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- EMDB-19944: cryoEM structure of the Drosophila melanogaster TOM core complex -

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Basic information

Entry
Database: EMDB / ID: EMD-19944
TitlecryoEM structure of the Drosophila melanogaster TOM core complex
Map dataMap of the translocase of the outer mitochondrial membrane of Drosophila melanogaster. Main 3D volume. Sharpened map.
Sample
  • Complex: Translocase of the outer mitochondrial membrane core complex of Drosophila melanogaster
    • Protein or peptide: Mitochondrial import receptor subunit TOM6
    • Protein or peptide: Mitochondrial import receptor subunit TOM5
    • Protein or peptide: Mitochondrial import receptor subunit TOM7
    • Protein or peptide: Mitochondrial import receptor subunit TOM22
    • Protein or peptide: Mitochondrial import receptor subunit TOM40
  • Ligand: DIUNDECYL PHOSPHATIDYL CHOLINE
KeywordsComplex / outer membrane / mitochondria / membrane protein / TOM / translocase
Function / homology
Function and homology information


mitochondrial outer membrane translocase complex / protein import into mitochondrial matrix / protein transmembrane transport / 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 ...mitochondrial outer membrane translocase complex / protein import into mitochondrial matrix / protein transmembrane transport / 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 / cellular response to hypoxia / mitochondrial outer membrane / mitochondrion
Similarity search - Function
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
GEO13367p1 / Mitochondrial import receptor subunit TOM7 homolog / RH17559p / Mitochondrial import receptor subunit TOM22 homolog / Mitochondrial import receptor subunit TOM40 homolog 1
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.35 Å
AuthorsOrnelas P / Kuehlbrandt W
Funding support Germany, 1 items
OrganizationGrant numberCountry
Max Planck Society Germany
CitationJournal: IUCrJ / Year: 2025
Title: Structure of an ex vivoDrosophila TOM complex determined by single-particle cryoEM.
Authors: Agalya Periasamy / Pamela Ornelas / Thomas Bausewein / Naomi Mitchell / Jiamin Zhao / Leonie M Quinn / Werner Kuehlbrandt / Jacqueline M Gulbis /
Abstract: Most mitochondrial precursor proteins are encoded in the cell nucleus and synthesized on cytoplasmic ribosomes. The translocase of the outer membrane (TOM) is the main protein-import pore of ...Most mitochondrial precursor proteins are encoded in the cell nucleus and synthesized on cytoplasmic ribosomes. The translocase of the outer membrane (TOM) is the main protein-import pore of mitochondria, recognizing nascent precursors of mitochondrially targeted proteins and transferring them across the outer membrane. A 3.3 Å resolution map and molecular model of a TOM complex from Drosophila melanogaster, obtained by single-particle electron cryomicroscopy, is presented. As the first reported structure of a transgenic protein expressed and purified ex vivo from Drosophila, the method provides impetus for parallel structural and genetic analyses of protein complexes linked to human pathology. The core TOM complex extracted from native membranes of the D. melanogaster retina contains transgenic Tom40 co-assembled with four endogenous TOM components: Tom22, Tom5, Tom6 and Tom7. The Drosophila TOM structure presented here shows that the human and Drosophila TOM are very similar, with small conformational changes at two subunit interfaces attributable to variation in lipid-binding residues. The new structure provides an opportunity to pinpoint general features that differentiate the TOM structures of higher and unicellular eukaryotes. While the quaternary fold of the assembly is retained, local nuances of structural elements implicated in precursor import are indicative of subtle evolutionary change.
History
DepositionMar 26, 2024-
Header (metadata) releaseDec 4, 2024-
Map releaseDec 4, 2024-
UpdateJan 22, 2025-
Current statusJan 22, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_19944.png

Downloads & links

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Map

FileDownload / File: emd_19944.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMap of the translocase of the outer mitochondrial membrane of Drosophila melanogaster. Main 3D volume. Sharpened map.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 360 pix.
= 301.32 Å		0.84 Å/pix.
x 360 pix.
= 301.32 Å		0.84 Å/pix.
x 360 pix.
= 301.32 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.837 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.11
Minimum - Maximum-0.6644163 - 0.9359728
Average (Standard dev.)0.00014972432 (±0.0154036265)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 301.32 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Volume half map A

Fileemd_19944_half_map_1.map
AnnotationVolume half map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Volume half map B

Fileemd_19944_half_map_2.map
AnnotationVolume half map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Translocase of the outer mitochondrial membrane core complex of D...

EntireName: Translocase of the outer mitochondrial membrane core complex of Drosophila melanogaster
Components
  • Complex: Translocase of the outer mitochondrial membrane core complex of Drosophila melanogaster
    • Protein or peptide: Mitochondrial import receptor subunit TOM6
    • Protein or peptide: Mitochondrial import receptor subunit TOM5
    • Protein or peptide: Mitochondrial import receptor subunit TOM7
    • Protein or peptide: Mitochondrial import receptor subunit TOM22
    • Protein or peptide: Mitochondrial import receptor subunit TOM40
  • Ligand: DIUNDECYL PHOSPHATIDYL CHOLINE

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Supramolecule #1: Translocase of the outer mitochondrial membrane core complex of D...

SupramoleculeName: Translocase of the outer mitochondrial membrane core complex of Drosophila melanogaster
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5
Source (natural)Organism: Drosophila melanogaster (fruit fly)

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Macromolecule #1: Mitochondrial import receptor subunit TOM6

MacromoleculeName: Mitochondrial import receptor subunit TOM6 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Drosophila melanogaster (fruit fly)
Molecular weightTheoretical: 4.883772 KDa
SequenceString:
PLSIVRSIYN NEFQWMLVKS YGLFFLGVRL AKEFVGVELM PS

UniProtKB: GEO13367p1

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Macromolecule #2: Mitochondrial import receptor subunit TOM5

MacromoleculeName: Mitochondrial import receptor subunit TOM5 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Drosophila melanogaster (fruit fly)
Molecular weightTheoretical: 4.308033 KDa
SequenceString:
SQPDPAEEQK RVAAEVRFNF ILFGAVIAAV RLAPIVLKH

UniProtKB: RH17559p

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Macromolecule #3: Mitochondrial import receptor subunit TOM7

MacromoleculeName: Mitochondrial import receptor subunit TOM7 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Drosophila melanogaster (fruit fly)
Molecular weightTheoretical: 5.138079 KDa
SequenceString:
DRLGFVVGVV QTGFHWGFVP LVLYLGFMKG AEPGMPPLNL FSLLWQ

UniProtKB: Mitochondrial import receptor subunit TOM7 homolog

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Macromolecule #4: Mitochondrial import receptor subunit TOM22

MacromoleculeName: Mitochondrial import receptor subunit TOM22 / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Drosophila melanogaster (fruit fly)
Molecular weightTheoretical: 5.352121 KDa
SequenceString:
ATVKSVKGFY SFSCNASWIF FTSAVILFAP VIFETERAQM EELHKSQ

UniProtKB: Mitochondrial import receptor subunit TOM22 homolog

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Macromolecule #5: Mitochondrial import receptor subunit TOM40

MacromoleculeName: Mitochondrial import receptor subunit TOM40 / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Drosophila melanogaster (fruit fly)
Molecular weightTheoretical: 31.382713 KDa
Recombinant expressionOrganism: Drosophila melanogaster (fruit fly)
SequenceString: AALENPGTVE ELHKKCKDIQ AITFEGAKIM LNKGLSNHFQ VSHTINMSNV VPSGYRFGAT YVGTKEFSPT EAFPVLLGDI DPAGNLNAN VIHQFSARLR CKFASQIQES KVVASQLTTD YRGSDYTLSL TVANPSIFTN SGVVVGQYLQ SVTPALALGS E LAYQFGPN ...String:
AALENPGTVE ELHKKCKDIQ AITFEGAKIM LNKGLSNHFQ VSHTINMSNV VPSGYRFGAT YVGTKEFSPT EAFPVLLGDI DPAGNLNAN VIHQFSARLR CKFASQIQES KVVASQLTTD YRGSDYTLSL TVANPSIFTN SGVVVGQYLQ SVTPALALGS E LAYQFGPN VPGRQIAIMS VVGRYTAGSS VWSGTLGQSG LHVCYYQKAS DQLQIGAEVE TSLRMQESVA TLAYQIDLPK AN LVFRGGI DSNWQIFGVL EKRLAPLPFT LALSGRMNHV KNNFRLGCGL MIG

UniProtKB: Mitochondrial import receptor subunit TOM40 homolog 1

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Macromolecule #6: DIUNDECYL PHOSPHATIDYL CHOLINE

MacromoleculeName: DIUNDECYL PHOSPHATIDYL CHOLINE / type: ligand / ID: 6 / Number of copies: 5 / Formula: PLC
Molecular weightTheoretical: 622.834 Da
Chemical component information

ChemComp-PLC:
DIUNDECYL PHOSPHATIDYL CHOLINE / 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: 7.4
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Detector mode: COUNTING / Average electron dose: 55.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.4 µm / Nominal defocus min: 1.4000000000000001 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.35 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 198185
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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