8W5K

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

• PDB DOI: https://doi.org/10.2210/pdb8W5K/pdb
• EM Map EMD-37295: EMDB EMDataResource

• Classification: TRANSLOCASE
• Organism(s): Saccharomyces cerevisiae S288C
• Expression System: Saccharomyces cerevisiae S288C
• Mutation(s): No 
• Membrane Protein: Yes  PDBTM


• Deposited: 2023-08-27 Released: 2024-03-13 
• Deposition Author(s): Wang, Q., Guan, Z.Y., Zhuang, J.J., Huang, R., Yin, P.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

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

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

• PubMed: 38360717 
• DOI: https://doi.org/10.1038/s41421-023-00643-y
• Primary Citation of Related Structures:  
  8W5J, 8W5K

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Organizational Affiliation: 

National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, Hubei, China.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 10-mer - A2B2C2D2E2 Pseudo Symmetry: Cyclic - C2  (Explore in 3D)
Pseudo Stoichiometry: Hetero 10-mer - A4B2C2D2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mitochondrial import receptor subunit TOM22	A [auth B], E [auth J]	152	Saccharomyces cerevisiae S288C	Mutation(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)) Explore P49334  Go to UniProtKB:  P49334

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Mitochondrial import receptor subunit TOM5	B [auth C], F [auth K]	50	Saccharomyces cerevisiae S288C	Mutation(s): 0  Gene Names: TOM5, MOM8A, YPR133W-A Membrane Entity: Yes
UniProt
Find proteins for P80967 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P80967  Go to UniProtKB:  P80967

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Mitochondrial import receptor subunit TOM6	C [auth D], G [auth L]	61	Saccharomyces cerevisiae S288C	Mutation(s): 0  Gene Names: TOM6, ISP6, YOR045W Membrane Entity: Yes
UniProt
Find proteins for P33448 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P33448  Go to UniProtKB:  P33448

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Mitochondrial import receptor subunit TOM7	D [auth E], H [auth M]	60	Saccharomyces cerevisiae S288C	Mutation(s): 0  Gene Names: TOM7, MOM7, YNL070W, N2378 Membrane Entity: Yes
UniProt
Find proteins for P53507 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P53507  Go to UniProtKB:  P53507

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Mitochondrial import receptor subunit TOM40	I [auth F], J [auth I]	387	Saccharomyces cerevisiae S288C	Mutation(s): 0  Gene Names: TOM40, ISP42, MOM38, YMR203W, YM8325.04 Membrane Entity: Yes
UniProt
Find proteins for P23644 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P23644  Go to UniProtKB:  P23644

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
46E (Subject of Investigation/LOI)	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 

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-03-13 
Deposition Author(s): Wang, Q., Guan, Z.Y., Zhuang, J.J., Huang, R., Yin, P.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	--

Revision History  

• Version 1.0: 2024-03-13
  Type: Initial release