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Yorodumi- PDB-8iar: Respiratory complex CIII2, focus-refined of type I, Wild type mou... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8iar | |||||||||
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Title | Respiratory complex CIII2, focus-refined of type I, Wild type mouse under thermoneutral temperature | |||||||||
Components |
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Keywords | ELECTRON TRANSPORT / Respiratory complex / Respiratory supercomplex | |||||||||
Function / homology | Function and homology information Complex III assembly / subthalamus development / pons development / cerebellar Purkinje cell layer development / respiratory chain complex III / Respiratory electron transport / pyramidal neuron development / response to mercury ion / mitochondrial respiratory chain complex III assembly / thalamus development ...Complex III assembly / subthalamus development / pons development / cerebellar Purkinje cell layer development / respiratory chain complex III / Respiratory electron transport / pyramidal neuron development / response to mercury ion / mitochondrial respiratory chain complex III assembly / thalamus development / Mitochondrial protein degradation / : / : / response to alkaloid / quinol-cytochrome-c reductase / response to copper ion / response to glucagon / ubiquinol-cytochrome-c reductase activity / cellular respiration / midbrain development / hypothalamus development / mitochondrial electron transport, ubiquinol to cytochrome c / response to cobalamin / electron transport coupled proton transport / response to hyperoxia / animal organ regeneration / response to cadmium ion / response to hormone / respiratory electron transport chain / response to activity / hippocampus development / mitochondrial membrane / metalloendopeptidase activity / 2 iron, 2 sulfur cluster binding / response to toxic substance / response to calcium ion / myelin sheath / response to ethanol / mitochondrial inner membrane / oxidoreductase activity / response to hypoxia / response to xenobiotic stimulus / ubiquitin protein ligase binding / heme binding / protein-containing complex binding / protein-containing complex / mitochondrion / proteolysis / nucleoplasm / membrane / metal ion binding Similarity search - Function | |||||||||
Biological species | Mus musculus (house mouse) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å | |||||||||
Authors | Shin, Y.-C. / Liao, M. | |||||||||
Funding support | United States, 2items
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Citation | Journal: To Be Published Title: Respiratory complex CIII2, focus-refined of type I, Wild type mouse under thermoneutral temperature Authors: Shin, Y.-C. / Liao, M. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8iar.cif.gz | 822.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8iar.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 8iar.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8iar_validation.pdf.gz | 2.6 MB | Display | wwPDB validaton report |
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Full document | 8iar_full_validation.pdf.gz | 2.7 MB | Display | |
Data in XML | 8iar_validation.xml.gz | 117.7 KB | Display | |
Data in CIF | 8iar_validation.cif.gz | 176.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ia/8iar ftp://data.pdbj.org/pub/pdb/validation_reports/ia/8iar | HTTPS FTP |
-Related structure data
Related structure data | 35316MC 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
-Cytochrome b-c1 complex subunit ... , 8 types, 18 molecules AAAaABAbAEAIAeAiAFAfAGAgAHAhAJAjAKAk
#1: Protein | Mass: 52910.594 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9CZ13 #2: Protein | Mass: 48289.730 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9DB77 #5: Protein | Mass: 29406.635 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9CR68, quinol-cytochrome-c reductase #6: Protein | Mass: 13587.532 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9CQB4 #7: Protein | Mass: 9783.245 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9CQ69 #8: Protein | Mass: 10452.694 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P99028 #9: Protein | Mass: 7457.526 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q8R1I1 #10: Protein | Mass: 6546.627 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9CPX8 |
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-Protein , 2 types, 4 molecules ACAcADAd
#3: Protein | Mass: 43240.305 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P00158 #4: Protein | Mass: 35374.652 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9D0M3, quinol-cytochrome-c reductase |
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-Non-polymers , 7 types, 22 molecules
#11: Chemical | ChemComp-3PE / #12: Chemical | ChemComp-HEM / #13: Chemical | #14: Chemical | #15: Chemical | #16: Chemical | ChemComp-CDL / #17: Chemical | ChemComp-PC1 / | |
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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: Respiratory complex / Type: COMPLEX / Entity ID: #1-#10 / Source: NATURAL |
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Source (natural) | Organism: Mus musculus (house mouse) |
Buffer solution | pH: 8 |
Specimen | Conc.: 0.33 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |
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Microscopy | Model: FEI TALOS ARCTICA |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: OTHER |
Electron lens | Mode: OTHER / Nominal defocus max: 2200 nm / Nominal defocus min: 1000 nm |
Image recording | Electron dose: 46.6 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
CTF correction | Type: NONE |
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3D reconstruction | Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 85845 / Symmetry type: POINT |