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- PDB-9j99: Substrate-engaged TOM complex from yeast -

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Basic information

Entry
Database: PDB / ID: 9j99
TitleSubstrate-engaged TOM complex from yeast
Components(Mitochondrial import receptor subunit ...) x 5
KeywordsPROTEIN TRANSPORT / Mitochondrial protein import / TOM / protein translocation
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 / transmembrane protein 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 / transmembrane protein transporter activity / monoatomic ion transport / intracellular protein 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
1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / UNDECANE / 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 S288C (yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.94 Å
AuthorsYang, Y.Q. / Wang, G.P.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32271269 China
CitationJournal: Nat Struct Mol Biol / Year: 2025
Title: Dynamic TOM-TIM23 supercomplex directs mitochondrial protein translocation and sorting.
Authors: Yuqi Yang / Shanshan Wang / Guopeng Wang / Yuke Lian / Lingfeng Xue / Wenhong Jiang / Qiang Guo / Chen Song / Long Li /
Abstract: The mitochondrial translocase of the outer membrane (TOM) and translocase of the inner membrane 23 (TIM23) complexes are coupled to control protein import across the outer and inner membranes, ...The mitochondrial translocase of the outer membrane (TOM) and translocase of the inner membrane 23 (TIM23) complexes are coupled to control protein import across the outer and inner membranes, respectively. However, the mechanisms of protein recognition and sorting in the TOM-TIM23 pathway remain unclear. Here we report cryo-electron microscopy structures of a translocating polypeptide substrate captured in the active TOM-TIM23 supercomplex from Saccharomyces cerevisiae. In the TOM complex, the polypeptide substrate adopts multiple conformations stabilized by hydrophilic residues from distinct regions of the Tom40 channel. In the TIM23 complex, the Tim17 and Mgr2 subunits create the translocation pathway, with a central restriction formed by four highly conserved hydrophobic residues. The substrate primarily interacts with hydrophobic residues along the Tim17-Mgr2 pathway. Substrate hydrophobicity modulates the association of Mgr2 with Tim17, enabling dynamic regulation of protein sorting toward either the matrix or membrane. These findings reveal a sophisticated translocation mechanism of the TOM-TIM23 supercomplex that ensures the efficient import of diverse mitochondrial proteins.
History
DepositionAug 22, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Sep 10, 2025Provider: repository / Type: Initial release
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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)180,12561
Polymers156,30810
Non-polymers23,81851
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 S288C (yeast) / Gene: TOM40, ISP42, MOM38, YMR203W, YM8325.04 / Production host: Saccharomyces cerevisiae (brewer's 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 S288C (yeast) / Gene: TOM22, MAS17, MAS22, MOM22, YNL131W, N1217, N1862 / Production host: Saccharomyces cerevisiae (brewer's 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 S288C (yeast) / Gene: TOM5, MOM8A, YPR133W-A / Production host: Saccharomyces cerevisiae (brewer's 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 S288C (yeast) / Gene: TOM6, ISP6, YOR045W / Production host: Saccharomyces cerevisiae (brewer's 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 S288C (yeast) / Gene: TOM7, MOM7, YNL070W, N2378 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P53507

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Non-polymers , 2 types, 51 molecules

#6: Chemical...
ChemComp-UND / UNDECANE / LIPID FRAGMENT


Mass: 156.308 Da / Num. of mol.: 26 / Source method: obtained synthetically / Formula: C11H24 / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical...
ChemComp-PC1 / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / 3-SN-PHOSPHATIDYLCHOLINE


Mass: 790.145 Da / Num. of mol.: 25 / Source method: obtained synthetically / Formula: C44H88NO8P / Comment: phospholipid*YM

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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: Substrate-engaged TOM complex from yeast / Type: COMPLEX / Entity ID: #1-#5 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)
Source (recombinant)Organism: Saccharomyces cerevisiae (brewer's yeast)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
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 magnification: 130000 X / Nominal defocus max: 1600 nm / Nominal defocus min: 1200 nm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 60 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM software
IDNameVersionCategory
2EPU3 5 1.6034image acquisition
13RELION3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.94 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1028127 / Algorithm: FOURIER SPACE / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0058964
ELECTRON MICROSCOPYf_angle_d0.72911899
ELECTRON MICROSCOPYf_dihedral_angle_d16.6013772
ELECTRON MICROSCOPYf_chiral_restr0.0491211
ELECTRON MICROSCOPYf_plane_restr0.0071402

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