7VKU | pdb_00007vku

Cryo-EM structure of SAM-Tom40 intermediate complex

• PDB DOI: https://doi.org/10.2210/pdb7VKU/pdb
• EM Map EMD-32019: EMDB EMDataResource

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


• Deposited: 2021-10-01 Released: 2023-01-04 
• Deposition Author(s): Takeda, H., Tsutsumi, A., Kikkawa, M., Endo, T.
• Funding Organization(s): Japan Society for the Promotion of Science (JSPS), Japan Science and Technology, Japan Agency for Medical Research and Development (AMED)

---

Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.20 Å
• Aggregation State: CELL 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Author Correction: A multipoint guidance mechanism for beta-barrel folding on the SAM complex.

Takeda, H., Busto, J.V., Lindau, C., Tsutsumi, A., Tomii, K., Imai, K., Yamamori, Y., Hirokawa, T., Motono, C., Ganesan, I., Wenz, L.S., Becker, T., Kikkawa, M., Pfanner, N., Wiedemann, N., Endo, T.

(2023) Nat Struct Mol Biol 30: 233-233

• PubMed: 36697808 
• DOI: https://doi.org/10.1038/s41594-023-00926-8
• Primary Citation Related Structures: 
  7VKU

---

Organizational Affiliation: 
• Faculty of Life Sciences, Kyoto Sangyo University, Kyoto, Japan.
Nara Institute of Science and Technology, Ikoma, Japan.
Institute of Biochemistry and Molecular Biology, Centre for Biochemistry and Molecular Cell Research, Faculty of Medicine, University of Freiburg, Freiburg, Germany.
Department of Cell Biology and Anatomy, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.
Artificial Intelligence Research Center, National Institute of Advanced Industrial Science and Technology (AIST), Tokyo, Japan.
Cellular and Molecular Biotechnology Research Institute, AIST, Tokyo, Japan.
Division of Biomedical Science, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan.
Transborder Medical Research Center, University of Tsukuba, Tsukuba, Japan.
Computational Bio Big-Data Open Innovation Laboratory, AIST, Waseda University, Tokyo, Japan.
Sanofi-Aventis Deutschland GmbH, Frankfurt, Germany.
Institute of Biochemistry and Molecular Biology, Faculty of Medicine, University of Bonn, Bonn, Germany.
Institute of Biochemistry and Molecular Biology, Centre for Biochemistry and Molecular Cell Research, Faculty of Medicine, University of Freiburg, Freiburg, Germany. [e-mail].
CIBSS Centre for Integrative Biological Signalling Studies, University of Freiburg, Freiburg, Germany. [e-mail].
BIOSS Centre for Biological Signalling Studies, University of Freiburg, Freiburg, Germany. [e-mail].
Institute of Biochemistry and Molecular Biology, Centre for Biochemistry and Molecular Cell Research, Faculty of Medicine, University of Freiburg, Freiburg, Germany. [e-mail].
CIBSS Centre for Integrative Biological Signalling Studies, University of Freiburg, Freiburg, Germany. [e-mail].
BIOSS Centre for Biological Signalling Studies, University of Freiburg, Freiburg, Germany. [e-mail].
Faculty of Life Sciences, Kyoto Sangyo University, Kyoto, Japan. [e-mail].
Institute for Protein Dynamics, Kyoto Sangyo University, Kyoto, Japan. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A1B1C1D1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 171.53 kDa 
• Atom Count: 9,219 
• Modeled Residue Count: 1,154 
• Deposited Residue Count: 1,527 
• Unique protein chains: 4

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sorting assembly machinery 50 kDa subunit	A	484	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  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	327	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 [auth X]	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

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.20 Å
• Aggregation State: CELL 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-01-04 
Deposition Author(s): Takeda, H., Tsutsumi, A., Kikkawa, M., Endo, T.

---

Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	--
Japan Science and Technology	Japan	--
Japan Agency for Medical Research and Development (AMED)	Japan	--

Revision History  

• Version 1.0: 2023-01-04
  Type: Initial release
  
• Version 1.1: 2024-06-19
  Changes: Data collection
• Version 1.2: 2024-07-17
  Changes: Data collection, Database references
• Version 1.3: 2025-06-25
  Changes: Data collection, Structure summary