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Yorodumi- PDB-8iaq: Respiratory complex Membrane domain of CI, focused map of type I,... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8iaq | |||||||||
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Title | Respiratory complex Membrane domain of CI, focused map 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 Protein lipoylation / Mitochondrial Fatty Acid Beta-Oxidation / Complex I biogenesis / Mitochondrial protein import / Respiratory electron transport / cellular response to oxygen levels / iron-sulfur cluster assembly complex / mitochondrial large ribosomal subunit binding / gliogenesis / neural precursor cell proliferation ...Protein lipoylation / Mitochondrial Fatty Acid Beta-Oxidation / Complex I biogenesis / Mitochondrial protein import / Respiratory electron transport / cellular response to oxygen levels / iron-sulfur cluster assembly complex / mitochondrial large ribosomal subunit binding / gliogenesis / neural precursor cell proliferation / negative regulation of non-canonical NF-kappaB signal transduction / [2Fe-2S] cluster assembly / oxygen sensor activity / positive regulation of mitochondrial membrane potential / iron-sulfur cluster assembly / positive regulation of ATP biosynthetic process / NADH:ubiquinone reductase (H+-translocating) / ubiquinone binding / : / NADH dehydrogenase activity / : / 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 / NADH dehydrogenase (ubiquinone) activity / quinone binding / ATP synthesis coupled electron transport / negative regulation of reactive oxygen species biosynthetic process / ionotropic glutamate receptor binding / aerobic respiration / Neutrophil degranulation / reactive oxygen species metabolic process / neurogenesis / cerebellum development / response to cocaine / electron transport chain / response to nicotine / response to hydrogen peroxide / mitochondrial intermembrane space / NAD binding / myelin sheath / 4 iron, 4 sulfur cluster binding / response to ethanol / in utero embryonic development / response to oxidative stress / mitochondrial inner membrane / response to hypoxia / nuclear speck / mitochondrial matrix / ubiquitin protein ligase binding / protein-containing complex binding / protein kinase binding / endoplasmic reticulum / mitochondrion / nucleoplasm / metal ion binding / cytoplasm 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 Membrane domain of CI, focused map 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 | 8iaq.cif.gz | 738.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8iaq.ent.gz | 591.9 KB | Display | PDB format |
PDBx/mmJSON format | 8iaq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8iaq_validation.pdf.gz | 2.3 MB | Display | wwPDB validaton report |
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Full document | 8iaq_full_validation.pdf.gz | 2.4 MB | Display | |
Data in XML | 8iaq_validation.xml.gz | 118.8 KB | Display | |
Data in CIF | 8iaq_validation.cif.gz | 175.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ia/8iaq ftp://data.pdbj.org/pub/pdb/validation_reports/ia/8iaq | HTTPS FTP |
-Related structure data
Related structure data | 35315MC 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 dehydrogenase [ubiquinone] iron-sulfur protein ... , 2 types, 2 molecules De
#1: 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) |
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#13: Protein | Mass: 12675.772 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q99LY9 |
-NADH-ubiquinone oxidoreductase chain ... , 5 types, 5 molecules JKLMN
#2: Protein | Mass: 18628.090 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) References: UniProt: P03925, NADH:ubiquinone reductase (H+-translocating) |
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#3: Protein | Mass: 10609.619 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) References: UniProt: P03903, NADH:ubiquinone reductase (H+-translocating) |
#4: Protein | Mass: 68519.289 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) References: UniProt: P03921, NADH:ubiquinone reductase (H+-translocating) |
#5: Protein | Mass: 51915.535 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) References: UniProt: P03911, NADH:ubiquinone reductase (H+-translocating) |
#6: Protein | Mass: 38772.219 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) References: UniProt: P03893, NADH:ubiquinone reductase (H+-translocating) |
-NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit ... , 3 types, 3 molecules OXY
#7: Protein | Mass: 40657.375 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q99LC3 |
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#9: 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 |
#10: Protein | Mass: 15130.416 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: G5E814 |
-Protein , 1 types, 1 molecules U
#8: 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 |
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-NADH dehydrogenase [ubiquinone] 1 subunit ... , 2 types, 2 molecules cd
#11: Protein | Mass: 8636.023 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9CQY9 |
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#12: Protein | Mass: 14185.692 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9CQ54 |
-NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit ... , 11 types, 11 molecules fghijklmnop
#14: Protein | Mass: 6965.109 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P0DN34 |
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#15: Protein | Mass: 17463.727 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: O09111 |
#16: Protein | Mass: 21742.197 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9CQH3 |
#17: Protein | Mass: 15540.085 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q3UIU2 |
#18: Protein | Mass: 11982.437 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9CPU2 |
#19: Protein | Mass: 11714.240 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9CQZ6 |
#20: Protein | Mass: 21903.828 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9D6J5 |
#21: Protein | Mass: 15105.287 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9CQC7 |
#22: Protein | Mass: 22020.123 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9CQJ8 |
#23: Protein | Mass: 16360.804 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9CR61 |
#24: Protein | Mass: 21054.832 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9DCS9 |
-Non-polymers , 5 types, 19 molecules
#25: Chemical | ChemComp-3PE / #26: Chemical | ChemComp-CDL / #27: Chemical | #28: Chemical | ChemComp-ADP / | #29: Chemical | ChemComp-EHZ / ~{ | |
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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-#24 / 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 |