+Open data
-Basic information
Entry | Database: PDB / ID: 8xva | ||||||
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Title | Human TOM complex with whole Tom20 | ||||||
Components | (Mitochondrial import receptor subunit ...) x 6 | ||||||
Keywords | PROTEIN TRANSPORT / mitochondria / transport / membrane protein complex | ||||||
Function / homology | Function and homology information tRNA import into mitochondrion / TOM complex / mitochondrion targeting sequence binding / mitochondrial outer membrane translocase complex / mitochondria-associated endoplasmic reticulum membrane contact site / migrasome / protein import into mitochondrial matrix / : / protein-transporting ATPase activity / Mitochondrial protein import ...tRNA import into mitochondrion / TOM complex / mitochondrion targeting sequence binding / mitochondrial outer membrane translocase complex / mitochondria-associated endoplasmic reticulum membrane contact site / migrasome / protein import into mitochondrial matrix / : / protein-transporting ATPase activity / 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 / sperm midpiece / PINK1-PRKN Mediated Mitophagy / cell periphery / regulation of protein stability / unfolded protein binding / mitochondrial outer membrane / mitochondrial inner membrane / Ub-specific processing proteases / mitochondrion / membrane / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 5.92 Å | ||||||
Authors | Tian, X.Y. / Su, J.Y. / Sui, S.F. | ||||||
Funding support | China, 1items
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Citation | Journal: PNAS Nexus / Year: 2024 Title: Structure of the intact Tom20 receptor in the human translocase of the outer membrane complex. Authors: Jiayue Su / Xuyang Tian / Ziyi Wang / Jiawen Yang / Shan Sun / Sen-Fang Sui / Abstract: The translocase of the outer membrane (TOM) complex serves as the main gate for preproteins entering mitochondria and thus plays a pivotal role in sustaining mitochondrial stability. Precursor ...The translocase of the outer membrane (TOM) complex serves as the main gate for preproteins entering mitochondria and thus plays a pivotal role in sustaining mitochondrial stability. Precursor proteins, featuring amino-terminal targeting signals (presequences) or internal targeting signals, are recognized by the TOM complex receptors Tom20, Tom22, and Tom70, and then translocated into mitochondria through Tom40. By using chemical cross-linking to stabilize Tom20 in the TOM complex, this study unveils the structure of the human TOM holo complex, encompassing the intact Tom20 component, at a resolution of approximately 6 Å by cryo-electron microscopy. Our structure shows the TOM holo complex containing only one Tom20 subunit, which is located right at the center of the complex and stabilized by extensive interactions with Tom22, Tom40, and Tom6. Based on the structure, we proposed a possible translocation mode of TOM complex, by which different receptors could work simultaneously to ensure that the preproteins recognized by them are all efficiently translocated into the mitochondria. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8xva.cif.gz | 168 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8xva.ent.gz | 110.9 KB | Display | PDB format |
PDBx/mmJSON format | 8xva.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8xva_validation.pdf.gz | 732.6 KB | Display | wwPDB validaton report |
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Full document | 8xva_full_validation.pdf.gz | 734.3 KB | Display | |
Data in XML | 8xva_validation.xml.gz | 28.6 KB | Display | |
Data in CIF | 8xva_validation.cif.gz | 46.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xv/8xva ftp://data.pdbj.org/pub/pdb/validation_reports/xv/8xva | HTTPS FTP |
-Related structure data
Related structure data | 38694MC 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 ... , 6 types, 11 molecules AFBICHDEGJK
#1: Protein | Mass: 8007.988 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: 293F / References: UniProt: Q96B49 #2: Protein | Mass: 37926.926 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: 293F / References: UniProt: O96008 #3: 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 / Cell line (production host): 293F / Production host: Homo sapiens (human) / References: UniProt: Q9NS69 #4: Protein | Mass: 6045.318 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: 293F / References: UniProt: Q8N4H5 #5: Protein | Mass: 6256.473 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9P0U1 #6: Protein | | Mass: 16319.862 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q15388 |
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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 complex with whole Tom20 / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT | ||||||||||||||||||||
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Molecular weight | Value: 168.3 kDa/nm / Experimental value: NO | ||||||||||||||||||||
Source (natural) | Organism: Homo sapiens (human) | ||||||||||||||||||||
Source (recombinant) | Organism: Homo sapiens (human) / Cell: 293F / Plasmid: 3X Flag-PCMV | ||||||||||||||||||||
Buffer solution | pH: 7.4 | ||||||||||||||||||||
Buffer component |
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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 R0.6/1 | ||||||||||||||||||||
Vitrification | Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 282 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 / Nominal defocus max: 1800 nm / Nominal defocus min: 1300 nm |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
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Particle selection | Num. of particles selected: 1151405 | ||||||||||||||||||||||||
3D reconstruction | Resolution: 5.92 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 189667 / Symmetry type: POINT | ||||||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT | ||||||||||||||||||||||||
Refine LS restraints |
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