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- PDB-6jnf: Cryo-EM structure of the translocator of the outer mitochondrial ... -

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Basic information

Entry
Database: PDB / ID: 6jnf
TitleCryo-EM structure of the translocator of the outer mitochondrial membrane
Components(Mitochondrial import receptor subunit ...) x 5
KeywordsTRANSLOCASE / alpha/beta translocator / membrane protein complex / Protein import / mitochondria
Function / homology
Function and homology information


mitochondrial outer membrane translocase complex assembly / mitochondrial outer membrane translocase complex / protein import into mitochondrial matrix / protein transmembrane transport / 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 assembly / mitochondrial outer membrane translocase complex / protein import into mitochondrial matrix / protein transmembrane transport / protein targeting to mitochondrion / porin activity / pore complex / protein insertion into mitochondrial outer membrane / protein transmembrane transporter activity / monoatomic ion 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 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 ...Mitochondrial import receptor subunit Tom6 / Mitochondrial import receptor subunit Tom22, fungi / Mitochondrial import receptor subunit Tom6, fungal / Mitochondrial import receptor subunit Tom40, fungi / 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
Chem-46E / 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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.81 Å
AuthorsAraiso, Y. / Tsutsumi, A. / Suzuki, J. / Yunoki, K. / Kawano, S. / Kikkawa, M. / Endo, T.
Funding support Japan, 5items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science15H05705 Japan
Japan Society for the Promotion of Science2222703 Japan
Japan Science and TechnologyJPMJCR12M1 Japan
Japan Society for the Promotion of Science15J07687 Japan
Japan Agency for Medical Research and Development (AMED)JP19am01011115 Japan
CitationJournal: Nature / Year: 2019
Title: Structure of the mitochondrial import gate reveals distinct preprotein paths.
Authors: Yuhei Araiso / Akihisa Tsutsumi / Jian Qiu / Kenichiro Imai / Takuya Shiota / Jiyao Song / Caroline Lindau / Lena-Sophie Wenz / Haruka Sakaue / Kaori Yunoki / Shin Kawano / Junko Suzuki / ...Authors: Yuhei Araiso / Akihisa Tsutsumi / Jian Qiu / Kenichiro Imai / Takuya Shiota / Jiyao Song / Caroline Lindau / Lena-Sophie Wenz / Haruka Sakaue / Kaori Yunoki / Shin Kawano / Junko Suzuki / Marilena Wischnewski / Conny Schütze / Hirotaka Ariyama / Toshio Ando / Thomas Becker / Trevor Lithgow / Nils Wiedemann / Nikolaus Pfanner / Masahide Kikkawa / Toshiya Endo /
Abstract: The translocase of the outer mitochondrial membrane (TOM) is the main entry gate for proteins. Here we use cryo-electron microscopy to report the structure of the yeast TOM core complex at 3.8-Å ...The translocase of the outer mitochondrial membrane (TOM) is the main entry gate for proteins. Here we use cryo-electron microscopy to report the structure of the yeast TOM core complex at 3.8-Å resolution. The structure reveals the high-resolution architecture of the translocator consisting of two Tom40 β-barrel channels and α-helical transmembrane subunits, providing insight into critical features that are conserved in all eukaryotes. Each Tom40 β-barrel is surrounded by small TOM subunits, and tethered by two Tom22 subunits and one phospholipid. The N-terminal extension of Tom40 forms a helix inside the channel; mutational analysis reveals its dual role in early and late steps in the biogenesis of intermembrane-space proteins in cooperation with Tom5. Each Tom40 channel possesses two precursor exit sites. Tom22, Tom40 and Tom7 guide presequence-containing preproteins to the exit in the middle of the dimer, whereas Tom5 and the Tom40 N extension guide preproteins lacking a presequence to the exit at the periphery of the dimer.
History
DepositionMar 14, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 16, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2019Group: Database references / Category: citation
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Nov 27, 2019Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)160,30311
Polymers159,66710
Non-polymers6361
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area17240 Å2
ΔGint-155 kcal/mol
Surface area55990 Å2

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Components

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

#1: Protein Mitochondrial import receptor subunit TOM40


Mass: 42071.141 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288c (yeast) / Strain: S288c / Gene: TOM40 / Production host: Saccharomyces cerevisiae (brewer's yeast) / Strain (production host): D273-10B yeast / References: UniProt: P23644
#2: Protein Mitochondrial import receptor subunit TOM7


Mass: 6876.955 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288c (yeast) / Strain: S288c / Gene: TOM7 / Production host: Saccharomyces cerevisiae (brewer's yeast) / Strain (production host): D273-10B yeast / References: UniProt: P53507
#3: Protein Mitochondrial import receptor subunit TOM22


Mass: 18481.139 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288c (yeast) / Strain: S288c / Gene: TOM22 / Production host: Saccharomyces cerevisiae (brewer's yeast) / Strain (production host): D273-10B yeast / References: UniProt: P49334
#4: Protein/peptide Mitochondrial import receptor subunit TOM5


Mass: 5993.924 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288c (yeast) / Strain: S288c / Gene: TOM5 / Production host: Saccharomyces cerevisiae (brewer's yeast) / Strain (production host): D273-10B yeast / References: UniProt: P80967
#5: Protein Mitochondrial import receptor subunit TOM6


Mass: 6410.460 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288c (yeast) / Strain: S288c / Gene: TOM6 / Production host: Saccharomyces cerevisiae (brewer's yeast) / Strain (production host): D273-10B yeast / References: UniProt: P33448

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Non-polymers , 1 types, 1 molecules

#6: Chemical ChemComp-46E / (2R)-3-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-(tetradecanoyloxy)propyl tetradecanoate


Mass: 635.853 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C33H66NO8P / Feature type: SUBJECT OF INVESTIGATION

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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: TOM complex / Type: COMPLEX / Entity ID: #1-#5 / Source: RECOMBINANT
Source (natural)Organism: Saccharomyces cerevisiae S288c (yeast) / Strain: S288c
Source (recombinant)Organism: Saccharomyces cerevisiae (brewer's yeast)
Buffer solutionpH: 7.4
SpecimenConc.: 5.4 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER/RHODIUM / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil, UltrAuFoil, R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 279 K

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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 / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 50 e/Å2 / Film or detector model: FEI FALCON III (4k x 4k)

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Processing

Software
NameVersionClassificationNB
phenix.real_space_refine1.14_3260refinement
PHENIX1.14_3260refinement
EM software
IDNameVersionCategory
1RELION3particle selection
2EPUimage acquisition
4CTFFIND4.1.13CTF correction
5RELION3CTF correction
11RELION3initial Euler assignment
12RELION3final Euler assignment
14RELION33D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 3.81 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 124653 / Symmetry type: POINT
RefinementStereochemistry target values: CDL v1.2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00847422
ELECTRON MICROSCOPYf_angle_d1.145510053
ELECTRON MICROSCOPYf_chiral_restr0.06311141
ELECTRON MICROSCOPYf_plane_restr0.00741272
ELECTRON MICROSCOPYf_dihedral_angle_d9.32574361

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