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 1.1 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 --: --

  • DOI: 10.1038/s41586-019-1680-7

  • PubMed Abstract: 
  • The translocase of the outer mitochondrial membrane (TOM) is the main entry gate for proteins <sup>1-4 </sup>. Here we use cryo-electron microscopy to report the structure of the yeast TOM core complex <sup>5-9 </sup> 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 conserved in all eukaryotes 1-3 . Each Tom40 β-barrel is surrounded by small Tom subunits, and tethered by two Tom22 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 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 midst of the dimer, whereas Tom5 and the Tom40 N-extension guide presequence-less preproteins to the exit at the dimer periphery.


    Organizational Affiliation

    Institute for Protein Dynamics, Kyoto Sangyo University, Kamigamo-motoyama, Kita-ku, Kyoto, Japan. tendo@cc.kyoto-su.ac.jp.,Nano Life Science Institute (WPI-Nano LSI), Kanazawa University, Kakuma-machi, Kanazawa, Japan.,Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, Freiburg, Germany.,Department of Clinical Laboratory Science, Division of Health Sciences, Graduate School of Medical Science, Kanazawa University, 5-11-80 Kodatsuno, Kanazawa, Ishikawa, Japan.,Molecular Profiling Research Center for Drug Discovery (molprof), National Institute of Advanced Industrial Science and Technology (AIST), 2-4-7 Aomi, Koto-ku, Tokyo, Japan.,Institute for Protein Dynamics, Kyoto Sangyo University, Kamigamo-motoyama, Kita-ku, Kyoto, Japan.,Sanofi Deutschland GmbH, Frankfurt am Main, Germany.,Organization for Promotion of Tenure Track, University of Miyazaki, 1-1 Gakuenkibanadai-nishi, Miyazaki, Japan.,Faculty of Life Sciences, Kyoto Sangyo University, Kamigamo-motoyama, Kita-ku, Kyoto, Japan. tendo@cc.kyoto-su.ac.jp.,Institute of Molecular Precision Medicine and Hunan Key Laboratory of Molecular Precision Medicine, Xiangya Hospital, Central South University, Changsha, Hunan, China.,Faculty of Life Sciences, Kyoto Sangyo University, Kamigamo-motoyama, Kita-ku, Kyoto, Japan.,Spemann Graduate School of Biology and Medicine, University of Freiburg, Freiburg, Germany.,Infection and Immunity Program, Biomedicine Discovery Institute and Department of Microbiology, Monash University, Melbourne, Victoria, Australia.,Department of Cell Biology and Anatomy, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, Japan.,Swiss Federal Institute of Technology (EPFL), Lausanne, Switzerland.,Faculty of Biology, University of Freiburg, Freiburg, Germany.,CIBSS Centre for Integrative Biological Signalling Studies, University of Freiburg, Freiburg, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Mitochondrial import receptor subunit TOM40
A, F
387Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: TOM40 (ISP42, MOM38)
Find proteins for P23644 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P23644
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Mitochondrial import receptor subunit TOM7
B, G
60Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: TOM7 (MOM7)
Find proteins for P53507 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P53507
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Mitochondrial import receptor subunit TOM22
C, H
166Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: TOM22 (MAS17, MAS22, MOM22)
Find proteins for P49334 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P49334
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Mitochondrial import receptor subunit TOM5
D, I
50Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: TOM5 (MOM8A)
Find proteins for P80967 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P80967
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
Mitochondrial import receptor subunit TOM6
E, J
61Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: TOM6 (ISP6)
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 SDF File 
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 
Software Package:
Software NamePurpose
phenix.real_space_refinerefinement
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



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
    Type: Database references