J:R.82, E:E.126 pi-Cation interactions: J:W.86, J:W.86 Hydrogen bonds: E:N.156

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

Serine/threonine-protein kinase PINK1, mitochondrial: A
Mitochondrial import receptor subunit TOM20 homolog: B
Voltage-dependent anion-selective channel protein 2: C
Mitochondrial import receptor subunit TOM40 homolog: DE
Mitochondrial import receptor subunit TOM5 homolog: FM
Mitochondrial import receptor subunit TOM7 homolog: GL
Mitochondrial import receptor subunit TOM6 homolog: HK
Mitochondrial import receptor subunit TOM22 homolog: IJ

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
D

C
F

D
I

E
J

F
L

M
Z

G
N

L
X

H
P

K
V

I
R

J
T

Membrane

We predict this structure to be a membrane protein.
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Serine/threonine-protein kinase PINK1, mitochondrial

Mitochondrial import receptor subunit TOM20 homolog

Voltage-dependent anion-selective channel protein 2

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

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