+Open data
-Basic information
Entry | Database: PDB / ID: 7ck6 | ||||||
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Title | Protein translocase of mitochondria | ||||||
Components | (Mitochondrial import receptor subunit ...) x 5 | ||||||
Keywords | STRUCTURAL PROTEIN / Complex / Mitochondria | ||||||
Function / homology | Function and homology information TOM complex / mitochondrion targeting sequence binding / mitochondrial outer membrane translocase complex / mitochondria-associated endoplasmic reticulum membrane contact site / positive regulation of mitophagy in response to mitochondrial depolarization / protein import into mitochondrial matrix / Mitochondrial protein import / protein targeting to mitochondrion / positive regulation of protein targeting to mitochondrion / protein insertion into mitochondrial outer membrane ...TOM complex / mitochondrion targeting sequence binding / mitochondrial outer membrane translocase complex / mitochondria-associated endoplasmic reticulum membrane contact site / positive regulation of mitophagy in response to mitochondrial depolarization / protein import into mitochondrial matrix / Mitochondrial protein import / protein targeting to mitochondrion / positive regulation of protein targeting to mitochondrion / protein insertion into mitochondrial outer membrane / porin activity / pore complex / protein transmembrane transporter activity / monoatomic ion transport / PINK1-PRKN Mediated Mitophagy / regulation of protein stability / mitochondrial outer membrane / mitochondrial inner membrane / mitochondrion / membrane / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å | ||||||
Authors | Yang, M. / Wang, W. / Zhang, L. / Chen, X. | ||||||
Funding support | China, 1items
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Citation | Journal: Cell Discov / Year: 2020 Title: Atomic structure of human TOM core complex. Authors: Wenhe Wang / Xudong Chen / Laixing Zhang / Jingbo Yi / Qingxi Ma / Jian Yin / Wei Zhuo / Jinke Gu / Maojun Yang / Abstract: The translocase of the outer mitochondrial membrane (TOM) complex is the main entry gate for mitochondrial precursor proteins synthesized on cytosolic ribosomes. Here we report the single-particle ...The translocase of the outer mitochondrial membrane (TOM) complex is the main entry gate for mitochondrial precursor proteins synthesized on cytosolic ribosomes. Here we report the single-particle cryo-electron microscopy (cryo-EM) structure of the dimeric human TOM core complex (TOM-CC). Two Tom40 β-barrel proteins, connected by two Tom22 receptor subunits and one phospholipid, form the protein-conducting channels. The small Tom proteins Tom5, Tom6, and Tom7 surround the channel and have notable configurations. The distinct electrostatic features of the complex, including the pronounced negative interior and the positive regions at the periphery and center of the dimer on the intermembrane space (IMS) side, provide insight into the preprotein translocation mechanism. Further, two dimeric TOM complexes may associate to form tetramer in the shape of a parallelogram, offering a potential explanation into the unusual structural features of Tom subunits and a new perspective of viewing the import of mitochondrial proteins. | ||||||
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 | 7ck6.cif.gz | 179.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7ck6.ent.gz | 140.1 KB | Display | PDB format |
PDBx/mmJSON format | 7ck6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7ck6_validation.pdf.gz | 841.7 KB | Display | wwPDB validaton report |
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Full document | 7ck6_full_validation.pdf.gz | 885.4 KB | Display | |
Data in XML | 7ck6_validation.xml.gz | 36.6 KB | Display | |
Data in CIF | 7ck6_validation.cif.gz | 52.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ck/7ck6 ftp://data.pdbj.org/pub/pdb/validation_reports/ck/7ck6 | HTTPS FTP |
-Related structure data
Related structure data | 30382MC 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 ABCDEFGHIJ
#1: Protein | Mass: 37926.926 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TOMM40, C19orf1, PEREC1, TOM40 / Production host: Homo sapiens (human) / References: UniProt: O96008 #2: Protein | Mass: 15532.528 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TOMM22, TOM22 / Production host: Homo sapiens (human) / References: UniProt: Q9NS69 #3: Protein | Mass: 8007.988 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TOMM6, OBTP, TOM6 / Production host: Homo sapiens (human) / References: UniProt: Q96B49 #4: Protein | Mass: 6256.473 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TOMM7, TOM7, TOMM07, AD-014 / Production host: Homo sapiens (human) / References: UniProt: Q9P0U1 #5: Protein | Mass: 6045.318 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TOMM5, C9orf105, TOM5 / Production host: Homo sapiens (human) / References: UniProt: Q8N4H5 |
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-Non-polymers , 1 types, 1 molecules
#6: Chemical | ChemComp-PC1 / |
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-Details
Has ligand of interest | N |
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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: The translocase of the outer mitochondrial membrane (TOM) complex Type: COMPLEX / Entity ID: #1-#5 / Source: RECOMBINANT |
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Source (natural) | Organism: Homo sapiens (human) |
Source (recombinant) | Organism: Homo sapiens (human) |
Buffer solution | pH: 7.8 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: NITROGEN |
-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: OTHER / Accelerating voltage: 300 kV / Illumination mode: OTHER |
Electron lens | Mode: OTHER |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING ONLY |
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3D reconstruction | Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 159369 / Symmetry type: POINT |