+Open data
-Basic information
Entry | Database: PDB / ID: 6g2j | ||||||||||||
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Title | Mouse mitochondrial complex I in the active state | ||||||||||||
Components |
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Keywords | OXIDOREDUCTASE / Complex I / mitochondria / proton pump / membrane protein | ||||||||||||
Function / homology | Function and homology information response to injury involved in regulation of muscle adaptation / Mitochondrial Fatty Acid Beta-Oxidation / Complex I biogenesis / reproductive system development / Mitochondrial protein import / Respiratory electron transport / Glyoxylate metabolism and glycine degradation / RHOG GTPase cycle / respiratory system process / response to light intensity ...response to injury involved in regulation of muscle adaptation / Mitochondrial Fatty Acid Beta-Oxidation / Complex I biogenesis / reproductive system development / Mitochondrial protein import / Respiratory electron transport / Glyoxylate metabolism and glycine degradation / RHOG GTPase cycle / respiratory system process / response to light intensity / protein insertion into mitochondrial inner membrane / blastocyst hatching / circulatory system development / psychomotor behavior / cellular response to oxygen levels / iron-sulfur cluster assembly complex / mitochondrial large ribosomal subunit binding / gliogenesis / cardiac muscle tissue development / neural precursor cell proliferation / ubiquinone-6 biosynthetic process / mitochondrial respirasome / [2Fe-2S] cluster assembly / oxygen sensor activity / adult walking behavior / negative regulation of non-canonical NF-kappaB signal transduction / cellular response to glucocorticoid stimulus / cellular respiration / positive regulation of mitochondrial membrane potential / response to hydroperoxide / iron-sulfur cluster assembly / mitochondrial ribosome / respiratory chain complex I / adult behavior / dopamine metabolic process / mitochondrial translation / NADH dehydrogenase activity / ubiquinone binding / NADH:ubiquinone reductase (H+-translocating) / positive regulation of ATP biosynthetic process / acyl binding / mitochondrial ATP synthesis coupled electron transport / proton motive force-driven mitochondrial ATP synthesis / electron transport coupled proton transport / mitochondrial respiratory chain complex I / apoptotic mitochondrial changes / mitochondrial electron transport, NADH to ubiquinone / acyl carrier activity / mitochondrial respiratory chain complex I assembly / NADH dehydrogenase (ubiquinone) activity / neuron development / quinone binding / cellular response to interferon-beta / ATP synthesis coupled electron transport / negative regulation of intrinsic apoptotic signaling pathway / ATP metabolic process / cellular response to retinoic acid / extrinsic apoptotic signaling pathway / negative regulation of reactive oxygen species biosynthetic process / aerobic respiration / response to cAMP / tricarboxylic acid cycle / response to organonitrogen compound / ionotropic glutamate receptor binding / visual perception / respiratory electron transport chain / Neutrophil degranulation / reactive oxygen species metabolic process / mitochondrion organization / cerebellum development / neurogenesis / fatty acid metabolic process / electron transport chain / regulation of mitochondrial membrane potential / response to nicotine / response to cocaine / kidney development / synaptic membrane / response to hormone / muscle contraction / apoptotic signaling pathway / mitochondrial membrane / sensory perception of sound / regulation of protein phosphorylation / multicellular organism growth / brain development / response to hydrogen peroxide / mitochondrial intermembrane space / negative regulation of cell growth / response to organic cyclic compound / 2 iron, 2 sulfur cluster binding / cognition / circadian rhythm / positive regulation of protein catabolic process / NAD binding / positive regulation of fibroblast proliferation / FMN binding / myelin sheath / nervous system development / 4 iron, 4 sulfur cluster binding Similarity search - Function | ||||||||||||
Biological species | Mus musculus (house mouse) | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å | ||||||||||||
Authors | Agip, A.N.A. / Blaza, J.N. / Bridges, H.R. / Viscomi, C. / Rawson, S. / Muench, S.P. / Hirst, J. | ||||||||||||
Funding support | United Kingdom, 3items
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Citation | Journal: Nat Struct Mol Biol / Year: 2018 Title: Cryo-EM structures of complex I from mouse heart mitochondria in two biochemically defined states. Authors: Ahmed-Noor A Agip / James N Blaza / Hannah R Bridges / Carlo Viscomi / Shaun Rawson / Stephen P Muench / Judy Hirst / Abstract: Complex I (NADH:ubiquinone oxidoreductase) uses the reducing potential of NADH to drive protons across the energy-transducing inner membrane and power oxidative phosphorylation in mammalian ...Complex I (NADH:ubiquinone oxidoreductase) uses the reducing potential of NADH to drive protons across the energy-transducing inner membrane and power oxidative phosphorylation in mammalian mitochondria. Recent cryo-EM analyses have produced near-complete models of all 45 subunits in the bovine, ovine and porcine complexes and have identified two states relevant to complex I in ischemia-reperfusion injury. Here, we describe the 3.3-Å structure of complex I from mouse heart mitochondria, a biomedically relevant model system, in the 'active' state. We reveal a nucleotide bound in subunit NDUFA10, a nucleoside kinase homolog, and define mechanistically critical elements in the mammalian enzyme. By comparisons with a 3.9-Å structure of the 'deactive' state and with known bacterial structures, we identify differences in helical geometry in the membrane domain that occur upon activation or that alter the positions of catalytically important charged residues. Our results demonstrate the capability of cryo-EM analyses to challenge and develop mechanistic models for mammalian complex I. | ||||||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
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PDBx/mmCIF format | 6g2j.cif.gz | 1.5 MB | Display | PDBx/mmCIF format |
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PDB format | pdb6g2j.ent.gz | 1.2 MB | Display | PDB format |
PDBx/mmJSON format | 6g2j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g2/6g2j ftp://data.pdbj.org/pub/pdb/validation_reports/g2/6g2j | HTTPS FTP |
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-Related structure data
Related structure data | 4345MC 4356C 6g72C 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
-NADH-ubiquinone oxidoreductase chain ... , 7 types, 7 molecules AHJKLMN
#1: Protein | Mass: 13251.785 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Organ: Heart References: UniProt: P03899, NADH:ubiquinone reductase (H+-translocating) |
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#8: Protein | Mass: 36105.027 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Organ: Heart References: UniProt: P03888, NADH:ubiquinone reductase (H+-translocating) |
#10: Protein | Mass: 18656.100 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Organ: Heart References: UniProt: P03925, NADH:ubiquinone reductase (H+-translocating) |
#11: Protein | Mass: 10637.629 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Organ: Heart References: UniProt: P03903, NADH:ubiquinone reductase (H+-translocating) |
#12: Protein | Mass: 68547.297 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Organ: Heart References: UniProt: P03921, NADH:ubiquinone reductase (H+-translocating) |
#13: Protein | Mass: 51943.547 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Organ: Heart References: UniProt: P03911, NADH:ubiquinone reductase (H+-translocating) |
#14: Protein | Mass: 38800.230 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Organ: Heart References: UniProt: P03893, NADH:ubiquinone reductase (H+-translocating) |
-NADH dehydrogenase [ubiquinone] iron-sulfur protein ... , 7 types, 7 molecules BCDIQRe
#2: Protein | Mass: 24715.912 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Organ: Heart References: UniProt: Q9DC70, NADH:ubiquinone reductase (H+-translocating), NADH dehydrogenase |
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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) / Organ: Heart References: UniProt: Q9DCT2, NADH:ubiquinone reductase (H+-translocating), NADH dehydrogenase |
#4: Protein | Mass: 52720.602 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Organ: Heart References: UniProt: Q91WD5, NADH:ubiquinone reductase (H+-translocating), NADH dehydrogenase |
#9: Protein | Mass: 24068.355 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Organ: Heart References: UniProt: Q8K3J1, NADH:ubiquinone reductase (H+-translocating), NADH dehydrogenase |
#17: Protein | Mass: 19814.725 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Organ: Heart / References: UniProt: Q9CXZ1 |
#18: Protein | Mass: 13041.828 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Organ: Heart / References: UniProt: P52503 |
#30: Protein | Mass: 12675.772 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Organ: Heart / References: UniProt: Q99LY9 |
-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) / Organ: Heart References: UniProt: Q9D6J6, NADH:ubiquinone reductase (H+-translocating), NADH dehydrogenase |
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#6: Protein | Mass: 47060.621 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Organ: Heart References: UniProt: Q91YT0, NADH:ubiquinone reductase (H+-translocating), NADH dehydrogenase |
#44: Protein | Mass: 11833.504 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Organ: Heart / References: UniProt: Q8BK30 |
-Protein , 3 types, 4 molecules GTUY
#7: Protein | Mass: 79866.688 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Organ: Heart References: UniProt: Q91VD9, NADH:ubiquinone reductase (H+-translocating), NADH dehydrogenase | ||
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#20: Protein | Mass: 17390.289 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Organ: Heart / References: UniProt: Q9CR21 #24: Protein | | Mass: 15130.416 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Organ: Heart / References: UniProt: G5E814 |
-NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit ... , 11 types, 11 molecules OPSVWXZabqr
#15: Protein | Mass: 40657.375 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Organ: Heart / References: UniProt: Q99LC3 |
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#16: Protein | Mass: 42588.129 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Organ: Heart / References: UniProt: Q9DC69 |
#19: Protein | Mass: 10932.675 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Organ: Heart / References: UniProt: Q9CQ75 |
#21: Protein | Mass: 13380.719 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Organ: Heart / References: UniProt: Q9CPP6 |
#22: Protein | Mass: 15311.858 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Organ: Heart / References: UniProt: Q9CQZ5 |
#23: Protein | Mass: 20025.127 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Organ: Heart / References: UniProt: Q9DCJ5 |
#25: Protein | Mass: 16881.588 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Organ: Heart / References: UniProt: Q9ERS2 |
#26: Protein | Mass: 7807.176 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Organ: Heart / References: UniProt: O35683 |
#27: Protein | Mass: 9380.904 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Organ: Heart / References: UniProt: Q9CQ91 |
#42: Protein | Mass: 17154.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Organ: Heart / References: UniProt: Q7TMF3 |
#43: Protein | Mass: 12637.629 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Organ: Heart / References: UniProt: Q9Z1P6 |
-NADH dehydrogenase [ubiquinone] 1 subunit ... , 2 types, 2 molecules cd
#28: Protein | Mass: 8636.023 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Organ: Heart / References: UniProt: Q9CQY9 |
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#29: Protein | Mass: 14185.692 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Organ: Heart / References: UniProt: Q9CQ54 |
-NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit ... , 11 types, 11 molecules fghijklmnop
#31: Protein | Mass: 6965.109 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Organ: Heart / References: UniProt: P0DN34 |
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#32: Protein | Mass: 17463.727 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Organ: Heart / References: UniProt: O09111 |
#33: Protein | Mass: 21742.197 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Organ: Heart / References: UniProt: Q9CQH3 |
#34: Protein | Mass: 15582.122 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Organ: Heart / References: UniProt: Q3UIU2 |
#35: Protein | Mass: 11982.437 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Organ: Heart / References: UniProt: Q9CPU2 |
#36: Protein | Mass: 11714.240 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Organ: Heart / References: UniProt: Q9CQZ6 |
#37: Protein | Mass: 21903.828 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Organ: Heart / References: UniProt: Q9D6J5 |
#38: Protein | Mass: 15105.287 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Organ: Heart / References: UniProt: Q9CQC7 |
#39: Protein | Mass: 22020.123 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Organ: Heart / References: UniProt: Q9CQJ8 |
#40: Protein | Mass: 16360.804 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Organ: Heart / References: UniProt: Q9CR61 |
#41: Protein | Mass: 21054.832 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Organ: Heart / References: UniProt: Q9DCS9 |
-Non-polymers , 10 types, 34 molecules
#45: Chemical | ChemComp-3PE / #46: Chemical | ChemComp-SF4 / #47: Chemical | #48: Chemical | ChemComp-FMN / | #49: Chemical | ChemComp-PC1 / #50: Chemical | ChemComp-CDL / #51: Chemical | ChemComp-ADP / | #52: Chemical | ChemComp-NDP / | #53: Chemical | ChemComp-ZN / | #54: Chemical | |
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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: Mitochondrial complex I from mouse in the active stateRespiratory complex I Type: COMPLEX / Entity ID: #1-#44 / Source: NATURAL | ||||||||||||||||||||
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Molecular weight | Value: 1.0 MDa / Experimental value: NO | ||||||||||||||||||||
Source (natural) | Organism: Mus musculus (house mouse) / Strain: C57BL/6 / Organ: Heart | ||||||||||||||||||||
Buffer solution | pH: 7.14 | ||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES Details: Peak fraction from a gel filtration column- monodisperse and not concentrated | ||||||||||||||||||||
Specimen support | Details: Gold was PEGylated prior to use in anaerobic ethanol in 5mM SPT-11P6 (Sensopath Technologies) for two days 0.6/1 holes Grid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil UltrAuFoil | ||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K / Details: 8-16s blotting. |
-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 FIELDBright-field microscopy / Calibrated magnification: 47600 X / Nominal defocus max: 3100 nm / Nominal defocus min: 1500 nm / Cs: 2.7 mm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 10 sec. / Electron dose: 50 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Num. of grids imaged: 1 |
EM imaging optics | Energyfilter name: GIF Quantum LS / Energyfilter upper: 20 eV / Energyfilter lower: 0 eV |
Image scans | Movie frames/image: 25 / Used frames/image: 1-12 |
-Processing
Software | Name: PHENIX / Version: 1.13_2998: / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | |||||||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 60851 | |||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | |||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 20370 / Algorithm: FOURIER SPACE / Symmetry type: POINT | |||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT / Space: REAL Details: Used default paramteres in phenix.real_space_refine |