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- EMDB-61257: Substrate-engaged TIM23 complex from yeast -

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Basic information

Entry
Database: EMDB / ID: EMD-61257
TitleSubstrate-engaged TIM23 complex from yeast
Map data
Sample
  • Complex: Substrate-engaged TIM23 complex from yeast
    • 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,L-lactate dehydrogenase (cytochrome),sfGFP
    • Protein or peptide: Protein MGR2
    • Protein or peptide: anti-Tim44-Fab H chain
    • Protein or peptide: anti-Tim44-Fab L chain
    • Protein or peptide: Substrate
  • Ligand: CARDIOLIPIN
KeywordsMitochondrial protein import / TOM / TIM23 protein translocation / PROTEIN TRANSPORT
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
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 (strain ATCC 204508 / S288c) (yeast) / Saccharomyces cerevisiae S288C (yeast) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.83 Å
AuthorsYang YQ / Wang GP / Wang SS
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32271269 China
CitationJournal: To Be Published
Title: Substrate-engaged TIM23 complex from yeast
Authors: Yang YQ / Wang GP
History
DepositionAug 22, 2024-
Header (metadata) releaseSep 10, 2025-
Map releaseSep 10, 2025-
UpdateSep 10, 2025-
Current statusSep 10, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_61257.png

Downloads & links

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Map

FileDownload / File: emd_61257.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.95 Å/pix.
x 300 pix.
= 285. Å		0.95 Å/pix.
x 300 pix.
= 285. Å		0.95 Å/pix.
x 300 pix.
= 285. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.95 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.44
Minimum - Maximum-1.3860798 - 2.1961918
Average (Standard dev.)0.0025949138 (±0.04197791)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 285.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_61257_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_61257_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Substrate-engaged TIM23 complex from yeast

EntireName: Substrate-engaged TIM23 complex from yeast
Components
  • Complex: Substrate-engaged TIM23 complex from yeast
    • 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,L-lactate dehydrogenase (cytochrome),sfGFP
    • Protein or peptide: Protein MGR2
    • Protein or peptide: anti-Tim44-Fab H chain
    • Protein or peptide: anti-Tim44-Fab L chain
    • Protein or peptide: Substrate
  • Ligand: CARDIOLIPIN

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Supramolecule #1: Substrate-engaged TIM23 complex from yeast

SupramoleculeName: Substrate-engaged TIM23 complex from yeast / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#7
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (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 S288C (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 S288C (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,L-l...

MacromoleculeName: Mitochondrial import inner membrane translocase subunit TIM44,L-lactate dehydrogenase (cytochrome),sfGFP
type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO / EC number: L-lactate dehydrogenase (cytochrome)
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 84.451133 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 GSRQFTPNHP GGQDVIKFNA GKDVTAIFEP LHAPNVIDKY IAPEKKLGPL QGSGS GSKG EELFTGVVPI LVELDGDVNG HKFSVRGEGE GDATNGKLTL KFICTTGKLP VPWPTLVTTL TYGVQCFSRY PDHMKR HDF FKSAMPEGYV QERTISFKDD GTYKTRAEVK FEGDTLVNRI ELKGIDFKED GNILGHKLEY NFNSHNVYIT ADKQKNG IK ANFKIRHNVE DGSVQLADHY QQNTPIGDGP VLLPDNHYLS TQSVLSKDPN EKRDHMVLLE FVTAAGITHG SAGLEVLF Q GPANGGSAWS HPQFEKGGGS GGGSGGGSWS HPQFEK

UniProtKB: Mitochondrial import inner membrane translocase subunit TIM44, L-lactate dehydrogenase (cytochrome)

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Macromolecule #4: Protein MGR2

MacromoleculeName: Protein MGR2 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)
Molecular weightTheoretical: 12.264158 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString:
MPPLPQNYAQ QQPSNWDKFK MGLMMGTTVG VCTGILFGGF AIATQGPGPD GVVRTLGKYI AGSAGTFGLF MSIGSIIRSD SESSPMSHP NLNLQQQARL EMWKLRAKYG IRKD

UniProtKB: Protein MGR2

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Macromolecule #5: anti-Tim44-Fab H chain

MacromoleculeName: anti-Tim44-Fab H chain / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)
Molecular weightTheoretical: 25.635932 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MDWTWRVFCL LAVAPGAHSQ VQLKQSGPGL VQPSQSLSIT CTVSGFSLTT YGVHWVRQSP GKGLEWLGVM WRGGSTDFNA AFMSRLSIT KDNSKSQVFF KMNSLQADDT AIYYCARYGN YDAMDYWGQG TSVTVSSAKT TPPSVYPLAP GSAAQTNSMV T LGCLVKGY ...String:
MDWTWRVFCL LAVAPGAHSQ 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: anti-Tim44-Fab L chain

MacromoleculeName: anti-Tim44-Fab L chain / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)
Molecular weightTheoretical: 26.14015 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MVLQTQVFIS LLLWISGAYG DIVLTQSPAS LAVSLGQRAT ISCRASESVD IYGISFMNWF QQKPGQPPKL LIYATSNQGS GVPARFSGS GSGTDFSLNI HPMEEDDTAM YFCQQSKEVP RTFGGGTKLE IKRADAAPTV SIFPPSSEQL TSGGASVVCF L NNFYPKDI ...String:
MVLQTQVFIS LLLWISGAYG 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 #7: Substrate

MacromoleculeName: Substrate / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)
Molecular weightTheoretical: 1.294587 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)

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Macromolecule #8: CARDIOLIPIN

MacromoleculeName: CARDIOLIPIN / type: ligand / ID: 8 / Number of copies: 1 / Formula: CDL
Molecular weightTheoretical: 1.464043 KDa
Chemical component information

ChemComp-CDL:
CARDIOLIPIN / phospholipid*YM

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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: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 60.0 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: 1.2 µm / Nominal magnification: 130000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.83 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 160770
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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