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Yorodumi- PDB-6ucu: Cryo-EM structure of the mitochondrial TOM complex from yeast (dimer) -
+Open data
-Basic information
Entry | Database: PDB / ID: 6ucu | |||||||||
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Title | Cryo-EM structure of the mitochondrial TOM complex from yeast (dimer) | |||||||||
Components | (Mitochondrial import receptor subunit ...) x 5 | |||||||||
Keywords | TRANSLOCASE / Membrane protein / mitochondrial protein import / mitochondrial outer membrane / protein translocation | |||||||||
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 / protein insertion into mitochondrial outer membrane / 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 / porin activity / protein insertion into mitochondrial outer membrane / pore complex / protein transmembrane transporter activity / monoatomic ion transport / mitochondrial intermembrane space / mitochondrial outer membrane / mitochondrion / cytosol Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.06 Å | |||||||||
Authors | Park, E. / Tucker, K. | |||||||||
Funding support | United States, 2items
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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 | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6ucu.cif.gz | 233 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ucu.ent.gz | 187.1 KB | Display | PDB format |
PDBx/mmJSON format | 6ucu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6ucu_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 6ucu_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 6ucu_validation.xml.gz | 40.8 KB | Display | |
Data in CIF | 6ucu_validation.cif.gz | 58.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uc/6ucu ftp://data.pdbj.org/pub/pdb/validation_reports/uc/6ucu | HTTPS FTP |
-Related structure data
Related structure data | 20728MC 6ucvC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Mitochondrial import receptor subunit ... , 5 types, 10 molecules AIBJCKDLEM
#1: Protein | Mass: 43227.387 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / Gene: TOM40, ISP42, MOM38, YMR203W, YM8325.04 Production host: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain (production host): ATCC 204508 / S288c / References: UniProt: P23644 #2: Protein | Mass: 18020.650 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / Gene: TOM22, MAS17, MAS22, MOM22, YNL131W, N1217, N1862 Production host: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain (production host): ATCC 204508 / S288c / References: UniProt: P49334 #3: Protein/peptide | Mass: 5993.924 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / Gene: TOM5, MOM8A, YPR133W-A Production host: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain (production host): ATCC 204508 / S288c / References: UniProt: P80967 #4: Protein | Mass: 6410.460 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / Gene: TOM6, ISP6, YOR045W Production host: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain (production host): ATCC 204508 / S288c / References: UniProt: P33448 #5: Protein | Mass: 6876.955 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / Gene: TOM7, MOM7, YNL070W, N2378 Production host: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain (production host): ATCC 204508 / S288c / References: UniProt: P53507 |
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-Sugars , 1 types, 60 molecules
#6: Sugar | ChemComp-LMT / |
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-Details
Has ligand of interest | Y |
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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: Dimeric TOM complex from yeast / Type: COMPLEX / Entity ID: #1-#5 / Source: RECOMBINANT |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c |
Source (recombinant) | Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: GOLD / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R1.2/1.3 |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 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 / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 61 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 QUANTUM (4k x 4k) |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||
Symmetry | Point symmetry: C2 (2 fold cyclic) | ||||||||||||||||||||
3D reconstruction | Resolution: 3.06 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 160577 / Symmetry type: POINT |