7E4I | pdb_00007e4i

Cryo-EM structure of the yeast mitochondrial SAM-Tom40/Tom5/Tom6 complex at 3.0 angstrom

• PDB DOI: https://doi.org/10.2210/pdb7E4I/pdb
• EM Map EMD-30986: EMDB EMDataResource

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


• Deposited: 2021-02-13 Released: 2021-09-01 
• Deposition Author(s): Wang, Q., Guan, Z.Y., Qi, L.B., Yan, C.Y., Yin, P.

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.05 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structural insight into the SAM-mediated assembly of the mitochondrial TOM core complex.

Wang, Q., Guan, Z., Qi, L., Zhuang, J., Wang, C., Hong, S., Yan, L., Wu, Y., Cao, X., Cao, J., Yan, J., Zou, T., Liu, Z., Zhang, D., Yan, C., Yin, P.

(2021) Science 373: 1377-1381

• PubMed: 34446444 
• DOI: https://doi.org/10.1126/science.abh0704
• Primary Citation Related Structures: 
  7E4H, 7E4I


• PubMed Abstract: 
  

  β barrel outer membrane proteins (β-OMPs) play vital roles in mitochondria, chloroplasts, and Gram-negative bacteria. Evolutionarily conserved complexes such as the mitochondrial sorting and assembly machinery (SAM) mediate the assembly of β-OMPs. We investigated the SAM-mediated assembly of the translocase of the outer membrane (TOM) core complex. Cryo–electron microscopy structures of SAM–fully folded Tom40 and the SAM-Tom40/Tom5/Tom6 complexes at ~3-angstrom resolution reveal that Sam37 stabilizes the mature Tom40 mainly through electrostatic interactions, thus facilitating subsequent TOM assembly. These results support the β barrel switching model and provide structural insights into the assembly and release of β barrel complexes.

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Organizational Affiliation: 
• National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China.
Public Laboratory of Electron Microscopy, Huazhong Agricultural University, Wuhan 430070, China.
College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China.
Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 6-mer - A1B1C1D1E1F1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 189.11 kDa 
• Atom Count: 11,336 
• Modeled Residue Count: 1,426 
• Deposited Residue Count: 1,685 
• Unique protein chains: 6

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sorting assembly machinery 50 kDa subunit	A	485	Saccharomyces cerevisiae S288C	Mutation(s): 0  Gene Names: SAM50, TOB55, YNL026W, N2802 Membrane Entity: Yes
UniProt
Find proteins for P53969 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P53969  Go to UniProtKB:  P53969

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Sorting assembly machinery 35 kDa subunit	B	329	Saccharomyces cerevisiae S288C	Mutation(s): 0  Gene Names: SAM35, OMP85, TOB38, TOM38, YHR083W Membrane Entity: Yes
UniProt
Find proteins for P14693 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P14693  Go to UniProtKB:  P14693

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Sorting assembly machinery 37 kDa subunit	C	351	Saccharomyces cerevisiae S288C	Mutation(s): 0  Gene Names: SAM37, MAS37, PET3027, TOM37, YMR060C, YM9796.13C Membrane Entity: Yes
UniProt
Find proteins for P50110 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P50110  Go to UniProtKB:  P50110

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Mitochondrial import receptor subunit TOM40	D	406	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

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Mitochondrial import receptor subunit TOM5	E	52	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: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Mitochondrial import receptor subunit TOM6	F	62	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

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.05 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX
RECONSTRUCTION	cryoSPARC	3.0

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-09-01 
Deposition Author(s): Wang, Q., Guan, Z.Y., Qi, L.B., Yan, C.Y., Yin, P.

Revision History  

• Version 1.0: 2021-09-01
  Type: Initial release
  
• Version 1.1: 2022-02-16
  Changes: Database references
• Version 1.2: 2024-06-05
  Changes: Data collection
• Version 1.3: 2025-07-02
  Changes: Data collection, Structure summary