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- EMDB-61256: Substrate-engaged TOM complex from yeast -

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Basic information

Entry
Database: EMDB / ID: EMD-61256
TitleSubstrate-engaged TOM complex from yeast
Map data
Sample
  • Complex: Substrate-engaged TOM complex from yeast
    • Protein or peptide: Mitochondrial import receptor subunit TOM40
    • Protein or peptide: Mitochondrial import receptor subunit TOM22
    • Protein or peptide: Mitochondrial import receptor subunit TOM5
    • Protein or peptide: Mitochondrial import receptor subunit TOM6
    • Protein or peptide: Mitochondrial import receptor subunit TOM7
  • Ligand: UNDECANE
  • Ligand: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE
KeywordsMitochondrial protein import / TOM / protein translocation / PROTEIN TRANSPORT
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
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.94 Å
AuthorsYang YQ / Wang GP / Wang SS
Funding support China, 1 items
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, 2024-
Header (metadata) releaseSep 10, 2025-
Map releaseSep 10, 2025-
UpdateMar 25, 2026-
Current statusMar 25, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_61256.png

Downloads & links

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Map

FileDownload / File: emd_61256.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

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Slices (1/3)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.95 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0082
Minimum - Maximum-0.031057417 - 0.055835664
Average (Standard dev.)0.00011555425 (±0.0011199592)
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_61256_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_61256_half_map_2.map
Projections & Slices
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Sample components

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Entire : Substrate-engaged TOM complex from yeast

EntireName: Substrate-engaged TOM complex from yeast
Components
  • Complex: Substrate-engaged TOM complex from yeast
    • Protein or peptide: Mitochondrial import receptor subunit TOM40
    • Protein or peptide: Mitochondrial import receptor subunit TOM22
    • Protein or peptide: Mitochondrial import receptor subunit TOM5
    • Protein or peptide: Mitochondrial import receptor subunit TOM6
    • Protein or peptide: Mitochondrial import receptor subunit TOM7
  • Ligand: UNDECANE
  • Ligand: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE

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Supramolecule #1: Substrate-engaged TOM complex from yeast

SupramoleculeName: Substrate-engaged TOM complex from yeast / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)

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Macromolecule #1: Mitochondrial import receptor subunit TOM40

MacromoleculeName: Mitochondrial import receptor subunit TOM40 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)
Molecular weightTheoretical: 42.071141 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MSAPTPLAEA SQIPTIPALS PLTAKQSKGN FFSSNPISSF VVDTYKQLHS HRQSLELVNP GTVENLNKEV SRDVFLSQYF FTGLRADLN KAFSMNPAFQ TSHTFSIGSQ ALPKYAFSAL FANDNLFAQG NIDNDLSVSG RLNYGWDKKN ISKVNLQISD G QPTMCQLE ...String:
MSAPTPLAEA SQIPTIPALS PLTAKQSKGN FFSSNPISSF VVDTYKQLHS HRQSLELVNP GTVENLNKEV SRDVFLSQYF FTGLRADLN KAFSMNPAFQ TSHTFSIGSQ ALPKYAFSAL FANDNLFAQG NIDNDLSVSG RLNYGWDKKN ISKVNLQISD G QPTMCQLE QDYQASDFSV NVKTLNPSFS EKGEFTGVAV ASFLQSVTPQ LALGLETLYS RTDGSAPGDA GVSYLTRYVS KK QDWIFSG QLQANGALIA SLWRKVAQNV EAGIETTLQA GMVPITDPLM GTPIGIQPTV EGSTTIGAKY EYRQSVYRGT LDS NGKVAC FLERKVLPTL SVLFCGEIDH FKNDTKIGCG LQFETAGNQE LLMLQQGLDA DGNPLQALPQ L

UniProtKB: Mitochondrial import receptor subunit TOM40

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Macromolecule #2: Mitochondrial import receptor subunit TOM22

MacromoleculeName: Mitochondrial import receptor subunit TOM22 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)
Molecular weightTheoretical: 16.801373 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString:
MVELTEIKDD VVQLDEPQFS RNQAIVEEKA SATNNDVVDD EDDSDSDFED EFDENETLLD RIVALKDIVP PGKRQTISNF FGFTSSFVR NAFTKSGNLA WTLTTTALLL GVPLSLSILA EQQLIEMEKT FDLQSDANNI LAQGEKDAAA TAN

UniProtKB: Mitochondrial import receptor subunit TOM22

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Macromolecule #3: Mitochondrial import receptor subunit TOM5

MacromoleculeName: Mitochondrial import receptor subunit TOM5 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)
Molecular weightTheoretical: 5.993924 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString:
MFGLPQQEVS EEEKRAHQEQ TEKTLKQAAY VAAFLWVSPM IWHLVKKQWK

UniProtKB: Mitochondrial import receptor subunit TOM5

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Macromolecule #4: Mitochondrial import receptor subunit TOM6

MacromoleculeName: Mitochondrial import receptor subunit TOM6 / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)
Molecular weightTheoretical: 6.41046 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString:
MDGMFAMPGA AAGAASPQQP KSRFQAFKES PLYTIALNGA FFVAGVAFIQ SPLMDMLAPQ L

UniProtKB: Mitochondrial import receptor subunit TOM6

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Macromolecule #5: Mitochondrial import receptor subunit TOM7

MacromoleculeName: Mitochondrial import receptor subunit TOM7 / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)
Molecular weightTheoretical: 6.876955 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString:
MSFLPSFILS DESKERISKI LTLTHNVAHY GWIPFVLYLG WAHTSNRPNF LNLLSPLPSV

UniProtKB: Mitochondrial import receptor subunit TOM7

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Macromolecule #6: UNDECANE

MacromoleculeName: UNDECANE / type: ligand / ID: 6 / Number of copies: 26 / Formula: UND
Molecular weightTheoretical: 156.308 Da
Chemical component information

ChemComp-UND:
UNDECANE

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Macromolecule #7: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE

MacromoleculeName: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / type: ligand / ID: 7 / Number of copies: 25 / Formula: PC1
Molecular weightTheoretical: 790.145 Da
Chemical component information

ChemComp-PC1:
1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / 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
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN 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 reconstructionAlgorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.94 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 1028127
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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