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Yorodumi- PDB-8w5k: Cryo-EM structure of the yeast TOM core complex crosslinked by BS... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8w5k | ||||||
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Title | Cryo-EM structure of the yeast TOM core complex crosslinked by BS3 (from TOM-TIM23 complex) | ||||||
Components | (Mitochondrial import receptor subunit ...) x 5 | ||||||
Keywords | TRANSLOCASE / TOM complex | ||||||
Function / homology | Function and homology information mitochondrial outer membrane translocase complex assembly / mitochondrial outer membrane translocase complex / protein transmembrane transport / 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 outer membrane translocase complex assembly / mitochondrial outer membrane translocase complex / protein transmembrane transport / 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 (brewer's yeast) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å | ||||||
Authors | Wang, Q. / Guan, Z.Y. / Zhuang, J.J. / Huang, R. / Yin, P. | ||||||
Funding support | China, 1items
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Citation | Journal: Cell Discov / Year: 2024 Title: The architecture of substrate-engaged TOM-TIM23 supercomplex reveals preprotein proximity sites for mitochondrial protein translocation. Authors: Qiang Wang / Jinjin Zhuang / Rui Huang / Zeyuan Guan / Ling Yan / Sixing Hong / Liying Zhang / Can Huang / Zhu Liu / Ping Yin / | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8w5k.cif.gz | 179.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8w5k.ent.gz | 138.7 KB | Display | PDB format |
PDBx/mmJSON format | 8w5k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w5/8w5k ftp://data.pdbj.org/pub/pdb/validation_reports/w5/8w5k | HTTPS FTP |
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-Related structure data
Related structure data | 37295MC 8w5jC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Mitochondrial import receptor subunit ... , 5 types, 10 molecules BJCKDLEMFI
#1: Protein | Mass: 16801.373 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Gene: TOM22, MAS17, MAS22, MOM22, YNL131W, N1217, N1862 Production host: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) References: UniProt: P49334 #2: 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) Gene: TOM5, MOM8A, YPR133W-A Production host: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) References: UniProt: P80967 #3: 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) Gene: TOM6, ISP6, YOR045W Production host: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) References: UniProt: P33448 #4: 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) Gene: TOM7, MOM7, YNL070W, N2378 Production host: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) References: UniProt: P53507 #5: Protein | Mass: 42071.141 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Gene: TOM40, ISP42, MOM38, YMR203W, YM8325.04 Production host: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) References: UniProt: P23644 |
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-Non-polymers , 1 types, 1 molecules
#6: Chemical | ChemComp-46E / ( |
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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: TOM-TIM23 complex / Type: COMPLEX / Entity ID: #1-#5 / Source: RECOMBINANT |
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Source (natural) | Organism: Saccharomyces cerevisiae S288C (yeast) |
Buffer solution | pH: 7.4 |
Specimen | Conc.: 3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-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 FIELDBright-field microscopy / Nominal defocus max: 2200 nm / Nominal defocus min: 1200 nm |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
-Processing
CTF correction | Type: NONE | ||||||||||||||||||||||||
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Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 356520 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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