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- PDB-9j9b: Substrate-engaged TIM23 complex from yeast -

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Basic information

Entry
Database: PDB / ID: 9j9b
TitleSubstrate-engaged TIM23 complex from yeast
Components
  • (Mitochondrial import inner membrane translocase subunit ...) x 3
  • (anti-Tim44-Fab ...) x 2
  • Protein MGR2
  • Substrate
KeywordsPROTEIN TRANSPORT / Mitochondrial protein import / TOM / TIM23 protein translocation
Function / homology
Function and homology information


PAM complex, Tim23 associated import motor / L-lactate dehydrogenase (cytochrome) / L-lactate dehydrogenase (cytochrome) activity / extrinsic component of mitochondrial inner membrane / Mitochondrial protein import / TIM23 mitochondrial import inner membrane translocase complex / mitochondrion targeting sequence binding / protein insertion into mitochondrial inner membrane / : / lactate metabolic process ...PAM complex, Tim23 associated import motor / L-lactate dehydrogenase (cytochrome) / L-lactate dehydrogenase (cytochrome) activity / extrinsic component of mitochondrial inner membrane / Mitochondrial protein import / TIM23 mitochondrial import inner membrane translocase complex / mitochondrion targeting sequence binding / protein insertion into mitochondrial inner membrane / : / lactate metabolic process / protein import into mitochondrial matrix / protein transmembrane transporter activity / intracellular protein transport / mitochondrial intermembrane space / protein-folding chaperone binding / protein-macromolecule adaptor activity / mitochondrial inner membrane / heme binding / mitochondrion / ATP binding / metal ion binding / nucleus / cytosol
Similarity search - Function
Romo1/Mgr2 / Reactive mitochondrial oxygen species modulator 1 / Reactive mitochondrial oxygen species modulator 1 / Mitochondrial inner membrane translocase complex, subunit Tim17 / Mitochondrial inner membrane translocase complex, subunit Tim23 / Tim23-like / Mitochondrial import inner membrane translocase subunit Tim44 / Tim44-like / L-mandelate/L-lactate dehydrogenase, FMN-binding domain / Cytochrome b5, heme-binding site ...Romo1/Mgr2 / Reactive mitochondrial oxygen species modulator 1 / Reactive mitochondrial oxygen species modulator 1 / Mitochondrial inner membrane translocase complex, subunit Tim17 / Mitochondrial inner membrane translocase complex, subunit Tim23 / Tim23-like / Mitochondrial import inner membrane translocase subunit Tim44 / Tim44-like / L-mandelate/L-lactate dehydrogenase, FMN-binding domain / Cytochrome b5, heme-binding site / Cytochrome b5 family, heme-binding domain signature. / FMN-dependent alpha-hydroxy acid dehydrogenase, active site / FMN hydroxy acid dehydrogenase domain / FMN-dependent alpha-hydroxy acid dehydrogenases active site. / FMN-dependent alpha-hydroxy acid dehydrogenase domain profile. / Cytochrome b5 family, heme-binding domain profile. / Cytochrome b5-like heme/steroid binding domain / Cytochrome b5-like heme/steroid binding domain superfamily / Cytochrome b5-like Heme/Steroid binding domain / Cytochrome b5-like Heme/Steroid binding domain / FMN-dependent dehydrogenase / FMN-dependent dehydrogenase / Tim44-like domain / Tim44-like domain / Tim44 / Tim17/Tim22/Tim23/Pmp24 family / NTF2-like domain superfamily / Aldolase-type TIM barrel
Similarity search - Domain/homology
CARDIOLIPIN / L-lactate dehydrogenase (cytochrome) / Mitochondrial import inner membrane translocase subunit TIM23 / Mitochondrial import inner membrane translocase subunit TIM17 / Mitochondrial import inner membrane translocase subunit TIM44 / Protein MGR2
Similarity search - Component
Biological speciesSaccharomyces cerevisiae S288C (yeast)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.83 Å
AuthorsYang, Y.Q. / Wang, G.P.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32271269 China
CitationJournal: To Be Published
Title: Substrate-engaged TIM23 complex from yeast
Authors: Yang, Y.Q. / Wang, G.P.
History
DepositionAug 22, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Sep 10, 2025Provider: repository / Type: Initial release
Revision 1.0Sep 10, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Sep 10, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Sep 10, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Sep 10, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Sep 10, 2025Data content type: Primary map / Data content type: Primary map / Provider: 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 inner membrane translocase subunit TIM17
B: Mitochondrial import inner membrane translocase subunit TIM23
C: Mitochondrial import inner membrane translocase subunit TIM44,L-lactate dehydrogenase (cytochrome),sfGFP
D: Protein MGR2
H: anti-Tim44-Fab H chain
L: anti-Tim44-Fab L chain
E: Substrate
hetero molecules


Theoretical massNumber of molelcules
Total (without water)191,1198
Polymers189,6557
Non-polymers1,4641
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 inner membrane translocase subunit ... , 3 types, 3 molecules ABC

#1: Protein Mitochondrial import inner membrane translocase subunit TIM17 / Mitochondrial inner membrane protein MIM17 / Mitochondrial protein import protein 2


Mass: 16602.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Gene: TIM17, MIM17, MPI2, SMS1, YJL143W, J0648 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P39515
#2: Protein Mitochondrial import inner membrane translocase subunit TIM23 / Membrane import machinery protein MIM23 / Mitochondrial protein import protein 3 / Mitochondrial ...Membrane import machinery protein MIM23 / Mitochondrial protein import protein 3 / Mitochondrial protein import protein MAS6


Mass: 23266.527 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Gene: TIM23, MAS6, MIM23, MPI3, YNR017W, N3180 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P32897
#3: Protein Mitochondrial import inner membrane translocase subunit TIM44,L-lactate dehydrogenase (cytochrome),sfGFP / Inner membrane import site protein 45 / ISP45 / Membrane import machinery protein MIM44 / ...Inner membrane import site protein 45 / ISP45 / Membrane import machinery protein MIM44 / Mitochondrial protein import protein 1 / Cytochrome b2 / Flavocytochrome b2 / FCB2 / L-lactate ferricytochrome c oxidoreductase / L-LCR


Mass: 84451.133 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast), (gene. exp.) synthetic construct (others)
Gene: TIM44, ISP45, MIM44, MPI1, YIL022W, CYB2, YML054C, YM9958.08C
Production host: Saccharomyces cerevisiae (brewer's yeast)
References: UniProt: Q01852, UniProt: P00175, L-lactate dehydrogenase (cytochrome)

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Antibody , 2 types, 2 molecules HL

#5: Antibody anti-Tim44-Fab H chain


Mass: 25635.932 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)
#6: Antibody anti-Tim44-Fab L chain


Mass: 26140.150 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)

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Protein / Protein/peptide / Non-polymers , 3 types, 3 molecules DE

#4: Protein Protein MGR2 / Mitochondrial genome-required protein 2


Mass: 12264.158 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Gene: MGR2, YPL098C / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q02889
#7: Protein/peptide Substrate


Mass: 1294.587 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)
#8: Chemical ChemComp-CDL / CARDIOLIPIN / DIPHOSPHATIDYL GLYCEROL / BIS-(1,2-DIACYL-SN-GLYCERO-3-PHOSPHO)-1',3'-SN-GLYCEROL


Mass: 1464.043 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C81H156O17P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: phospholipid*YM

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Details

Has ligand of interestY
Has protein modificationY

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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 TIM23 complex from yeast / Type: COMPLEX / Entity ID: #1-#7 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / 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
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS 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
8PHENIXmodel refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.83 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 160770 / Symmetry type: POINT
RefinementHighest resolution: 3.83 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0046166
ELECTRON MICROSCOPYf_angle_d0.7238310
ELECTRON MICROSCOPYf_dihedral_angle_d14.2062254
ELECTRON MICROSCOPYf_chiral_restr0.048900
ELECTRON MICROSCOPYf_plane_restr0.0061065

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