9J9B | pdb_00009j9b

Substrate-engaged TIM23 complex from yeast


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.83 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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This is version 1.1 of the entry. See complete history


Literature

Dynamic TOM-TIM23 supercomplex directs mitochondrial protein translocation and sorting.

Yang, Y.Wang, S.Wang, G.Lian, Y.Xue, L.Jiang, W.Guo, Q.Song, C.Li, L.

(2025) Nat Struct Mol Biol 32: 2231-2241

  • DOI: https://doi.org/10.1038/s41594-025-01662-x
  • Primary Citation of Related Structures:  
    9J99, 9J9B

  • PubMed Abstract: 

    The mitochondrial translocase of the outer membrane (TOM) and translocase of the inner membrane 23 (TIM23) complexes are coupled to control protein import across the outer and inner membranes, respectively. However, the mechanisms of protein recognition and sorting in the TOM-TIM23 pathway remain unclear. Here we report cryo-electron microscopy structures of a translocating polypeptide substrate captured in the active TOM-TIM23 supercomplex from Saccharomyces cerevisiae. In the TOM complex, the polypeptide substrate adopts multiple conformations stabilized by hydrophilic residues from distinct regions of the Tom40 channel. In the TIM23 complex, the Tim17 and Mgr2 subunits create the translocation pathway, with a central restriction formed by four highly conserved hydrophobic residues. The substrate primarily interacts with hydrophobic residues along the Tim17-Mgr2 pathway. Substrate hydrophobicity modulates the association of Mgr2 with Tim17, enabling dynamic regulation of protein sorting toward either the matrix or membrane. These findings reveal a sophisticated translocation mechanism of the TOM-TIM23 supercomplex that ensures the efficient import of diverse mitochondrial proteins.


  • Organizational Affiliation
    • State Key Laboratory of Membrane Biology, School of Life Sciences, Peking University, Beijing, China.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial import inner membrane translocase subunit TIM17158Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: TIM17MIM17MPI2SMS1YJL143WJ0648
UniProt
Find proteins for P39515 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Go to UniProtKB:  P39515
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UniProt GroupP39515
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial import inner membrane translocase subunit TIM23222Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: TIM23MAS6MIM23MPI3YNR017WN3180
UniProt
Find proteins for P32897 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Go to UniProtKB:  P32897
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UniProt GroupP32897
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial import inner membrane translocase subunit TIM44,L-lactate dehydrogenase (cytochrome),sfGFP757Saccharomyces cerevisiae S288Csynthetic constructMutation(s): 0 
Gene Names: TIM44ISP45MIM44MPI1YIL022WCYB2YML054CYM9958.08C
EC: 1.1.2.3
UniProt
Find proteins for P00175 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Find proteins for Q01852 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Go to UniProtKB:  Q01852
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UniProt GroupsQ01852P00175
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Protein MGR2113Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: MGR2YPL098C
UniProt
Find proteins for Q02889 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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UniProt GroupQ02889
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
anti-Tim44-Fab H chainE [auth H]238Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
anti-Tim44-Fab L chainF [auth L]238Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
SubstrateG [auth E]15Saccharomyces cerevisiae S288CMutation(s): 0 
Sequence Annotations
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Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CDL (Subject of Investigation/LOI)
Query on CDL

Download Ideal Coordinates CCD File 
H [auth A]CARDIOLIPIN
C81 H156 O17 P2
XVTUQDWPJJBEHJ-KZCWQMDCSA-L
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.83 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX
RECONSTRUCTIONcryoSPARC

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China32271269

Revision History  (Full details and data files)

  • Version 1.0: 2025-09-10
    Type: Initial release
  • Version 1.1: 2026-03-25
    Changes: Data collection, Database references