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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-4356 | ||||||||||||
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Title | Mouse mitochondrial complex I in the deactive state | ||||||||||||
![]() | Mouse mitochondrial complex I in the deactive state | ||||||||||||
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![]() | Complex I / mitochondria / proton pump / membrane protein / oxidoreductase | ||||||||||||
Function / homology | ![]() Mitochondrial protein import / response to injury involved in regulation of muscle adaptation / Protein lipoylation / Mitochondrial Fatty Acid Beta-Oxidation / Complex I biogenesis / RHOG GTPase cycle / Respiratory electron transport / protein insertion into mitochondrial inner membrane / blastocyst hatching / respiratory system process ...Mitochondrial protein import / response to injury involved in regulation of muscle adaptation / Protein lipoylation / Mitochondrial Fatty Acid Beta-Oxidation / Complex I biogenesis / RHOG GTPase cycle / Respiratory electron transport / protein insertion into mitochondrial inner membrane / blastocyst hatching / respiratory system process / psychomotor behavior / Mitochondrial protein degradation / mesenchymal stem cell proliferation / cellular response to oxygen levels / response to light intensity / respiratory chain complex / reproductive system development / mitochondrial [2Fe-2S] assembly complex / iron-sulfur cluster assembly complex / mitochondrial large ribosomal subunit binding / gliogenesis / mesenchymal stem cell differentiation / circulatory system development / negative regulation of non-canonical NF-kappaB signal transduction / cardiac muscle tissue development / neural precursor cell proliferation / positive regulation of mitochondrial membrane potential / [2Fe-2S] cluster assembly / oxygen sensor activity / adult walking behavior / response to hydroperoxide / stem cell division / cellular response to glucocorticoid stimulus / iron-sulfur cluster assembly / mitochondrial ATP synthesis coupled electron transport / NADH:ubiquinone reductase (H+-translocating) / dopamine metabolic process / adult behavior / positive regulation of ATP biosynthetic process / NADH dehydrogenase activity / mitochondrial respiratory chain complex I assembly / mitochondrial electron transport, NADH to ubiquinone / proton motive force-driven mitochondrial ATP synthesis / positive regulation of execution phase of apoptosis / respiratory chain complex I / NADH dehydrogenase (ubiquinone) activity / neuron development / quinone binding / cellular response to interferon-beta / ATP synthesis coupled electron transport / extrinsic apoptotic signaling pathway / negative regulation of reactive oxygen species biosynthetic process / tricarboxylic acid cycle / cellular response to retinoic acid / neurogenesis / Neutrophil degranulation / visual perception / muscle contraction / reactive oxygen species metabolic process / aerobic respiration / cerebellum development / respiratory electron transport chain / regulation of mitochondrial membrane potential / response to nicotine / mitochondrion organization / DNA damage response, signal transduction by p53 class mediator / response to cocaine / kidney development / fatty acid metabolic process / sensory perception of sound / response to hydrogen peroxide / monooxygenase activity / electron transport chain / mitochondrial membrane / brain development / mitochondrial intermembrane space / 2 iron, 2 sulfur cluster binding / multicellular organism growth / cognition / circadian rhythm / NAD binding / positive regulation of protein catabolic process / fatty acid biosynthetic process / cellular senescence / FMN binding / nervous system development / myelin sheath / 4 iron, 4 sulfur cluster binding / response to ethanol / neuron apoptotic process / in utero embryonic development / response to oxidative stress / gene expression / response to hypoxia / electron transfer activity / mitochondrial inner membrane / nuclear speck / nuclear body / inflammatory response / mitochondrial matrix Similarity search - Function | ||||||||||||
Biological species | ![]() ![]() | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.9 Å | ||||||||||||
![]() | Agip ANA / Blaza JN | ||||||||||||
Funding support | ![]()
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![]() | ![]() 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
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 172 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 70.5 KB 70.5 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 12.9 KB | Display | ![]() |
Images | ![]() | 97.2 KB | ||
Filedesc metadata | ![]() | 14.3 KB | ||
Others | ![]() ![]() | 146.1 MB 146 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
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Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 19.7 KB | Display | |
Data in CIF | ![]() | 26.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6g72MC ![]() 4345C ![]() 6g2jC C: citing same article ( M: atomic model generated by this map |
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Similar structure data | |
EM raw data | ![]() Data size: 2.7 TB Data #1: Single particle cryo-EM dataset of Mus musculus mitochondrial complex I in the deactive state [micrographs - multiframe]) |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | Mouse mitochondrial complex I in the deactive state | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.33 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Half map: Half-1
File | emd_4356_half_map_1.map | ||||||||||||
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Annotation | Half-1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half-2
File | emd_4356_half_map_2.map | ||||||||||||
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Annotation | Half-2 | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
+Entire : Mitochondrial complex I from mouse in the deactive state
+Supramolecule #1: Mitochondrial complex I from mouse in the deactive state
+Macromolecule #1: NADH-ubiquinone oxidoreductase chain 3
+Macromolecule #2: NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial
+Macromolecule #3: NADH dehydrogenase [ubiquinone] iron-sulfur protein 3, mitochondrial
+Macromolecule #4: NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial
+Macromolecule #5: NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial
+Macromolecule #6: NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial
+Macromolecule #7: NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial
+Macromolecule #8: NADH-ubiquinone oxidoreductase chain 1
+Macromolecule #9: NADH dehydrogenase [ubiquinone] iron-sulfur protein 8, mitochondrial
+Macromolecule #10: NADH-ubiquinone oxidoreductase chain 6
+Macromolecule #11: NADH-ubiquinone oxidoreductase chain 4L
+Macromolecule #12: NADH-ubiquinone oxidoreductase chain 5
+Macromolecule #13: NADH-ubiquinone oxidoreductase chain 4
+Macromolecule #14: NADH-ubiquinone oxidoreductase chain 2
+Macromolecule #15: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mi...
+Macromolecule #16: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9, mit...
+Macromolecule #17: NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial
+Macromolecule #18: NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial
+Macromolecule #19: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2
+Macromolecule #20: Acyl carrier protein, mitochondrial
+Macromolecule #21: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5
+Macromolecule #22: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6
+Macromolecule #23: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8
+Macromolecule #24: MCG5603
+Macromolecule #25: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13
+Macromolecule #26: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1
+Macromolecule #27: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3
+Macromolecule #28: NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrial
+Macromolecule #29: NADH dehydrogenase [ubiquinone] 1 subunit C2
+Macromolecule #30: NADH dehydrogenase [ubiquinone] iron-sulfur protein 5
+Macromolecule #31: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1
+Macromolecule #32: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 11, mit...
+Macromolecule #33: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 5, mito...
+Macromolecule #34: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6
+Macromolecule #35: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2, mito...
+Macromolecule #36: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3
+Macromolecule #37: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mito...
+Macromolecule #38: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4
+Macromolecule #39: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9
+Macromolecule #40: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7
+Macromolecule #41: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10
+Macromolecule #42: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12
+Macromolecule #43: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7
+Macromolecule #44: NADH dehydrogenase [ubiquinone] flavoprotein 3, mitochondrial
+Macromolecule #45: IRON/SULFUR CLUSTER
+Macromolecule #46: FE2/S2 (INORGANIC) CLUSTER
+Macromolecule #47: FLAVIN MONONUCLEOTIDE
+Macromolecule #48: ADENOSINE-5'-DIPHOSPHATE
+Macromolecule #49: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
+Macromolecule #50: ZINC ION
+Macromolecule #51: ~{S}-[2-[3-[[(2~{R})-3,3-dimethyl-2-oxidanyl-4-phosphonooxy-butan...
+Macromolecule #52: ACETYL GROUP
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 3 mg/mL | ||||||||||||
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Buffer | pH: 7.14 Component:
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Grid | Model: Quantifoil UltrAuFoil / Material: GOLD / Mesh: 300 Details: Gold was PEGylated prior to use in anaerobic ethanol in 5mM SPT-11P6 (Sensopath Technologies) for two days 0.6/1 holes | ||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV / Details: 8-16s blotting.. | ||||||||||||
Details | Peak fraction from a gel filtration column- monodisperse and not concentrated. The complex was put into the deactive state by heating at 37degC for 30 mins before isolation in detergent. |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Name: GIF Quantum LS / Energy filter - Lower energy threshold: 0 eV / Energy filter - Upper energy threshold: 20 eV |
Image recording | Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: COUNTING / Digitization - Frames/image: 1-30 / Number grids imaged: 1 / Average exposure time: 15.0 sec. / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Calibrated magnification: 37600 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.4 µm / Nominal defocus min: 2.2 µm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
-Atomic model buiding 1
Details | Used default paramteres in phenix.real_space_refine |
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Refinement | Space: REAL / Protocol: FLEXIBLE FIT |
Output model | ![]() PDB-6g72: |