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- PDB-9n84: Yeast TIM23 complex inhibited by stendomycin -

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Basic information

Entry
Database: PDB / ID: 9n84
TitleYeast TIM23 complex inhibited by stendomycin
Components
  • (Antibody Fab fragment ...) x 2
  • (Mitochondrial import inner membrane translocase subunit ...) x 3
  • Stendomycin V
KeywordsMEMBRANE PROTEIN/INHIBITOR / TIM23 / Tim17 / stendomycin / mitochondrial inner membrane / mitochondrial protein import / mitochondria / protein translocation / translocase / MEMBRANE PROTEIN / MEMBRANE PROTEIN-INHIBITOR complex
Function / homology
Function and homology information


mitochondrial protein-transporting ATPase / negative regulation of mitochondrial DNA metabolic process / extrinsic component of mitochondrial inner membrane / PAM complex, Tim23 associated import motor / Mitochondrial protein import / TIM23 mitochondrial import inner membrane translocase complex / mitochondrion targeting sequence binding / protein insertion into mitochondrial inner membrane / protein import into mitochondrial matrix / transmembrane protein transporter activity ...mitochondrial protein-transporting ATPase / negative regulation of mitochondrial DNA metabolic process / extrinsic component of mitochondrial inner membrane / PAM complex, Tim23 associated import motor / Mitochondrial protein import / TIM23 mitochondrial import inner membrane translocase complex / mitochondrion targeting sequence binding / protein insertion into mitochondrial inner membrane / protein import into mitochondrial matrix / transmembrane protein transporter activity / intracellular protein transport / mitochondrial intermembrane space / protein-folding chaperone binding / protein-macromolecule adaptor activity / mitochondrial inner membrane / mitochondrion / ATP binding
Similarity search - Function
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 / Tim44-like domain / Tim44-like domain / Tim44 / Tim17/Tim22/Tim23/Pmp24 family / NTF2-like domain superfamily
Similarity search - Domain/homology
CARDIOLIPIN / 10-METHYLUNDECANOIC ACID / PHOSPHATIDYLETHANOLAMINE / Mitochondrial import inner membrane translocase subunit TIM23 / Mitochondrial import inner membrane translocase subunit TIM17 / Mitochondrial import inner membrane translocase subunit TIM44
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Mus musculus (house mouse)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsPark, E.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM147628 United States
The Pew Charitable Trusts United States
CitationJournal: Nat Chem Biol / Year: 2026
Title: Topogenic sequence recognition at TIM complexes revealed by a stendomycin-bound structure.
Authors: Yuanyuan Chen / Antony Lurie / Kevin Wu / Kihong Nam / Samantha N Garcia / Nathaniel W M Dempsey / Esben B Svenningsen / Thomas Tørring / Thomas B Poulsen / Alban Ordureau / Eunyong Park /
Abstract: In the mitochondrial inner membrane (IM), topogenesis of imported proteins is mediated by TIM23 and TIM22 complexes. TIM23 translocates soluble polypeptides across the IM into the matrix, whereas ...In the mitochondrial inner membrane (IM), topogenesis of imported proteins is mediated by TIM23 and TIM22 complexes. TIM23 translocates soluble polypeptides across the IM into the matrix, whereas TIM22 inserts polytopic membrane proteins into the IM. Although functionally distinct, both rely on homologous subunits, Tim17 in TIM23 and Tim22 in TIM22. The underlying mechanisms, however, remain elusive. Here we use structural and functional approaches with yeast Tim17, Tim22 and the TIM23 inhibitor stendomycin. Cryogenic-electron microscopy shows that stendomycin binds to the protein translocation cavity of Tim17, mimicking α-helical topogenic sequences. While Tim22 does not bind stendomycin, a single mutation in its equivalent cavity suffices to enable binding. The cavities of Tim17 and Tim22 are largely interchangeable without disrupting their functions. Lastly, stendomycin triggers a collapse of the membrane potential, likely via its Tim17- or Tim22-dependent translocation across the IM. These findings reveal a mechanistic overlap between protein translocases and insertases.
History
DepositionFeb 7, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 16, 2026Provider: repository / Type: Initial release
Revision 1.0Sep 16, 2026Data content type: EM metadata / Data content type: EM metadata / 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: Antibody Fab fragment light chain
H: Antibody Fab fragment heavy chain
D: Stendomycin V
hetero molecules


Theoretical massNumber of molelcules
Total (without water)144,3059
Polymers141,9076
Non-polymers2,3983
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 (brewer's 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 (brewer's 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 / 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


Mass: 48933.418 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: TIM44, ISP45, MIM44, MPI1, YIL022W / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q01852

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Protein/peptide , 1 types, 1 molecules D

#6: Protein/peptide Stendomycin V


Mass: 1436.695 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Antibody , 2 types, 2 molecules LH

#4: Antibody Antibody Fab fragment light chain


Mass: 26173.201 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#5: Antibody Antibody Fab fragment heavy chain


Mass: 25494.990 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)

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Non-polymers , 3 types, 3 molecules

#7: 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 / Comment: phospholipid*YM
#8: Chemical ChemComp-PTY / PHOSPHATIDYLETHANOLAMINE


Mass: 734.039 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C40H80NO8P / Comment: phospholipid*YM
#9: Chemical ChemComp-M12 / 10-METHYLUNDECANOIC ACID


Mass: 200.318 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H24O2 / Feature type: SUBJECT OF INVESTIGATION

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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: TIM23 complex inhibited by stendomycin / Type: COMPLEX / Entity ID: #1-#5 / Source: MULTIPLE SOURCES
Molecular weightExperimental value: NO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's 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
Specimen supportGrid material: GOLD / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen 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 defocus max: 1600 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameCategory
2SerialEMimage acquisition
4cryoSPARCCTF correction
9cryoSPARCinitial Euler assignment
10cryoSPARCfinal Euler assignment
12cryoSPARC3D reconstruction
13PHENIXmodel 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: 105256 / Symmetry type: POINT
Atomic model buildingPDB-ID: 8SCX

8scx


Accession code: 8SCX / Source name: PDB / Type: experimental model
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 69.03 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00265970
ELECTRON MICROSCOPYf_angle_d0.52968061
ELECTRON MICROSCOPYf_chiral_restr0.0395875
ELECTRON MICROSCOPYf_plane_restr0.00641045
ELECTRON MICROSCOPYf_dihedral_angle_d10.3424976

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