6JNF

Cryo-EM structure of the translocator of the outer mitochondrial membrane


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.81 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structure of the mitochondrial import gate reveals distinct preprotein paths.

Araiso, Y.Tsutsumi, A.Qiu, J.Imai, K.Shiota, T.Song, J.Lindau, C.Wenz, L.S.Sakaue, H.Yunoki, K.Kawano, S.Suzuki, J.Wischnewski, M.Schutze, C.Ariyama, H.Ando, T.Becker, T.Lithgow, T.Wiedemann, N.Pfanner, N.Kikkawa, M.Endo, T.

(2019) Nature 575: 395-401

  • DOI: 10.1038/s41586-019-1680-7
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • The translocase of the outer mitochondrial membrane (TOM) is the main entry gate for proteins 1-4 . Here we use cryo-electron microscopy to report the structure of the yeast TOM core complex 5-9 at 3.8-Å resolution. The structu ...

    The translocase of the outer mitochondrial membrane (TOM) is the main entry gate for proteins 1-4 . Here we use cryo-electron microscopy to report the structure of the yeast TOM core complex 5-9 at 3.8-Å resolution. The structure reveals the high-resolution architecture of the translocator consisting of two Tom40 β-barrel channels and α-helical transmembrane subunits, providing insight into critical features that are conserved in all eukaryotes 1-3 . Each Tom40 β-barrel is surrounded by small TOM subunits, and tethered by two Tom22 subunits and one phospholipid. The N-terminal extension of Tom40 forms a helix inside the channel; mutational analysis reveals its dual role in early and late steps in the biogenesis of intermembrane-space proteins in cooperation with Tom5. Each Tom40 channel possesses two precursor exit sites. Tom22, Tom40 and Tom7 guide presequence-containing preproteins to the exit in the middle of the dimer, whereas Tom5 and the Tom40 N extension guide preproteins lacking a presequence to the exit at the periphery of the dimer.


    Organizational Affiliation

    Institute for Protein Dynamics, Kyoto Sangyo University, Kyoto, Japan. tendo@cc.kyoto-su.ac.jp.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Mitochondrial import receptor subunit TOM40
A, F
387Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: TOM40ISP42MOM38YMR203WYM8325.04
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: BETA-BARREL
Sub Group: 
Beta-Barrel Membrane Proteins: Mitochondrial Outer Membrane
Protein: 
translocase of the outer mitochondrial membrane (TOM) complex
Find proteins for P23644 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P23644

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Mitochondrial import receptor subunit TOM7
B, G
60Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: TOM7MOM7YNL070WN2378
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: BETA-BARREL
Sub Group: 
Beta-Barrel Membrane Proteins: Mitochondrial Outer Membrane
Protein: 
translocase of the outer mitochondrial membrane (TOM) complex
Find proteins for P53507 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P53507

Find similar proteins by: Sequence  |  Structure

Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Mitochondrial import receptor subunit TOM22
C, H
166Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: TOM22MAS17MAS22MOM22YNL131WN1217N1862
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: BETA-BARREL
Sub Group: 
Beta-Barrel Membrane Proteins: Mitochondrial Outer Membrane
Protein: 
translocase of the outer mitochondrial membrane (TOM) complex
Find proteins for P49334 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P49334

Find similar proteins by: Sequence  |  Structure

Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Mitochondrial import receptor subunit TOM5
D, I
50Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: TOM5MOM8AYPR133W-A
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: BETA-BARREL
Sub Group: 
Beta-Barrel Membrane Proteins: Mitochondrial Outer Membrane
Protein: 
translocase of the outer mitochondrial membrane (TOM) complex
Find proteins for P80967 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P80967

Find similar proteins by: Sequence  |  Structure

Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
Mitochondrial import receptor subunit TOM6
E, J
61Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: TOM6ISP6YOR045W
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: BETA-BARREL
Sub Group: 
Beta-Barrel Membrane Proteins: Mitochondrial Outer Membrane
Protein: 
translocase of the outer mitochondrial membrane (TOM) complex
Find proteins for P33448 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P33448
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
46E
Query on 46E

Download CCD File 
A
(2R)-3-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-(tetradecanoyloxy)propyl tetradecanoate
C33 H66 N O8 P
NEZDNQCXEZDCBI-WJOKGBTCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.81 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of ScienceJapan15H05705
Japan Society for the Promotion of ScienceJapan2222703
Japan Science and TechnologyJapanJPMJCR12M1
Japan Society for the Promotion of ScienceJapan15J07687
Japan Agency for Medical Research and Development (AMED)JapanJP19am01011115

Revision History 

  • Version 1.0: 2019-10-16
    Type: Initial release
  • Version 1.1: 2019-11-13
    Changes: Database references
  • Version 1.2: 2019-11-27
    Changes: Database references