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Yorodumi- EMDB-20729: Cryo-EM structure of the mitochondrial TOM complex from yeast (te... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-20729 | |||||||||
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Title | Cryo-EM structure of the mitochondrial TOM complex from yeast (tetramer) | |||||||||
Map data | Filtered, sharpened map | |||||||||
Sample |
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Keywords | Membrane protein / mitochondrial protein import / mitochondrial outer membrane / protein translocation / TRANSLOCASE | |||||||||
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 / protein insertion into mitochondrial outer membrane / porin activity / pore complex / 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 / 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 (strain ATCC 204508 / S288c) (yeast) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.1 Å | |||||||||
Authors | Park E / Tucker K | |||||||||
Funding support | United States, 2 items
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Citation | Journal: Nat Struct Mol Biol / Year: 2019 Title: Cryo-EM structure of the mitochondrial protein-import channel TOM complex at near-atomic resolution. Authors: Kyle Tucker / Eunyong Park / Abstract: Nearly all mitochondrial proteins are encoded by the nuclear genome and imported into mitochondria after synthesis on cytosolic ribosomes. These precursor proteins are translocated into mitochondria ...Nearly all mitochondrial proteins are encoded by the nuclear genome and imported into mitochondria after synthesis on cytosolic ribosomes. These precursor proteins are translocated into mitochondria by the TOM complex, a protein-conducting channel in the mitochondrial outer membrane. We have determined high-resolution cryo-EM structures of the core TOM complex from Saccharomyces cerevisiae in dimeric and tetrameric forms. Dimeric TOM consists of two copies each of five proteins arranged in two-fold symmetry: pore-forming β-barrel protein Tom40 and four auxiliary α-helical transmembrane proteins. The pore of each Tom40 has an overall negatively charged inner surface attributed to multiple functionally important acidic patches. The tetrameric complex is essentially a dimer of dimeric TOM, which may be capable of forming higher-order oligomers. Our study reveals the detailed molecular organization of the TOM complex and provides new insights about the mechanism of protein translocation into mitochondria. | |||||||||
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_20729.map.gz | 229.9 MB | EMDB map data format | |
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Header (meta data) | emd-20729-v30.xml emd-20729.xml | 18.8 KB 18.8 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_20729_fsc.xml | 14.5 KB | Display | FSC data file |
Images | emd_20729.png | 181.6 KB | ||
Filedesc metadata | emd-20729.cif.gz | 6 KB | ||
Others | emd_20729_additional.map.gz | 226.2 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-20729 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-20729 | HTTPS FTP |
-Validation report
Summary document | emd_20729_validation.pdf.gz | 515.4 KB | Display | EMDB validaton report |
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Full document | emd_20729_full_validation.pdf.gz | 515 KB | Display | |
Data in XML | emd_20729_validation.xml.gz | 13.5 KB | Display | |
Data in CIF | emd_20729_validation.cif.gz | 18.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-20729 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-20729 | HTTPS FTP |
-Related structure data
Related structure data | 6ucvMC 6ucuC C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_20729.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Filtered, sharpened map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.15 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Additional map: Raw combined map
File | emd_20729_additional.map | ||||||||||||
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Annotation | Raw combined map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Tetrameric TOM complex from yeast
Entire | Name: Tetrameric TOM complex from yeast |
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Components |
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-Supramolecule #1: Tetrameric TOM complex from yeast
Supramolecule | Name: Tetrameric TOM complex from yeast / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5 |
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Source (natural) | Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c |
-Macromolecule #1: Mitochondrial import receptor subunit TOM40
Macromolecule | Name: Mitochondrial import receptor subunit TOM40 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c |
Molecular weight | Theoretical: 43.227387 KDa |
Recombinant expression | Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (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 LGGWSHPQFE K UniProtKB: Mitochondrial import receptor subunit TOM40 |
-Macromolecule #2: Mitochondrial import receptor subunit TOM22
Macromolecule | Name: Mitochondrial import receptor subunit TOM22 / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c |
Molecular weight | Theoretical: 18.02065 KDa |
Recombinant expression | Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) |
Sequence | String: MVELTEIKDD VVQLDEPQFS RNQAIVEEKA SATNNDVVDD EDDSDSDFED EFDENETLLD RIVALKDIVP PGKRQTISNF FGFTSSFVR NAFTKSGNLA WTLTTTALLL GVPLSLSILA EQQLIEMEKT FDLQSDANNI LAQGEKDAAA TANGGHHHHH H HH UniProtKB: Mitochondrial import receptor subunit TOM22 |
-Macromolecule #3: Mitochondrial import receptor subunit TOM5
Macromolecule | Name: Mitochondrial import receptor subunit TOM5 / type: protein_or_peptide / ID: 3 / Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c |
Molecular weight | Theoretical: 5.993924 KDa |
Recombinant expression | Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) |
Sequence | String: MFGLPQQEVS EEEKRAHQEQ TEKTLKQAAY VAAFLWVSPM IWHLVKKQWK UniProtKB: Mitochondrial import receptor subunit TOM5 |
-Macromolecule #4: Mitochondrial import receptor subunit TOM6
Macromolecule | Name: Mitochondrial import receptor subunit TOM6 / type: protein_or_peptide / ID: 4 / Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c |
Molecular weight | Theoretical: 6.41046 KDa |
Recombinant expression | Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) |
Sequence | String: MDGMFAMPGA AAGAASPQQP KSRFQAFKES PLYTIALNGA FFVAGVAFIQ SPLMDMLAPQ L UniProtKB: Mitochondrial import receptor subunit TOM6 |
-Macromolecule #5: Mitochondrial import receptor subunit TOM7
Macromolecule | Name: Mitochondrial import receptor subunit TOM7 / type: protein_or_peptide / ID: 5 / Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c |
Molecular weight | Theoretical: 6.876955 KDa |
Recombinant expression | Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) |
Sequence | String: MSFLPSFILS DESKERISKI LTLTHNVAHY GWIPFVLYLG WAHTSNRPNF LNLLSPLPSV UniProtKB: Mitochondrial import receptor subunit TOM7 |
-Macromolecule #6: 1,2-DIMYRISTOYL-RAC-GLYCERO-3-PHOSPHOCHOLINE
Macromolecule | Name: 1,2-DIMYRISTOYL-RAC-GLYCERO-3-PHOSPHOCHOLINE / type: ligand / ID: 6 / Number of copies: 2 / Formula: MC3 |
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Molecular weight | Theoretical: 677.933 Da |
Chemical component information | ChemComp-MC3: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Grid | Support film - Material: CARBON / Support film - topology: HOLEY / Details: unspecified |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: COUNTING / Average electron dose: 43.9 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |