+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-9851 | ||||||||||||||||||
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Title | membrane structure | ||||||||||||||||||
Map data | |||||||||||||||||||
Sample |
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Keywords | alpha/beta translocator / membrane protein complex / Protein import / mitochondria / TRANSLOCASE | ||||||||||||||||||
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 | single particle reconstruction / cryo EM / Resolution: 3.81 Å | ||||||||||||||||||
Authors | Araiso Y / Tsutsumi A | ||||||||||||||||||
Funding support | Japan, 5 items
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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 | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_9851.map.gz | 16.9 MB | EMDB map data format | |
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Header (meta data) | emd-9851-v30.xml emd-9851.xml | 22.4 KB 22.4 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_9851_fsc.xml | 8 KB | Display | FSC data file |
Images | emd_9851.png | 114.7 KB | ||
Masks | emd_9851_msk_1.map | 27 MB | Mask map | |
Filedesc metadata | emd-9851.cif.gz | 6.5 KB | ||
Others | emd_9851_half_map_1.map.gz emd_9851_half_map_2.map.gz | 19.7 MB 19.7 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-9851 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-9851 | HTTPS FTP |
-Validation report
Summary document | emd_9851_validation.pdf.gz | 731.7 KB | Display | EMDB validaton report |
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Full document | emd_9851_full_validation.pdf.gz | 731.2 KB | Display | |
Data in XML | emd_9851_validation.xml.gz | 12.4 KB | Display | |
Data in CIF | emd_9851_validation.cif.gz | 17.1 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-9851 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-9851 | HTTPS FTP |
-Related structure data
Related structure data | 6jnfMC M: atomic model generated by this map 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
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_9851.map.gz / Format: CCP4 / Size: 27 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.2915 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
File | emd_9851_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_9851_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_9851_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : TOM complex
Entire | Name: TOM complex |
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Components |
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-Supramolecule #1: TOM complex
Supramolecule | Name: TOM complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5 |
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Source (natural) | Organism: Saccharomyces cerevisiae S288c (yeast) / Strain: S288c |
-Macromolecule #1: Mitochondrial import receptor subunit TOM40
Macromolecule | Name: Mitochondrial import receptor subunit TOM40 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Saccharomyces cerevisiae S288c (yeast) / Strain: S288c |
Molecular weight | Theoretical: 42.071141 KDa |
Recombinant expression | Organism: Saccharomyces cerevisiae (brewer's yeast) |
Sequence | String: MSAPTPLAEA SQIPTIPALS PLTAKQSKGN FFSSNPISSF VVDTYKQLHS HRQSLELVNP GTVENLNKEV SRDVFLSQYF FTGLRADLN KAFSMNPAFQ TSHTFSIGSQ ALPKYAFSAL FANDNLFAQG NIDNDLSVSG RLNYGWDKKN ISKVNLQISD G QPTMCQLE ...String: MSAPTPLAEA SQIPTIPALS PLTAKQSKGN FFSSNPISSF VVDTYKQLHS HRQSLELVNP GTVENLNKEV SRDVFLSQYF FTGLRADLN KAFSMNPAFQ TSHTFSIGSQ ALPKYAFSAL FANDNLFAQG NIDNDLSVSG RLNYGWDKKN ISKVNLQISD G QPTMCQLE QDYQASDFSV NVKTLNPSFS EKGEFTGVAV ASFLQSVTPQ LALGLETLYS RTDGSAPGDA GVSYLTRYVS KK QDWIFSG QLQANGALIA SLWRKVAQNV EAGIETTLQA GMVPITDPLM GTPIGIQPTV EGSTTIGAKY EYRQSVYRGT LDS NGKVAC FLERKVLPTL SVLFCGEIDH FKNDTKIGCG LQFETAGNQE LLMLQQGLDA DGNPLQALPQ L UniProtKB: Mitochondrial import receptor subunit TOM40 |
-Macromolecule #2: Mitochondrial import receptor subunit TOM7
Macromolecule | Name: Mitochondrial import receptor subunit TOM7 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Saccharomyces cerevisiae S288c (yeast) / Strain: S288c |
Molecular weight | Theoretical: 6.876955 KDa |
Recombinant expression | Organism: Saccharomyces cerevisiae (brewer's yeast) |
Sequence | String: MSFLPSFILS DESKERISKI LTLTHNVAHY GWIPFVLYLG WAHTSNRPNF LNLLSPLPSV UniProtKB: Mitochondrial import receptor subunit TOM7 |
-Macromolecule #3: Mitochondrial import receptor subunit TOM22
Macromolecule | Name: Mitochondrial import receptor subunit TOM22 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Saccharomyces cerevisiae S288c (yeast) / Strain: S288c |
Molecular weight | Theoretical: 18.481139 KDa |
Recombinant expression | Organism: Saccharomyces cerevisiae (brewer's yeast) |
Sequence | String: MVELTEIKDD VVQLDEPQFS RNQAIVEEKA SATNNDVVDD EDDSDSDFED EFDENETLLD RIVALKDIVP PGKRQTISNF FGFTSSFVR NAFTKSGNLA WTLTTTALLL GVPLSLSILA EQQLIEMEKT FDLQSDANNI LAQGEKDAAA TANGSPGHHH H HHHHHH UniProtKB: Mitochondrial import receptor subunit TOM22 |
-Macromolecule #4: Mitochondrial import receptor subunit TOM5
Macromolecule | Name: Mitochondrial import receptor subunit TOM5 / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Saccharomyces cerevisiae S288c (yeast) / Strain: S288c |
Molecular weight | Theoretical: 5.993924 KDa |
Recombinant expression | Organism: Saccharomyces cerevisiae (brewer's yeast) |
Sequence | String: MFGLPQQEVS EEEKRAHQEQ TEKTLKQAAY VAAFLWVSPM IWHLVKKQWK UniProtKB: Mitochondrial import receptor subunit TOM5 |
-Macromolecule #5: Mitochondrial import receptor subunit TOM6
Macromolecule | Name: Mitochondrial import receptor subunit TOM6 / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Saccharomyces cerevisiae S288c (yeast) / Strain: S288c |
Molecular weight | Theoretical: 6.41046 KDa |
Recombinant expression | Organism: Saccharomyces cerevisiae (brewer's yeast) |
Sequence | String: MDGMFAMPGA AAGAASPQQP KSRFQAFKES PLYTIALNGA FFVAGVAFIQ SPLMDMLAPQ L UniProtKB: Mitochondrial import receptor subunit TOM6 |
-Macromolecule #6: (2R)-3-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-(tetradeca...
Macromolecule | Name: (2R)-3-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-(tetradecanoyloxy)propyl tetradecanoate type: ligand / ID: 6 / Number of copies: 1 / Formula: 46E |
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Molecular weight | Theoretical: 635.853 Da |
Chemical component information | ChemComp-46E: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 5.4 mg/mL |
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Buffer | pH: 7.4 |
Grid | Model: Quantifoil, UltrAuFoil, R1.2/1.3 / Material: COPPER/RHODIUM / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 279 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |