SMTL ID : 8b4i.1

Cryo-EM structure of the Neurospora crassa TOM core complex at 3.3 angstrom

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

8 x DU0: 2-[2-[(1~{S},2~{S},4~{S},5'~{R},6~{R},7~{S},8~{R},9~{S},12~{S},13~{R},16~{S})-5',7,9,13-tetramethylspiro[5-oxapentacyclo[10.8.0.0^{2,9}.0^{4,8}.0^{13,18}]icos-18-ene-6,2'-oxane]-16-yl]oxyethyl]propane-1,3-diol(Non-covalent)

DU0.1: 8 residues within 4Å: Chain A: I.286, S.288, K.289, G.290, V.316 Chain G: R.37, F.41 Ligands: DU0.4 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain G Hydrophobic interactions: A:I.286, A:V.316, G:F.41 DU0.3: 8 residues within 4Å: Chain B: I.286, S.288, K.289, G.290, V.316 Chain H: R.37, F.41 Ligands: DU0.7 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain H Hydrophobic interactions: B:I.286, B:V.316, H:F.41, H:F.41 DU0.4: 7 residues within 4Å: Chain A: H.315 Chain C: F.81, R.84, A.88, S.92 Ligands: DU0.1, DU0.6 5 PLIP interactions: 1 interactions with chain A, 4 interactions with chain C Hydrophobic interactions: A:H.315, C:F.81, C:F.81, C:F.81, C:A.88 DU0.5: 12 residues within 4Å: Chain B: L.300, A.303, V.305, I.328 Chain C: G.93, L.94, V.98, A.101, I.102, A.105, N.109 Chain J: L.52 9 PLIP interactions: 5 interactions with chain C, 3 interactions with chain B, 1 interactions with chain J Hydrophobic interactions: C:L.94, C:V.98, C:I.102, C:A.105, B:L.300, B:A.303, B:I.328, J:L.52 Hydrogen bonds: C:N.109 DU0.6: 7 residues within 4Å: Chain C: S.92, G.93, I.96, G.97, F.100, A.101 Ligands: DU0.4 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:I.96, C:F.100, C:A.101 DU0.7: 7 residues within 4Å: Chain B: H.315 Chain D: F.81, R.84, A.88, S.92 Ligands: DU0.3, DU0.9 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain D Hydrophobic interactions: B:H.315, D:F.81, D:F.81, D:A.88 DU0.8: 12 residues within 4Å: Chain A: L.300, A.303, V.305, I.328 Chain D: G.93, L.94, V.98, A.101, I.102, A.105, N.109 Chain I: L.52 10 PLIP interactions: 4 interactions with chain A, 5 interactions with chain D, 1 interactions with chain I Hydrophobic interactions: A:L.300, A:L.300, A:A.303, A:I.328, D:L.94, D:V.98, D:I.102, D:A.105, I:L.52 Hydrogen bonds: D:N.109 DU0.9: 7 residues within 4Å: Chain D: V.89, S.92, G.93, I.96, G.97, F.100 Ligands: DU0.7 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:V.89, D:I.96, D:F.100

1 x PLC: DIUNDECYL PHOSPHATIDYL CHOLINE(Non-covalent)

PLC.2: 23 residues within 4Å: Chain A: L.65, R.66, M.87, L.296, K.298, L.300, F.309, M.324, V.326 Chain B: R.66, A.67, L.296, K.298, L.307, F.309, M.324, V.326 Chain C: V.98, E.106 Chain D: L.94, V.98, I.102, E.106 14 PLIP interactions: 3 interactions with chain D, 4 interactions with chain B, 5 interactions with chain A, 2 interactions with chain C Hydrophobic interactions: D:L.94, D:V.98, B:A.67, B:F.309, B:V.326, A:L.65, A:L.296, A:F.309, A:V.326, C:V.98 Salt bridges: D:E.106, B:K.298, A:K.298, C:E.106

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ornelas, P. et al., Two conformations of the Tom20 preprotein receptor in the TOM holo complex. Proc.Natl.Acad.Sci.USA (2023)

Release Date

2023-08-09

Peptides

Mitochondrial import receptor subunit Tom40: AB
Mitochondrial import receptor subunit Tom22: CD
Translocase of outer mitochondrial membrane subunit 5: EF
TOM6: GH
TOM7: IJ

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

I
I

J
J

Membrane

We predict this structure to be a membrane protein.
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Mitochondrial import receptor subunit Tom40

Mitochondrial import receptor subunit Tom22

Translocase of outer mitochondrial membrane subunit 5

TOM6

TOM7

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