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- PDB-9etm: cryoEM structure of the Drosophila melanogaster TOM core complex -

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Basic information

Entry
Database: PDB / ID: 9etm
TitlecryoEM structure of the Drosophila melanogaster TOM core complex
Components(Mitochondrial import receptor subunit ...) x 5
KeywordsMEMBRANE PROTEIN / Complex / outer membrane / mitochondria / TOM / translocase
Function / homology
Function and homology information


mitochondrial outer membrane translocase complex / protein insertion into mitochondrial outer membrane / protein transmembrane transport / positive regulation of protein targeting to mitochondrion / protein targeting to mitochondrion / porin activity / pore complex / protein import into mitochondrial matrix / protein transmembrane transporter activity / monoatomic ion transport ...mitochondrial outer membrane translocase complex / protein insertion into mitochondrial outer membrane / protein transmembrane transport / positive regulation of protein targeting to mitochondrion / protein targeting to mitochondrion / porin activity / pore complex / protein import into mitochondrial matrix / protein transmembrane transporter activity / monoatomic ion transport / cellular response to hypoxia / mitochondrial outer membrane / mitochondrion
Similarity search - Function
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
DIUNDECYL PHOSPHATIDYL CHOLINE / 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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.35 Å
AuthorsOrnelas, P. / Kuehlbrandt, W.
Funding support Germany, 1items
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, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 4, 2024Provider: repository / Type: Initial release
Revision 1.0Dec 4, 2024Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Dec 4, 2024Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Dec 4, 2024Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Dec 4, 2024Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Dec 4, 2024Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Dec 4, 2024Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.0Dec 4, 2024Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Dec 4, 2024Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Dec 4, 2024Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Dec 4, 2024Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Dec 4, 2024Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Jan 22, 2025Group: Data collection / Database references / Category: citation / em_admin
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _em_admin.last_update
Revision 1.2Jul 9, 2025Group: Data collection / Category: em_admin / em_software / Item: _em_admin.last_update / _em_software.name
Revision 1.1Jul 9, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Data processing / Experimental summary / Data content type: EM metadata / EM metadata / Category: em_admin / em_software / Data content type: EM metadata / EM metadata / Item: _em_admin.last_update / _em_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
G: Mitochondrial import receptor subunit TOM6
I: Mitochondrial import receptor subunit TOM5
E: Mitochondrial import receptor subunit TOM7
C: Mitochondrial import receptor subunit TOM22
A: Mitochondrial import receptor subunit TOM40
H: Mitochondrial import receptor subunit TOM6
J: Mitochondrial import receptor subunit TOM5
F: Mitochondrial import receptor subunit TOM7
D: Mitochondrial import receptor subunit TOM22
B: Mitochondrial import receptor subunit TOM40
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,24415
Polymers102,12910
Non-polymers3,1145
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Mitochondrial import receptor subunit ... , 5 types, 10 molecules GHIJEFCDAB

#1: Protein/peptide Mitochondrial import receptor subunit TOM6 / Mitochondrial import receptor subunit Tom6 / Translocase of outer membrane 6 kDa subunit homolog / ...Mitochondrial import receptor subunit Tom6 / Translocase of outer membrane 6 kDa subunit homolog / dtom6 / GEO13367p1


Mass: 4883.772 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt: Q6IGW6
#2: Protein/peptide Mitochondrial import receptor subunit TOM5 / Mitochondrial import receptor subunit Tom5 / Translocase of outer membrane 5 kDa subunit homolog / ...Mitochondrial import receptor subunit Tom5 / Translocase of outer membrane 5 kDa subunit homolog / dtom5 / RH17559p


Mass: 4308.033 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt: Q8IRD0
#3: Protein/peptide Mitochondrial import receptor subunit TOM7 / Mitochondrial import receptor subunit Tom7 / Translocase of outer membrane 7 kDa subunit homolog / ...Mitochondrial import receptor subunit Tom7 / Translocase of outer membrane 7 kDa subunit homolog / dtom7 / Mitochondrial import receptor subunit TOM7 homolog


Mass: 5138.079 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt: Q7K036
#4: Protein/peptide Mitochondrial import receptor subunit TOM22 / Mitochondrial import receptor subunit Tom22 / Translocase of outer membrane 22 kDa subunit homolog ...Mitochondrial import receptor subunit Tom22 / Translocase of outer membrane 22 kDa subunit homolog / dtom22 / itochondrial import receptor subunit TOM22 homolog


Mass: 5352.121 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt: Q9I7T5
#5: Protein Mitochondrial import receptor subunit TOM40 / Mitochondrial import receptor subunit Tom40 / Translocase of outer membrane 40 kDa subunit homolog ...Mitochondrial import receptor subunit Tom40 / Translocase of outer membrane 40 kDa subunit homolog / dtom40 / Male sterile protein 15 / Translocase of outer membrane 40 kDa subunit homolog 1


Mass: 31382.713 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: Tom40, mit, ms(1)15, CG12157 / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: Q9U4L6

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Non-polymers , 1 types, 5 molecules

#6: Chemical
ChemComp-PLC / DIUNDECYL PHOSPHATIDYL CHOLINE


Mass: 622.834 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C32H65NO8P / Comment: phospholipid*YM

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Details

Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Translocase of the outer mitochondrial membrane core complex of Drosophila melanogaster
Type: COMPLEX / Entity ID: #1-#5 / Source: RECOMBINANT
Source (natural)Organism: Drosophila melanogaster (fruit fly)
Source (recombinant)Organism: Drosophila melanogaster (fruit fly)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2400 nm / Nominal defocus min: 1400 nm
Image recordingElectron dose: 55 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.35 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 198185 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0037565
ELECTRON MICROSCOPYf_angle_d0.6410221
ELECTRON MICROSCOPYf_dihedral_angle_d13.8282747
ELECTRON MICROSCOPYf_chiral_restr0.0441127
ELECTRON MICROSCOPYf_plane_restr0.0071286

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