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Yorodumi- PDB-6jnf: Cryo-EM structure of the translocator of the outer mitochondrial ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6jnf | ||||||||||||||||||
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Title | Cryo-EM structure of the translocator of the outer mitochondrial membrane | ||||||||||||||||||
Components | (Mitochondrial import receptor subunit ...) x 5 | ||||||||||||||||||
Keywords | TRANSLOCASE / 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 targeting to mitochondrion / protein insertion into mitochondrial outer membrane / porin activity / pore complex / protein transmembrane transporter activity / monoatomic ion transport / mitochondrial intermembrane space ...mitochondrial outer membrane translocase complex assembly / mitochondrial outer membrane translocase complex / protein import into mitochondrial matrix / protein targeting to mitochondrion / protein insertion into mitochondrial outer membrane / porin activity / pore complex / protein transmembrane transporter activity / monoatomic ion transport / mitochondrial intermembrane space / mitochondrial outer membrane / mitochondrion / cytosol Similarity search - Function | ||||||||||||||||||
Biological species | Saccharomyces cerevisiae S288c (yeast) | ||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.81 Å | ||||||||||||||||||
Authors | Araiso, Y. / Tsutsumi, A. / Suzuki, J. / Yunoki, K. / Kawano, S. / Kikkawa, M. / Endo, T. | ||||||||||||||||||
Funding support | Japan, 5items
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Citation | Journal: 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 |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6jnf.cif.gz | 185.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6jnf.ent.gz | 138.1 KB | Display | PDB format |
PDBx/mmJSON format | 6jnf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6jnf_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 6jnf_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 6jnf_validation.xml.gz | 37.4 KB | Display | |
Data in CIF | 6jnf_validation.cif.gz | 56.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jn/6jnf ftp://data.pdbj.org/pub/pdb/validation_reports/jn/6jnf | HTTPS FTP |
-Related structure data
Related structure data | 9851MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | |
EM raw data | EMPIAR-10332 (Title: Cryo-EM structure of the translocator of the outer mitochondrial membrane Data size: 1.9 TB Data #1: Unaligned multi-frame micrographs of yeast TOM complex [micrographs - multiframe]) |
-Links
-Assembly
Deposited unit |
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-Components
-Mitochondrial import receptor subunit ... , 5 types, 10 molecules AFBGCHDIEJ
#1: Protein | 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 | 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 | 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 | 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 | 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 / ( |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: TOM complex / Type: COMPLEX / Entity ID: #1-#5 / Source: RECOMBINANT |
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Source (natural) | Organism: Saccharomyces cerevisiae S288c (yeast) / Strain: S288c |
Source (recombinant) | Organism: Saccharomyces cerevisiae (brewer's yeast) |
Buffer solution | pH: 7.4 |
Specimen | Conc.: 5.4 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER/RHODIUM / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil, UltrAuFoil, R1.2/1.3 |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 279 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: FEI FALCON III (4k x 4k) |
-Processing
Software |
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C2 (2 fold cyclic) | ||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.81 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 124653 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||
Refinement | Stereochemistry target values: CDL v1.2 | ||||||||||||||||||||||||||||||||
Refine LS restraints |
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