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- PDB-8w5j: Cryo-EM structure of the yeast TOM core complex (from TOM-TIM23 c... -

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Basic information

Entry
Database: PDB / ID: 8w5j
TitleCryo-EM structure of the yeast TOM core complex (from TOM-TIM23 complex)
Components(Mitochondrial import receptor subunit ...) x 5
KeywordsTRANSLOCASE / TOM complex
Function / homology
Function and homology information


mitochondrial outer membrane translocase complex assembly / mitochondrial outer membrane translocase complex / protein insertion into mitochondrial outer membrane / protein transmembrane transport / : / porin activity / pore complex / protein import into mitochondrial matrix / protein transmembrane transporter activity / monoatomic ion transport ...mitochondrial outer membrane translocase complex assembly / mitochondrial outer membrane translocase complex / protein insertion into mitochondrial outer membrane / protein transmembrane transport / : / porin activity / pore complex / protein import into mitochondrial matrix / protein transmembrane transporter activity / monoatomic ion transport / mitochondrial intermembrane space / mitochondrial outer membrane / mitochondrion / cytosol
Similarity search - Function
Mitochondrial import receptor subunit Tom6 / Mitochondrial import receptor subunit Tom22, fungi / Mitochondrial import receptor subunit Tom6, fungal / Mitochondrial import receptor subunit Tom40, fungi / Mitochondrial outer membrane translocase complex, subunit Tom5 / Mitochondrial import receptor subunit or translocase / Mitochondrial import receptor subunit Tom22 / Mitochondrial import receptor subunit TOM7 / Mitochondrial import receptor subunit Tom22 / TOM7 family ...Mitochondrial import receptor subunit Tom6 / Mitochondrial import receptor subunit Tom22, fungi / Mitochondrial import receptor subunit Tom6, fungal / Mitochondrial import receptor subunit Tom40, fungi / Mitochondrial outer membrane translocase complex, subunit Tom5 / Mitochondrial import receptor subunit or translocase / Mitochondrial import receptor subunit Tom22 / Mitochondrial import receptor subunit TOM7 / Mitochondrial import receptor subunit Tom22 / TOM7 family / Tom40 / Eukaryotic porin/Tom40 / Eukaryotic porin / Porin domain superfamily
Similarity search - Domain/homology
Chem-46E / Mitochondrial import receptor subunit TOM40 / Mitochondrial import receptor subunit TOM6 / Mitochondrial import receptor subunit TOM22 / Mitochondrial import receptor subunit TOM7 / Mitochondrial import receptor subunit TOM5
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.4 Å
AuthorsWang, Q. / Guan, Z.Y. / Zhuang, J.J. / Huang, R. / Yin, P.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Cell Discov / Year: 2024
Title: The architecture of substrate-engaged TOM-TIM23 supercomplex reveals preprotein proximity sites for mitochondrial protein translocation.
Authors: Qiang Wang / Jinjin Zhuang / Rui Huang / Zeyuan Guan / Ling Yan / Sixing Hong / Liying Zhang / Can Huang / Zhu Liu / Ping Yin /
History
DepositionAug 27, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Feb 28, 2024Provider: repository / Type: Initial release
Revision 1.0Feb 28, 2024Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Feb 28, 2024Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Feb 28, 2024Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Feb 28, 2024Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Feb 28, 2024Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Jul 23, 2025Group: Data collection / Structure summary / Category: em_admin / em_software / pdbx_entry_details
Item: _em_admin.last_update / _em_software.name / _pdbx_entry_details.has_protein_modification
Revision 1.1Jul 23, 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: Mitochondrial import receptor subunit TOM40
B: Mitochondrial import receptor subunit TOM22
C: Mitochondrial import receptor subunit TOM5
D: Mitochondrial import receptor subunit TOM6
E: Mitochondrial import receptor subunit TOM7
I: Mitochondrial import receptor subunit TOM40
J: Mitochondrial import receptor subunit TOM22
K: Mitochondrial import receptor subunit TOM5
L: Mitochondrial import receptor subunit TOM6
M: Mitochondrial import receptor subunit TOM7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)156,94411
Polymers156,30810
Non-polymers6361
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Mitochondrial import receptor subunit ... , 5 types, 10 molecules AIBJCKDLEM

#1: 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.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Gene: TOM40, ISP42, MOM38, YMR203W, YM8325.04
Production host: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P23644
#2: Protein Mitochondrial import receptor subunit TOM22 / Mitochondrial 17 kDa assembly protein / Mitochondrial 22 kDa outer membrane protein / Protein MAS17 ...Mitochondrial 17 kDa assembly protein / Mitochondrial 22 kDa outer membrane protein / Protein MAS17 / Translocase of outer membrane 22 kDa subunit


Mass: 16801.373 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Gene: TOM22, MAS17, MAS22, MOM22, YNL131W, N1217, N1862
Production host: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P49334
#3: Protein/peptide Mitochondrial import receptor subunit TOM5 / Translocase of outer membrane 5 kDa subunit


Mass: 5993.924 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Gene: TOM5, MOM8A, YPR133W-A
Production host: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P80967
#4: Protein Mitochondrial import receptor subunit TOM6 / Mitochondrial import site protein ISP6 / Translocase of outer membrane 6 kDa subunit


Mass: 6410.460 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Gene: TOM6, ISP6, YOR045W
Production host: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P33448
#5: Protein Mitochondrial import receptor subunit TOM7 / Translocase of outer membrane 7 kDa subunit


Mass: 6876.955 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Gene: TOM7, MOM7, YNL070W, N2378
Production host: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P53507

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Non-polymers , 1 types, 1 molecules

#6: Chemical ChemComp-46E / (2R)-3-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-(tetradecanoyloxy)propyl tetradecanoate


Mass: 635.853 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C33H66NO8P / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: TOM-TIM23 complex / Type: COMPLEX / Entity ID: #1-#5 / Source: RECOMBINANT
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Buffer solutionpH: 7.4
SpecimenConc.: 2.5 mg/ml / Embedding 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: 2200 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM softwareName: PHENIX / Category: model refinement
CTF correctionType: NONE
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 4.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 50070 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0027515
ELECTRON MICROSCOPYf_angle_d0.60310196
ELECTRON MICROSCOPYf_dihedral_angle_d4.627988
ELECTRON MICROSCOPYf_chiral_restr0.0391157
ELECTRON MICROSCOPYf_plane_restr0.0051298

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