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- EMDB-49111: Yeast TIM23 complex inhibited by stendomycin -

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Basic information

Entry
Database: EMDB / ID: EMD-49111
TitleYeast TIM23 complex inhibited by stendomycin
Map dataCombined, sharpened map
Sample
  • Complex: TIM23 complex inhibited by stendomycin
    • Protein or peptide: Mitochondrial import inner membrane translocase subunit TIM17
    • Protein or peptide: Mitochondrial import inner membrane translocase subunit TIM23
    • Protein or peptide: Mitochondrial import inner membrane translocase subunit TIM44
    • Protein or peptide: Antibody Fab fragment light chain
    • Protein or peptide: Antibody Fab fragment heavy chain
  • Protein or peptide: Stendomycin V
  • Ligand: CARDIOLIPIN
  • Ligand: PHOSPHATIDYLETHANOLAMINE
  • Ligand: 10-METHYLUNDECANOIC ACID
KeywordsTIM23 / 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
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsPark E
Funding support United States, 2 items
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, 2025-
Header (metadata) releaseSep 16, 2026-
Map releaseSep 16, 2026-
UpdateSep 16, 2026-
Current statusSep 16, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_49111.png

Downloads & links

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Map

FileDownload / File: emd_49111.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCombined, sharpened map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 256 pix.
= 268.8 Å		1.05 Å/pix.
x 256 pix.
= 268.8 Å		1.05 Å/pix.
x 256 pix.
= 268.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.05 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.3
Minimum - Maximum-1.7262614 - 2.2375736
Average (Standard dev.)0.001295944 (±0.03978911)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 268.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: half map 1

Fileemd_49111_half_map_1.map
Annotationhalf map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map 2

Fileemd_49111_half_map_2.map
Annotationhalf map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : TIM23 complex inhibited by stendomycin

EntireName: TIM23 complex inhibited by stendomycin
Components
  • Complex: TIM23 complex inhibited by stendomycin
    • Protein or peptide: Mitochondrial import inner membrane translocase subunit TIM17
    • Protein or peptide: Mitochondrial import inner membrane translocase subunit TIM23
    • Protein or peptide: Mitochondrial import inner membrane translocase subunit TIM44
    • Protein or peptide: Antibody Fab fragment light chain
    • Protein or peptide: Antibody Fab fragment heavy chain
  • Protein or peptide: Stendomycin V
  • Ligand: CARDIOLIPIN
  • Ligand: PHOSPHATIDYLETHANOLAMINE
  • Ligand: 10-METHYLUNDECANOIC ACID

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Supramolecule #1: TIM23 complex inhibited by stendomycin

SupramoleculeName: TIM23 complex inhibited by stendomycin / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)

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Macromolecule #1: Mitochondrial import inner membrane translocase subunit TIM17

MacromoleculeName: Mitochondrial import inner membrane translocase subunit TIM17
type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 16.602156 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString:
MSADHSRDPC PIVILNDFGG AFAMGAIGGV VWHGIKGFRN SPLGERGSGA MSAIKARAPV LGGNFGVWGG LFSTFDCAVK AVRKREDPW NAIIAGFFTG GALAVRGGWR HTRNSSITCA CLLGVIEGVG LMFQRYAAWQ AKPMAPPLPE APSSQPLQA

UniProtKB: Mitochondrial import inner membrane translocase subunit TIM17

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Macromolecule #2: Mitochondrial import inner membrane translocase subunit TIM23

MacromoleculeName: Mitochondrial import inner membrane translocase subunit TIM23
type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 23.266527 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MSWLFGDKTP TDDANAAVGG QDTTKPKELS LKQSLGFEPN INNIISGPGG MHVDTARLHP LAGLDKGVEY LDLEEEQLSS LEGSQGLIP SRGWTDDLCY GTGAVYLLGL GIGGFSGMMQ GLQNIPPNSP GKLQLNTVLN HITKRGPFLG NNAGILALSY N IINSTIDA ...String:
MSWLFGDKTP TDDANAAVGG QDTTKPKELS LKQSLGFEPN INNIISGPGG MHVDTARLHP LAGLDKGVEY LDLEEEQLSS LEGSQGLIP SRGWTDDLCY GTGAVYLLGL GIGGFSGMMQ GLQNIPPNSP GKLQLNTVLN HITKRGPFLG NNAGILALSY N IINSTIDA LRGKHDTAGS IGAGALTGAL FKSSKGLKPM GYSSAMVAAA CAVWCSVKKR LLEK

UniProtKB: Mitochondrial import inner membrane translocase subunit TIM23

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Macromolecule #3: Mitochondrial import inner membrane translocase subunit TIM44

MacromoleculeName: Mitochondrial import inner membrane translocase subunit TIM44
type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 48.933418 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MHRSTFIRTS GTSSRTLTAR YRSQYTGLLV ARVLFSTSTT RAQGGNPRSP LQIFRDTFKK EWEKSQELQE NIKTLQDASG KLGESEAYK KAREAYLKAQ RGSTIVGKTL KKTGETMEHI ATKAWESELG KNTRKAAAAT AKKLDESFEP VRQTKIYKEV S EVIDDGES ...String:
MHRSTFIRTS GTSSRTLTAR YRSQYTGLLV ARVLFSTSTT RAQGGNPRSP LQIFRDTFKK EWEKSQELQE NIKTLQDASG KLGESEAYK KAREAYLKAQ RGSTIVGKTL KKTGETMEHI ATKAWESELG KNTRKAAAAT AKKLDESFEP VRQTKIYKEV S EVIDDGES SRYGGFITKE QRRLKRERDL ASGKRHRAVK SNEDAGTAVV ATNIESKESF GKKVEDFKEK TVVGRSIQSL KN KLWDESE NPLIVVMRKI TNKVGGFFAE TESSRVYSQF KLMDPTFSNE SFTRHLREYI VPEILEAYVK GDVKVLKKWF SEA PFNVYA AQQKIFKEQD VYADGRILDI RGVEIVSAKL LAPQDIPVLV VGCRAQEINL YRKKKTGEIA AGDEANILMS SYAM VFTRD PEQIDDDETE GWKILEFVRG GSRQFT

UniProtKB: Mitochondrial import inner membrane translocase subunit TIM44

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Macromolecule #4: Antibody Fab fragment light chain

MacromoleculeName: Antibody Fab fragment light chain / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 26.173201 KDa
SequenceString: MEKDTLLLWV LLLWVPGSTG DIVLTQSPAS LAVSLGQRAT ISCRASESVD IYGISFMNWF QQKPGQPPKL LIYATSNQGS GVPARFSGS GSGTDFSLNI HPMEEDDTAM YFCQQSKEVP RTFGGGTKLE IKRADAAPTV SIFPPSSEQL TSGGASVVCF L NNFYPKDI ...String:
MEKDTLLLWV LLLWVPGSTG DIVLTQSPAS LAVSLGQRAT ISCRASESVD IYGISFMNWF QQKPGQPPKL LIYATSNQGS GVPARFSGS GSGTDFSLNI HPMEEDDTAM YFCQQSKEVP RTFGGGTKLE IKRADAAPTV SIFPPSSEQL TSGGASVVCF L NNFYPKDI NVKWKIDGSE RQNGVLNSWT DQDSKDSTYS MSSTLTLTKD EYERHNSYTC EATHKTSTSP IVKSFNRNEC

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Macromolecule #5: Antibody Fab fragment heavy chain

MacromoleculeName: Antibody Fab fragment heavy chain / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 25.49499 KDa
SequenceString: MAVLVLLLCL VTFPSCVLSQ VQLKQSGPGL VQPSQSLSIT CTVSGFSLTT YGVHWVRQSP GKGLEWLGVM WRGGSTDFNA AFMSRLSIT KDNSKSQVFF KMNSLQADDT AIYYCARYGN YDAMDYWGQG TSVTVSSAKT TPPSVYPLAP GSAAQTNSMV T LGCLVKGY ...String:
MAVLVLLLCL VTFPSCVLSQ VQLKQSGPGL VQPSQSLSIT CTVSGFSLTT YGVHWVRQSP GKGLEWLGVM WRGGSTDFNA AFMSRLSIT KDNSKSQVFF KMNSLQADDT AIYYCARYGN YDAMDYWGQG TSVTVSSAKT TPPSVYPLAP GSAAQTNSMV T LGCLVKGY FPEPVTVTWN SGSLSSGVHT FPAVLQSDLY TLSSSVTVPS SPRPSETVTC NVAHPASSTK VDKKIVPRDC

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Macromolecule #6: Stendomycin V

MacromoleculeName: Stendomycin V / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 1.436695 KDa
SequenceString:
P(NZC)G(DVA)(28J)(DAL)(DBU)(2TL)(DVA)V (2TL)S(28J)(A1BW3)

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Macromolecule #7: CARDIOLIPIN

MacromoleculeName: CARDIOLIPIN / type: ligand / ID: 7 / Number of copies: 1 / Formula: CDL
Molecular weightTheoretical: 1.464043 KDa
Chemical component information

ChemComp-CDL:
CARDIOLIPIN / phospholipid*YM

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Macromolecule #8: PHOSPHATIDYLETHANOLAMINE

MacromoleculeName: PHOSPHATIDYLETHANOLAMINE / type: ligand / ID: 8 / Number of copies: 1 / Formula: PTY
Molecular weightTheoretical: 734.039 Da
Chemical component information

ChemComp-PTY:
PHOSPHATIDYLETHANOLAMINE / phospholipid*YM

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Macromolecule #9: 10-METHYLUNDECANOIC ACID

MacromoleculeName: 10-METHYLUNDECANOIC ACID / type: ligand / ID: 9 / Number of copies: 1 / Formula: M12
Molecular weightTheoretical: 200.318 Da
Chemical component information

ChemComp-M12:
10-METHYLUNDECANOIC ACID

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 105256
Initial angle assignmentType: RANDOM ASSIGNMENT / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

8scx


Chain - Source name: PDB / Chain - Initial model type: experimental model
Output model

PDB-9n84:
Yeast TIM23 complex inhibited by stendomycin

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