8W5K | pdb_00008w5k

Cryo-EM structure of the yeast TOM core complex crosslinked by BS3 (from TOM-TIM23 complex)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

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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

Macromolecule Content 

  • Total Structure Weight: 156.94 kDa 
  • Atom Count: 7,379 
  • Modeled Residue Count: 942 
  • Deposited Residue Count: 1,420 
  • Unique protein chains: 5

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Mitochondrial import receptor subunit TOM22A [auth B],
E [auth J]
152Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: TOM22MAS17MAS22MOM22YNL131WN1217N1862
Membrane Entity: Yes 
UniProt
Find proteins for P49334 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P49334 
Go to UniProtKB:  P49334
Entity Groups
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UniProt GroupP49334
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Mitochondrial import receptor subunit TOM5B [auth C],
F [auth K]
50Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: TOM5MOM8AYPR133W-A
Membrane Entity: Yes 
UniProt
Find proteins for P80967 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P80967 
Go to UniProtKB:  P80967
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UniProt GroupP80967
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Mitochondrial import receptor subunit TOM6C [auth D],
G [auth L]
61Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: TOM6ISP6YOR045W
Membrane Entity: Yes 
UniProt
Find proteins for P33448 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P33448 
Go to UniProtKB:  P33448
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UniProt GroupP33448
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Mitochondrial import receptor subunit TOM7D [auth E],
H [auth M]
60Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: TOM7MOM7YNL070WN2378
Membrane Entity: Yes 
UniProt
Find proteins for P53507 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P53507 
Go to UniProtKB:  P53507
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Reference Sequence
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
Mitochondrial import receptor subunit TOM40I [auth F],
J [auth I]
387Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: TOM40ISP42MOM38YMR203WYM8325.04
Membrane Entity: Yes 
UniProt
Find proteins for P23644 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P23644 
Go to UniProtKB:  P23644
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UniProt GroupP23644
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Reference Sequence

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: 3.60 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: 2024-03-13
    Type: Initial release
  • Version 1.1: 2025-07-16
    Changes: Data collection, Structure summary