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Yorodumi- EMDB-3761: Cryo-EM structure of the TOM core complex from Neurospora crassa -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-3761 | |||||||||
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Title | Cryo-EM structure of the TOM core complex from Neurospora crassa | |||||||||
Map data | TOM core complex consisting of Tom40, Tom22, Tom5, Tom6 and Tom7 | |||||||||
Sample |
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Keywords | TOM-Complex / Protein Import / Mitochondria / Cryo-EM / PROTEIN TRANSPORT | |||||||||
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) / Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987) (fungus) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 6.8 Å | |||||||||
Authors | Bausewein T / Mills DJ | |||||||||
Funding support | Germany, 1 items
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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
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_3761.map.gz | 21.5 MB | EMDB map data format | |
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Header (meta data) | emd-3761-v30.xml emd-3761.xml | 9.5 KB 9.5 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_3761_fsc.xml | 6.3 KB | Display | FSC data file |
Images | emd_3761.png | 73.3 KB | ||
Filedesc metadata | emd-3761.cif.gz | 4.8 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-3761 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-3761 | HTTPS FTP |
-Validation report
Summary document | emd_3761_validation.pdf.gz | 259.9 KB | Display | EMDB validaton report |
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Full document | emd_3761_full_validation.pdf.gz | 259 KB | Display | |
Data in XML | emd_3761_validation.xml.gz | 9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-3761 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-3761 | HTTPS FTP |
-Related structure data
Related structure data | 5o8oMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_3761.map.gz / Format: CCP4 / Size: 23 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | TOM core complex consisting of Tom40, Tom22, Tom5, Tom6 and Tom7 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.12 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : TOM core complex consisting of Tom40, Tom22, Tom5, Tom6 and Tom7
Entire | Name: TOM core complex consisting of Tom40, Tom22, Tom5, Tom6 and Tom7 |
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Components |
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-Supramolecule #1: TOM core complex consisting of Tom40, Tom22, Tom5, Tom6 and Tom7
Supramolecule | Name: TOM core complex consisting of Tom40, Tom22, Tom5, Tom6 and Tom7 type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Neurospora crassa (fungus) / Strain: GR-107 |
-Macromolecule #1: Mitochondrial import receptor subunit tom40
Macromolecule | Name: Mitochondrial import receptor subunit tom40 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: 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 |
Molecular weight | Theoretical: 38.184797 KDa |
Sequence | String: MASFSTESPL AMLRDNAIYS SLSDAFNAFQ ERRKQFGLSN PGTIETIARE VQRDTLLTNY MFSGLRADVT KAFSLAPLFQ VSHQFAMGE RLNPYAFAAL YGTNQIFAQG NLDNEGALST RFNYRWGDRT ITKTQFSIGG GQDMAQFEHE HLGDDFSASL K AINPSFLD ...String: MASFSTESPL AMLRDNAIYS SLSDAFNAFQ ERRKQFGLSN PGTIETIARE VQRDTLLTNY MFSGLRADVT KAFSLAPLFQ VSHQFAMGE RLNPYAFAAL YGTNQIFAQG NLDNEGALST RFNYRWGDRT ITKTQFSIGG GQDMAQFEHE HLGDDFSASL K AINPSFLD GGLTGIFVGD YLQAVTPRLG LGLQAVWQRQ GLTQGPDTAI SYFARYKAGD WVASAQLQAQ GALNTSFWKK LT DRVQAGV DMTLSVAPSQ SMMGGLTKEG ITTFGAKYDF RMSTFRAQID SKGKLSCLLE KRLGAAPVTL TFAADVDHVT QQA KLGMSV SIEASDVDLQ EQQEGAQSLN IPF UniProtKB: Mitochondrial import receptor subunit tom40 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 1 mg/mL |
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Buffer | pH: 7.2 |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | JEOL 3200FSC |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 60.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
+Image processing
-Atomic model buiding 1
Refinement | Protocol: FLEXIBLE FIT |
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Output model | PDB-5o8o: |