8W5J | pdb_00008w5j

Cryo-EM structure of the yeast TOM core complex (from TOM-TIM23 complex)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.40 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

The architecture of substrate-engaged TOM-TIM23 supercomplex reveals preprotein proximity sites for mitochondrial protein translocation.

Wang, Q., Zhuang, J., Huang, R., Guan, Z., Yan, L., Hong, S., Zhang, L., Huang, C., Liu, Z., Yin, P.

(2024) Cell Discov 10: 19-19

  • DOI: https://doi.org/10.1038/s41421-023-00643-y
  • Primary Citation of Related Structures:  
    8W5J, 8W5K
    • Organizational Affiliation: 
    • National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, Hubei, China.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial import receptor subunit TOM40A,
F [auth I]		387Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: TOM40, ISP42, MOM38, YMR203W, YM8325.04
Membrane Entity: Yes 
UniProt
Find proteins for P23644 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Go to UniProtKB:  P23644
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UniProt GroupP23644
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial import receptor subunit TOM22B,
G [auth J]		152Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: TOM22, MAS17, MAS22, MOM22, YNL131W, N1217, N1862
Membrane Entity: Yes 
UniProt
Find proteins for P49334 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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UniProt GroupP49334
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial import receptor subunit TOM5C,
H [auth K]		50Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: TOM5, MOM8A, YPR133W-A
Membrane Entity: Yes 
UniProt
Find proteins for P80967 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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UniProt GroupP80967
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial import receptor subunit TOM6D,
I [auth L]		61Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: TOM6, ISP6, YOR045W
Membrane Entity: Yes 
UniProt
Find proteins for P33448 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial import receptor subunit TOM7E,
J [auth M]		60Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: TOM7, MOM7, YNL070W, N2378
Membrane Entity: Yes 
UniProt
Find proteins for P53507 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
46E (Subject of Investigation/LOI)
Query on 46E
Download Ideal Coordinates CCD File 
K [auth I](2R)-3-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-(tetradecanoyloxy)propyl tetradecanoate
C33 H66 N O8 P
NEZDNQCXEZDCBI-WJOKGBTCSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

Structure Validation

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Entry History & Funding Information

Deposition Data

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

Revision History  (Full details and data files)

  • Version 1.0: 2024-02-28
    Type: Initial release
  • Version 1.1: 2025-07-23
    Changes: Data collection, Structure summary