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- PDB-7vku: Cryo-EM structure of SAM-Tom40 intermediate complex -

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Basic information

Entry
Database: PDB / ID: 7vku
TitleCryo-EM structure of SAM-Tom40 intermediate complex
Components
  • Mitochondrial import receptor subunit TOM40
  • Sorting assembly machinery 35 kDa subunit
  • Sorting assembly machinery 37 kDa subunit
  • Sorting assembly machinery 50 kDa subunit
KeywordsTRANSLOCASE / Mitochondrial protein assembly gate
Function / homology
Function and homology information


membrane insertase activity / mitochondrial outer membrane translocase complex assembly / SAM complex / mitochondrial outer membrane translocase complex / protein insertion into mitochondrial outer membrane / phospholipid transport / porin activity / pore complex / protein import into mitochondrial matrix / protein transmembrane transporter activity ...membrane insertase activity / mitochondrial outer membrane translocase complex assembly / SAM complex / mitochondrial outer membrane translocase complex / protein insertion into mitochondrial outer membrane / phospholipid transport / porin activity / pore complex / protein import into mitochondrial matrix / protein transmembrane transporter activity / monoatomic ion transport / mitochondrion organization / mitochondrial intermembrane space / protein-containing complex assembly / mitochondrial outer membrane / mitochondrion / cytosol / cytoplasm
Similarity search - Function
Sorting assembly machinery 35kDa subunit / Tom37, C-terminal domain / SAM35, subunit of SAM coomplex / Tom37 C-terminal domain / Mitochondrial outer membrane transport complex Sam37/metaxin, N-terminal domain / : / Outer mitochondrial membrane transport complex protein / Mitochondrial import receptor subunit Tom40, fungi / membrane protein fhac: a member of the omp85/tpsb transporter family / Tom40 ...Sorting assembly machinery 35kDa subunit / Tom37, C-terminal domain / SAM35, subunit of SAM coomplex / Tom37 C-terminal domain / Mitochondrial outer membrane transport complex Sam37/metaxin, N-terminal domain / : / Outer mitochondrial membrane transport complex protein / Mitochondrial import receptor subunit Tom40, fungi / membrane protein fhac: a member of the omp85/tpsb transporter family / Tom40 / Eukaryotic porin/Tom40 / Eukaryotic porin / Porin domain superfamily / Bacterial surface antigen (D15) / Omp85 superfamily domain / Porin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Sorting assembly machinery 35 kDa subunit / Mitochondrial import receptor subunit TOM40 / Sorting assembly machinery 37 kDa subunit / Sorting assembly machinery 50 kDa subunit
Similarity search - Component
Biological speciesSaccharomyces cerevisiae S288C (yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsTakeda, H. / Tsutsumi, A. / Kikkawa, M. / Endo, T.
Funding support Japan, 3items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS) Japan
Japan Science and Technology Japan
Japan Agency for Medical Research and Development (AMED) Japan
CitationJournal: Nat Struct Mol Biol / Year: 2023
Title: Author Correction: A multipoint guidance mechanism for β-barrel folding on the SAM complex.
Authors: Hironori Takeda / Jon V Busto / Caroline Lindau / Akihisa Tsutsumi / Kentaro Tomii / Kenichiro Imai / Yu Yamamori / Takatsugu Hirokawa / Chie Motono / Iniyan Ganesan / Lena-Sophie Wenz / ...Authors: Hironori Takeda / Jon V Busto / Caroline Lindau / Akihisa Tsutsumi / Kentaro Tomii / Kenichiro Imai / Yu Yamamori / Takatsugu Hirokawa / Chie Motono / Iniyan Ganesan / Lena-Sophie Wenz / Thomas Becker / Masahide Kikkawa / Nikolaus Pfanner / Nils Wiedemann / Toshiya Endo /
History
DepositionOct 1, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 4, 2023Provider: repository / Type: Initial release
Revision 1.0Jan 4, 2023Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jan 4, 2023Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jan 4, 2023Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jan 4, 2023Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.0Jan 4, 2023Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jan 4, 2023Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jan 4, 2023Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.0Jan 4, 2023Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jan 4, 2023Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jan 4, 2023Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.2Jul 17, 2024Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _em_admin.last_update
Revision 1.3Jun 25, 2025Group: Data collection / Structure summary / Category: em_admin / em_software / pdbx_entry_details / Item: _em_admin.last_update / _em_software.name
Revision 1.1Jun 25, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Data processing / Experimental summary / Data content type: EM metadata / EM metadata / Category: em_admin / em_software / Data content type: EM metadata / EM metadata / Item: _em_admin.last_update / _em_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Sorting assembly machinery 50 kDa subunit
B: Sorting assembly machinery 35 kDa subunit
C: Sorting assembly machinery 37 kDa subunit
X: Mitochondrial import receptor subunit TOM40


Theoretical massNumber of molelcules
Total (without water)171,5294
Polymers171,5294
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Sorting assembly machinery 50 kDa subunit / TOB complex 55 kDa subunit


Mass: 54473.840 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Gene: SAM50, TOB55, YNL026W, N2802 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P53969
#2: Protein Sorting assembly machinery 35 kDa subunit / Sam35


Mass: 37446.070 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P14693
#3: Protein Sorting assembly machinery 37 kDa subunit / Sam37


Mass: 37537.797 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Gene: SAM37, MAS37, PET3027, TOM37, YMR060C, YM9796.13C / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P50110
#4: Protein Mitochondrial import receptor subunit TOM40 / Mitochondrial import site protein ISP42 / Translocase of outer membrane 40 kDa subunit


Mass: 42071.141 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Gene: TOM40, ISP42, MOM38, YMR203W, YM8325.04 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P23644
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: CELL / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: SAM-Tom40 / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Source (recombinant)Organism: Saccharomyces cerevisiae (brewer's yeast)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1800 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm
Image recordingElectron dose: 48 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.14_3260: / Classification: refinement
EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 23542 / Symmetry type: POINT

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