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Yorodumi- PDB-8iba: Respiratory complex Peripheral Arm of CI, focus-refined map of ty... -
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-Basic information
Entry | Database: PDB / ID: 8iba | |||||||||
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Title | Respiratory complex Peripheral Arm of CI, focus-refined map of type IB, Wild type mouse under cold temperature | |||||||||
Components |
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Keywords | ELECTRON TRANSPORT / Respiratory complex / Respiratory supercomplex | |||||||||
Function / homology | Function and homology information response to injury involved in regulation of muscle adaptation / Protein lipoylation / reproductive system development / Mitochondrial Fatty Acid Beta-Oxidation / Complex I biogenesis / RHOG GTPase cycle / Respiratory electron transport / protein insertion into mitochondrial inner membrane / circulatory system development / blastocyst hatching ...response to injury involved in regulation of muscle adaptation / Protein lipoylation / reproductive system development / Mitochondrial Fatty Acid Beta-Oxidation / Complex I biogenesis / RHOG GTPase cycle / Respiratory electron transport / protein insertion into mitochondrial inner membrane / circulatory system development / blastocyst hatching / respiratory system process / psychomotor behavior / Mitochondrial protein degradation / response to light intensity / cellular response to oxygen levels / iron-sulfur cluster assembly complex / ubiquinone-6 biosynthetic process / mitochondrial large ribosomal subunit binding / gliogenesis / neural precursor cell proliferation / cardiac muscle tissue development / : / [2Fe-2S] cluster assembly / adult walking behavior / oxygen sensor activity / cellular response to glucocorticoid stimulus / response to hydroperoxide / cellular respiration / respiratory chain complex I / iron-sulfur cluster assembly / mitochondrial ribosome / adult behavior / mitochondrial translation / dopamine metabolic process / positive regulation of execution phase of apoptosis / NADH:ubiquinone reductase (H+-translocating) / NADH dehydrogenase activity / apoptotic mitochondrial changes / : / mitochondrial ATP synthesis coupled electron transport / mitochondrial electron transport, NADH to ubiquinone / mitochondrial respiratory chain complex I assembly / proton motive force-driven mitochondrial ATP synthesis / electron transport coupled proton transport / acyl binding / acyl carrier activity / cellular response to interferon-beta / NADH dehydrogenase (ubiquinone) activity / neuron development / quinone binding / cellular response to retinoic acid / negative regulation of intrinsic apoptotic signaling pathway / muscle contraction / ATP metabolic process / extrinsic apoptotic signaling pathway / tricarboxylic acid cycle / visual perception / aerobic respiration / response to hormone / respiratory electron transport chain / reactive oxygen species metabolic process / neurogenesis / regulation of mitochondrial membrane potential / kidney development / mitochondrion organization / fatty acid metabolic process / cognition / synaptic membrane / mitochondrial membrane / apoptotic signaling pathway / sensory perception of sound / regulation of protein phosphorylation / multicellular organism growth / brain development / response to organic cyclic compound / negative regulation of cell growth / mitochondrial intermembrane space / 2 iron, 2 sulfur cluster binding / circadian rhythm / positive regulation of protein catabolic process / NAD binding / FMN binding / myelin sheath / nervous system development / 4 iron, 4 sulfur cluster binding / protease binding / neuron apoptotic process / response to oxidative stress / mitochondrial inner membrane / electron transfer activity / response to hypoxia / nuclear body / structural constituent of ribosome / mitochondrial matrix / inflammatory response / response to xenobiotic stimulus / innate immune response / negative regulation of DNA-templated transcription / neuronal cell body / ubiquitin protein ligase binding Similarity search - Function | |||||||||
Biological species | Mus musculus (house mouse) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å | |||||||||
Authors | Shin, Y.-C. / Liao, M. | |||||||||
Funding support | United States, 2items
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Citation | Journal: To Be Published Title: Respiratory complex Peripheral Arm of CI, focus-refined map of type IB, Wild type mouse under cold 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 | 8iba.cif.gz | 783.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8iba.ent.gz | 622.4 KB | Display | PDB format |
PDBx/mmJSON format | 8iba.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8iba_validation.pdf.gz | 2.2 MB | Display | wwPDB validaton report |
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Full document | 8iba_full_validation.pdf.gz | 2.2 MB | Display | |
Data in XML | 8iba_validation.xml.gz | 122.4 KB | Display | |
Data in CIF | 8iba_validation.cif.gz | 185.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ib/8iba ftp://data.pdbj.org/pub/pdb/validation_reports/ib/8iba | HTTPS FTP |
-Related structure data
Related structure data | 35337MC 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
-NADH-ubiquinone oxidoreductase chain ... , 2 types, 2 molecules AH
#1: Protein | Mass: 13223.775 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) References: UniProt: P03899, NADH:ubiquinone reductase (H+-translocating) |
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#8: Protein | Mass: 36077.016 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) References: UniProt: P03888, NADH:ubiquinone reductase (H+-translocating) |
-NADH dehydrogenase [ubiquinone] iron-sulfur protein ... , 6 types, 6 molecules BCDIQR
#2: Protein | Mass: 24715.912 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) References: UniProt: Q9DC70, NADH:ubiquinone reductase (H+-translocating) |
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#3: Protein | Mass: 30191.307 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) References: UniProt: Q9DCT2, NADH:ubiquinone reductase (H+-translocating) |
#4: Protein | Mass: 52693.559 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) References: UniProt: Q91WD5, NADH:ubiquinone reductase (H+-translocating) |
#9: Protein | Mass: 24068.355 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) References: UniProt: Q8K3J1, NADH:ubiquinone reductase (H+-translocating) |
#11: Protein | Mass: 19814.725 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9CXZ1 |
#12: Protein | Mass: 13041.828 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P52503 |
-NADH dehydrogenase [ubiquinone] flavoprotein ... , 3 types, 3 molecules EFs
#5: Protein | Mass: 27318.336 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) References: UniProt: Q9D6J6, NADH:ubiquinone reductase (H+-translocating) |
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#6: Protein | Mass: 50904.152 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) References: UniProt: Q91YT0, NADH:ubiquinone reductase (H+-translocating) |
#23: Protein | Mass: 11833.504 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q8BK30 |
-Protein , 2 types, 2 molecules GT
#7: Protein | Mass: 79866.688 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) References: UniProt: Q91VD9, NADH:ubiquinone reductase (H+-translocating) |
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#14: Protein | Mass: 17390.289 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9CR21 |
-NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit ... , 10 types, 10 molecules PSVWXZabqr
#10: Protein | Mass: 42588.129 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9DC69 |
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#13: Protein | Mass: 10932.675 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9CQ75 |
#15: Protein | Mass: 13380.719 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9CPP6 |
#16: Protein | Mass: 15311.858 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9CQZ5 |
#17: Protein | Mass: 20025.127 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9DCJ5 |
#18: Protein | Mass: 16881.588 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9ERS2 |
#19: Protein | Mass: 8149.524 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: O35683 |
#20: Protein | Mass: 9338.867 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9CQ91 |
#21: Protein | Mass: 17112.416 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q7TMF3 |
#22: Protein | Mass: 12595.592 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9Z1P6 |
-Non-polymers , 11 types, 20 molecules
#24: Chemical | #25: Chemical | ChemComp-SF4 / #26: Chemical | ChemComp-UQ1 / | #27: Chemical | #28: Chemical | #29: Chemical | ChemComp-FMN / | #30: Chemical | ChemComp-UQ9 / | #31: Chemical | ChemComp-NDP / | #32: Chemical | ChemComp-ZN / | #33: Chemical | ChemComp-EHZ / ~{ | #34: Chemical | ChemComp-CDL / | |
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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 Supercomplex CI:CIII2 / Type: COMPLEX / Entity ID: #1-#23 / Source: NATURAL |
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Molecular weight | Value: 1.32 MDa / Experimental value: NO |
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 |
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-Processing
CTF correction | Type: NONE |
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3D reconstruction | Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 147426 / Symmetry type: POINT |