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Yorodumi- PDB-5o8o: N. crassa Tom40 model based on cryo-EM structure of the TOM core ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5o8o | ||||||
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Title | N. crassa Tom40 model based on cryo-EM structure of the TOM core complex at 6.8 A | ||||||
Components | Mitochondrial import receptor subunit tom40 | ||||||
Keywords | PROTEIN TRANSPORT / TOM-Complex / Protein Import / Mitochondria / Cryo-EM | ||||||
Function / homology | Function and homology information mitochondrial outer membrane translocase complex / protein import into mitochondrial matrix / porin activity / pore complex / protein transmembrane transporter activity Similarity search - Function | ||||||
Biological species | Neurospora crassa (fungus) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 6.8 Å | ||||||
Authors | Bausewein, T. / Mills, D.J. / Nussberger, S. / Nitschke, B. / Kuehlbrandt, W. | ||||||
Funding support | Germany, 1items
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Citation | Journal: Cell / Year: 2017 Title: Cryo-EM Structure of the TOM Core Complex from Neurospora crassa. Authors: Thomas Bausewein / Deryck J Mills / Julian D Langer / Beate Nitschke / Stephan Nussberger / Werner Kühlbrandt / Abstract: The TOM complex is the main entry gate for protein precursors from the cytosol into mitochondria. We have determined the structure of the TOM core complex by cryoelectron microscopy (cryo-EM). The ...The TOM complex is the main entry gate for protein precursors from the cytosol into mitochondria. We have determined the structure of the TOM core complex by cryoelectron microscopy (cryo-EM). The complex is a 148 kDa symmetrical dimer of ten membrane protein subunits that create a shallow funnel on the cytoplasmic membrane surface. In the core of the dimer, the β-barrels of the Tom40 pore form two identical preprotein conduits. Each Tom40 pore is surrounded by the transmembrane segments of the α-helical subunits Tom5, Tom6, and Tom7. Tom22, the central preprotein receptor, connects the two Tom40 pores at the dimer interface. Our structure offers detailed insights into the molecular architecture of the mitochondrial preprotein import machinery. | ||||||
History |
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-Structure visualization
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Structure viewer | Molecule: MolmilJmol/JSmol |
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PDBx/mmCIF format | 5o8o.cif.gz | 113.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5o8o.ent.gz | 87.3 KB | Display | PDB format |
PDBx/mmJSON format | 5o8o.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5o8o_validation.pdf.gz | 720.2 KB | Display | wwPDB validaton report |
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Full document | 5o8o_full_validation.pdf.gz | 721.7 KB | Display | |
Data in XML | 5o8o_validation.xml.gz | 20 KB | Display | |
Data in CIF | 5o8o_validation.cif.gz | 28.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o8/5o8o ftp://data.pdbj.org/pub/pdb/validation_reports/o8/5o8o | HTTPS FTP |
-Related structure data
Related structure data | 3761MC 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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-Components
#1: Protein | Mass: 38184.797 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987) (fungus) Strain: ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987 References: UniProt: P24391 |
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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 core complex consisting of Tom40, Tom22, Tom5, Tom6 and Tom7 Type: COMPLEX / Entity ID: all / Source: NATURAL |
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Source (natural) | Organism: Neurospora crassa (fungus) / Strain: GR-107 |
Buffer solution | pH: 7.2 |
Specimen | Conc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Microscopy | Model: JEOL 3200FSC |
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Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 60 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (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: 6.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 92144 / Symmetry type: POINT | |||||||||
Atomic model building | Protocol: FLEXIBLE FIT |