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- EMDB-38282: TOM complex with small molecule -

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ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-38282
TitleTOM complex with small molecule
Map data
Sample
  • Complex: The translocase of the outer mitochondrial membrane (TOM) complex
    • Protein or peptide: Mitochondrial import receptor subunit TOM40 homolog
    • Protein or peptide: Mitochondrial import receptor subunit TOM22 homolog
    • Protein or peptide: Mitochondrial import receptor subunit TOM6 homolog
    • Protein or peptide: Mitochondrial import receptor subunit TOM7 homolog
    • Protein or peptide: Mitochondrial import receptor subunit TOM5 homolog
  • Ligand: D-fructose
  • Ligand: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE
Keywordsremodeling / TRANSLOCASE
Function / homology
Function and homology information


TOM complex / mitochondrion targeting sequence binding / mitochondrial outer membrane translocase complex / mitochondria-associated endoplasmic reticulum membrane contact site / protein import into mitochondrial matrix / positive regulation of type 2 mitophagy / Mitochondrial protein import / protein targeting to mitochondrion / positive regulation of protein targeting to mitochondrion / porin activity ...TOM complex / mitochondrion targeting sequence binding / mitochondrial outer membrane translocase complex / mitochondria-associated endoplasmic reticulum membrane contact site / protein import into mitochondrial matrix / positive regulation of type 2 mitophagy / Mitochondrial protein import / protein targeting to mitochondrion / positive regulation of protein targeting to mitochondrion / porin activity / pore complex / protein insertion into mitochondrial outer membrane / protein transmembrane transporter activity / monoatomic ion transport / PINK1-PRKN Mediated Mitophagy / regulation of protein stability / mitochondrial outer membrane / mitochondrial inner membrane / mitochondrion / membrane / cytosol
Similarity search - Function
Mitochondrial import receptor subunit TOM5, metazoa / Mitochondrial import receptor subunit TOM6 homologue / Mitochondrial import receptor subunit TOM6 homolog / Mitochondrial import receptor subunit Tom22 / Mitochondrial import receptor subunit TOM7 / Mitochondrial import receptor subunit Tom22 / TOM7 family / Mitochondrial outer membrane translocase complex, subunit Tom5 / Mitochondrial import receptor subunit or translocase / Tom40 ...Mitochondrial import receptor subunit TOM5, metazoa / Mitochondrial import receptor subunit TOM6 homologue / Mitochondrial import receptor subunit TOM6 homolog / Mitochondrial import receptor subunit Tom22 / Mitochondrial import receptor subunit TOM7 / Mitochondrial import receptor subunit Tom22 / TOM7 family / Mitochondrial outer membrane translocase complex, subunit Tom5 / Mitochondrial import receptor subunit or translocase / Tom40 / Eukaryotic porin/Tom40 / Eukaryotic porin / Porin domain superfamily
Similarity search - Domain/homology
Mitochondrial import receptor subunit TOM40 homolog / Mitochondrial import receptor subunit TOM5 homolog / Mitochondrial import receptor subunit TOM6 homolog / Mitochondrial import receptor subunit TOM22 homolog / Mitochondrial import receptor subunit TOM7 homolog
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.93 Å
AuthorsWang WH / Yang MJ
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32030056 China
CitationJournal: To Be Published
Title: TOM complex with small molecule
Authors: Wang WH / Yang MJ
History
DepositionDec 11, 2023-
Header (metadata) releaseJun 11, 2025-
Map releaseJun 11, 2025-
UpdateJun 11, 2025-
Current statusJun 11, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_38282.png

Downloads & links

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Map

FileDownload / File: emd_38282.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 320 pix.
= 267.968 Å		0.84 Å/pix.
x 320 pix.
= 267.968 Å		0.84 Å/pix.
x 320 pix.
= 267.968 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8374 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.22
Minimum - Maximum-1.4309222 - 2.5891445
Average (Standard dev.)0.002881811 (±0.04318992)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 267.96802 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_38282_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_38282_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_38282_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 : The translocase of the outer mitochondrial membrane (TOM) complex

EntireName: The translocase of the outer mitochondrial membrane (TOM) complex
Components
  • Complex: The translocase of the outer mitochondrial membrane (TOM) complex
    • Protein or peptide: Mitochondrial import receptor subunit TOM40 homolog
    • Protein or peptide: Mitochondrial import receptor subunit TOM22 homolog
    • Protein or peptide: Mitochondrial import receptor subunit TOM6 homolog
    • Protein or peptide: Mitochondrial import receptor subunit TOM7 homolog
    • Protein or peptide: Mitochondrial import receptor subunit TOM5 homolog
  • Ligand: D-fructose
  • Ligand: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE

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Supramolecule #1: The translocase of the outer mitochondrial membrane (TOM) complex

SupramoleculeName: The translocase of the outer mitochondrial membrane (TOM) complex
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Mitochondrial import receptor subunit TOM40 homolog

MacromoleculeName: Mitochondrial import receptor subunit TOM40 homolog / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 37.926926 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MGNVLAASSP PAGPPPPPAP ALVGLPPPPP SPPGFTLPPL GGSLGAGTST SRSSERTPGA ATASASGAAE DGACGCLPNP GTFEECHRK CKELFPIQME GVKLTVNKGL SNHFQVNHTV ALSTIGESNY HFGVTYVGTK QLSPTEAFPV LVGDMDNSGS L NAQVIHQL ...String:
MGNVLAASSP PAGPPPPPAP ALVGLPPPPP SPPGFTLPPL GGSLGAGTST SRSSERTPGA ATASASGAAE DGACGCLPNP GTFEECHRK CKELFPIQME GVKLTVNKGL SNHFQVNHTV ALSTIGESNY HFGVTYVGTK QLSPTEAFPV LVGDMDNSGS L NAQVIHQL GPGLRSKMAI QTQQSKFVNW QVDGEYRGSD FTAAVTLGNP DVLVGSGILV AHYLQSITPC LALGGELVYH RR PGEEGTV MSLAGKYTLN NWLATVTLGQ AGMHATYYHK ASDQLQVGVE FEASTRMQDT SVSFGYQLDL PKANLLFKGS VDS NWIVGA TLEKKLPPLP LTLALGAFLN HRKNKFQCGF GLTIG

UniProtKB: Mitochondrial import receptor subunit TOM40 homolog

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Macromolecule #2: Mitochondrial import receptor subunit TOM22 homolog

MacromoleculeName: Mitochondrial import receptor subunit TOM22 homolog / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 15.532528 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
MAAAVAAAGA GEPQSPDELL PKGDAEKPEE ELEEDDDEEL DETLSERLWG LTEMFPERVR SAAGATFDLS LFVAQKMYRF SRAALWIGT TSFMILVLPV VFETEKLQME QQQQLQQRQI LLGPNTGLSG GMPGALPSLP GKI

UniProtKB: Mitochondrial import receptor subunit TOM22 homolog

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Macromolecule #3: Mitochondrial import receptor subunit TOM6 homolog

MacromoleculeName: Mitochondrial import receptor subunit TOM6 homolog / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 8.007988 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
MASSTVPVSA AGSANETPEI PDNVGDWLRG VYRFATDRND FRRNLILNLG LFAAGVWLAR NLSDIDLMAP QPGV

UniProtKB: Mitochondrial import receptor subunit TOM6 homolog

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Macromolecule #4: Mitochondrial import receptor subunit TOM7 homolog

MacromoleculeName: Mitochondrial import receptor subunit TOM7 homolog / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 6.256473 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
MVKLSKEAKQ RLQQLFKGSQ FAIRWGFIPL VIYLGFKRGA DPGMPEPTVL SLLWG

UniProtKB: Mitochondrial import receptor subunit TOM7 homolog

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Macromolecule #5: Mitochondrial import receptor subunit TOM5 homolog

MacromoleculeName: Mitochondrial import receptor subunit TOM5 homolog / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 6.045318 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
MFRIEGLAPK LDPEEMKRKM REDVISSIRN FLIYVALLRV TPFILKKLDS I

UniProtKB: Mitochondrial import receptor subunit TOM5 homolog

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Macromolecule #6: D-fructose

MacromoleculeName: D-fructose / type: ligand / ID: 6 / Number of copies: 1 / Formula: FUD
Molecular weightTheoretical: 180.156 Da
Chemical component information

ChemComp-FUD:
D-fructose

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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: 1 / 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: 7.8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: OTHER
Electron opticsIllumination mode: OTHER / Imaging mode: OTHER / Nominal defocus max: 5.0 µm / Nominal defocus min: 1.2 µm
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: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.93 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 309574
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER
FSC plot (resolution estimation)

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