+Open data
-Basic information
Entry | Database: PDB / ID: 6lo8 | ||||||
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Title | Cryo-EM structure of the TIM22 complex from yeast | ||||||
Components |
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Keywords | PROTEIN TRANSPORT / mitochondrial import / Tim22 / protein translocation / membrane protein insertion | ||||||
Function / homology | Function and homology information mitochondrial intermembrane space protein transporter complex / Citric acid cycle (TCA cycle) / lipid kinase activity / Mitochondrial protein import / mitochondrion targeting sequence binding / succinate dehydrogenase activity / TIM22 mitochondrial import inner membrane insertion complex / : / mitochondrial electron transport, succinate to ubiquinone / protein transmembrane transport ...mitochondrial intermembrane space protein transporter complex / Citric acid cycle (TCA cycle) / lipid kinase activity / Mitochondrial protein import / mitochondrion targeting sequence binding / succinate dehydrogenase activity / TIM22 mitochondrial import inner membrane insertion complex / : / mitochondrial electron transport, succinate to ubiquinone / protein transmembrane transport / protein transporter activity / protein insertion into mitochondrial inner membrane / sphingolipid metabolic process / response to arsenic-containing substance / cellular respiration / response to osmotic stress / protein transmembrane transporter activity / quinone binding / tricarboxylic acid cycle / mitochondrial intermembrane space / phospholipid binding / unfolded protein binding / cellular response to oxidative stress / mitochondrial inner membrane / membrane => GO:0016020 / electron transfer activity / phosphorylation / apoptotic process / mitochondrion / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.83 Å | ||||||
Authors | Zhang, Y. / Zhou, X. / Wu, X. / Li, L. | ||||||
Citation | Journal: Cell Res / Year: 2021 Title: Structure of the mitochondrial TIM22 complex from yeast. Authors: Yutong Zhang / Xiaomin Ou / Xuezheng Wang / Dongjie Sun / Xueyin Zhou / Xiaofei Wu / Qing Li / Long Li / | ||||||
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 | 6lo8.cif.gz | 191.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6lo8.ent.gz | 151.2 KB | Display | PDB format |
PDBx/mmJSON format | 6lo8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6lo8_validation.pdf.gz | 712.3 KB | Display | wwPDB validaton report |
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Full document | 6lo8_full_validation.pdf.gz | 719 KB | Display | |
Data in XML | 6lo8_validation.xml.gz | 31.8 KB | Display | |
Data in CIF | 6lo8_validation.cif.gz | 47.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lo/6lo8 ftp://data.pdbj.org/pub/pdb/validation_reports/lo/6lo8 | HTTPS FTP |
-Related structure data
Related structure data | 0935MC 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 inner membrane translocase subunit ... , 6 types, 9 molecules ABDEGIFHJ
#1: Protein | Mass: 21751.740 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / References: UniProt: Q12328 | ||||
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#2: Protein | Mass: 54252.637 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / References: UniProt: P47045 | ||||
#4: Protein | Mass: 21994.391 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / References: UniProt: Q08749 | ||||
#5: Protein | Mass: 10216.649 Da / Num. of mol.: 3 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / References: UniProt: O74700 #6: Protein | | Mass: 12299.962 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / References: UniProt: P32830 #7: Protein | Mass: 10313.589 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / References: UniProt: P87108 |
-Protein , 1 types, 1 molecules C
#3: Protein | Mass: 22094.963 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / References: UniProt: P33421 |
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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: TIM22 complex / Type: COMPLEX / Entity ID: #1-#6 / Source: NATURAL |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) |
Source (recombinant) | Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: BJ5465 |
Buffer solution | pH: 7.5 |
Specimen | Conc.: 1.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 297 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 |
Specimen holder | Cryogen: NITROGEN |
Image recording | Electron dose: 57 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
Software |
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EM software |
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CTF correction | Type: NONE | |||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 3663107 | |||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | |||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.83 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 251984 / Symmetry type: POINT | |||||||||||||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT / Space: REAL | |||||||||||||||||||||||||||
Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | |||||||||||||||||||||||||||
Displacement parameters | Biso mean: 93.66 Å2 | |||||||||||||||||||||||||||
Refine LS restraints |
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