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Yorodumi- EMDB-53477: Complex I from Ovis aries in presence of D1 inhibitor, Open state -
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Open data
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Basic information
| Entry | ![]() | |||||||||
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| Title | Complex I from Ovis aries in presence of D1 inhibitor, Open state | |||||||||
Map data | Composite map of Complex I from Ovis aries in presence of D1 inhibitor, Open state | |||||||||
Sample |
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Keywords | Complex I / inhibitor / respiration / proton pump / NADH:ubiquinone oxidoreductase / membrane protein / mitochondria / PROTON TRANSPORT | |||||||||
| Function / homology | Function and homology informationmyoblast migration involved in skeletal muscle regeneration / negative regulation of skeletal muscle satellite cell proliferation / positive regulation of macrophage chemotaxis / NADH:ubiquinone reductase (H+-translocating) / ubiquinone binding / mitochondrial ATP synthesis coupled electron transport / mitochondrial electron transport, NADH to ubiquinone / electron transport coupled proton transport / acyl binding / mitochondrial respiratory chain complex I assembly ...myoblast migration involved in skeletal muscle regeneration / negative regulation of skeletal muscle satellite cell proliferation / positive regulation of macrophage chemotaxis / NADH:ubiquinone reductase (H+-translocating) / ubiquinone binding / mitochondrial ATP synthesis coupled electron transport / mitochondrial electron transport, NADH to ubiquinone / electron transport coupled proton transport / acyl binding / mitochondrial respiratory chain complex I assembly / oxidoreductase activity, acting on NAD(P)H / NADH dehydrogenase activity / respiratory chain complex I / NADH dehydrogenase (ubiquinone) activity / positive regulation of myoblast differentiation / acyl carrier activity / quinone binding / ATP synthesis coupled electron transport / positive regulation of lamellipodium assembly / reactive oxygen species metabolic process / aerobic respiration / transcription coregulator activity / electron transport chain / mitochondrial intermembrane space / 2 iron, 2 sulfur cluster binding / mitochondrial membrane / NAD binding / FMN binding / 4 iron, 4 sulfur cluster binding / response to oxidative stress / mitochondrial inner membrane / chromatin / positive regulation of transcription by RNA polymerase II / mitochondrion / membrane / metal ion binding / nucleus Similarity search - Function | |||||||||
| Biological species | ![]() | |||||||||
| Method | single particle reconstruction / cryo EM / Resolution: 3.2 Å | |||||||||
Authors | Sazanov L / Petrova O | |||||||||
| Funding support | United States, 1 items
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Citation | Journal: To Be PublishedTitle: Complex I from Ovis aries in presence of D1 inhibitor Authors: Sazanov L / Petrova O #1: Journal: To Be PublishedTitle: Real-space refinement in PHENIX for cryo-EM and crystallography Authors: Sazanov L | |||||||||
| History |
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Structure visualization
| Supplemental images |
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Downloads & links
-EMDB archive
| Map data | emd_53477.map.gz | 4.1 MB | EMDB map data format | |
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| Header (meta data) | emd-53477-v30.xml emd-53477.xml | 67.2 KB 67.2 KB | Display Display | EMDB header |
| Images | emd_53477.png | 118.9 KB | ||
| Filedesc metadata | emd-53477.cif.gz | 14.7 KB | ||
| Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-53477 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-53477 | HTTPS FTP |
-Related structure data
| Related structure data | ![]() 9r03MC ![]() 9r01C C: citing same article ( M: atomic model generated by this map |
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| Similar structure data | Similarity search - Function & homology F&H Search |
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Links
| EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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| Related items in Molecule of the Month |
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Map
| File | Download / File: emd_53477.map.gz / Format: CCP4 / Size: 20.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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| Annotation | Composite map of Complex I from Ovis aries in presence of D1 inhibitor, Open state | ||||||||||||||||||||||||||||||||||||
| Projections & slices | Image control
Images are generated by Spider. generated in cubic-lattice coordinate | ||||||||||||||||||||||||||||||||||||
| Voxel size | X=Y=Z: 1.22 Å | ||||||||||||||||||||||||||||||||||||
| Density |
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| Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
| Details | EMDB XML:
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-Supplemental data
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Sample components
+Entire : Complex I from Ovis aries in presence of D1 inhibitor, Open state
+Supramolecule #1: Complex I from Ovis aries in presence of D1 inhibitor, Open state
+Macromolecule #1: NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial
+Macromolecule #2: NADH-ubiquinone oxidoreductase chain 3
+Macromolecule #3: NADH-ubiquinone oxidoreductase chain 1
+Macromolecule #4: NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial
+Macromolecule #5: NADH-ubiquinone oxidoreductase chain 6
+Macromolecule #6: NADH-ubiquinone oxidoreductase chain 4L
+Macromolecule #7: NADH-ubiquinone oxidoreductase chain 5
+Macromolecule #8: NADH-ubiquinone oxidoreductase chain 4
+Macromolecule #9: NADH-ubiquinone oxidoreductase chain 2
+Macromolecule #10: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11
+Macromolecule #11: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 5, mito...
+Macromolecule #12: Acyl carrier protein
+Macromolecule #13: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8
+Macromolecule #14: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10
+Macromolecule #15: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mi...
+Macromolecule #16: NADH dehydrogenase [ubiquinone] iron-sulfur protein 5
+Macromolecule #17: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3
+Macromolecule #18: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3
+Macromolecule #19: NADH dehydrogenase [ubiquinone] 1 subunit C2
+Macromolecule #20: NADH:ubiquinone oxidoreductase subunit B4
+Macromolecule #21: Mitochondrial complex I, B17 subunit
+Macromolecule #22: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7
+Macromolecule #23: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9
+Macromolecule #24: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2, mito...
+Macromolecule #25: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mito...
+Macromolecule #26: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 11, mit...
+Macromolecule #27: NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrial
+Macromolecule #28: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1
+Macromolecule #29: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1
+Macromolecule #30: NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial
+Macromolecule #31: Mitochondrial complex I, 24 kDa subunit
+Macromolecule #32: NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial
+Macromolecule #33: NADH:ubiquinone oxidoreductase core subunit S3
+Macromolecule #34: Complex I-23kD
+Macromolecule #35: NADH dehydrogenase [ubiquinone] flavoprotein 3, mitochondrial
+Macromolecule #36: NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial
+Macromolecule #37: NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial
+Macromolecule #38: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9, mit...
+Macromolecule #39: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2
+Macromolecule #40: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5
+Macromolecule #41: NADH:ubiquinone oxidoreductase subunit A6
+Macromolecule #42: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7
+Macromolecule #43: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12
+Macromolecule #44: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13
+Macromolecule #45: 1,2-Distearoyl-sn-glycerophosphoethanolamine
+Macromolecule #46: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE
+Macromolecule #47: (7~{S})-7-[(2~{S})-1-(6-azanylpurin-3-yl)propan-2-yl]-3-methyl-6,...
+Macromolecule #48: IRON/SULFUR CLUSTER
+Macromolecule #49: 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE
+Macromolecule #50: MAGNESIUM ION
+Macromolecule #51: MYRISTIC ACID
+Macromolecule #52: S-[2-({N-[(2S)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-b...
+Macromolecule #53: FLAVIN MONONUCLEOTIDE
+Macromolecule #54: 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE
+Macromolecule #55: FE2/S2 (INORGANIC) CLUSTER
+Macromolecule #56: POTASSIUM ION
+Macromolecule #57: ZINC ION
+Macromolecule #58: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
-Experimental details
-Structure determination
| Method | cryo EM |
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Processing | single particle reconstruction |
| Aggregation state | particle |
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Sample preparation
| Concentration | 3 mg/mL |
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| Buffer | pH: 7.4 / Component - Concentration: 20.0 mM / Component - Formula: C8H18N2O4S / Component - Name: Hepes / Details: 50mM NaCl, 1mM EDTA, 0.02% LMNG |
| Grid | Model: Quantifoil R0.6/1 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE |
| Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
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Electron microscopy
| Microscope | TFS GLACIOS |
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| Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Number grids imaged: 1 / Number real images: 4167 / Average exposure time: 3.39 sec. / Average electron dose: 90.0 e/Å2 |
| Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
| Electron optics | C2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 120000 |
| Sample stage | Cooling holder cryogen: NITROGEN |
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Image processing
-Atomic model buiding 1
| Initial model | PDB ID: Chain - Source name: PDB / Chain - Initial model type: experimental model |
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| Software | Name: Coot (ver. 0.9.8.95) |
| Refinement | Space: REAL / Protocol: FLEXIBLE FIT / Target criteria: correlation coefficient |
| Output model | ![]() PDB-9r03: |
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Keywords
Authors
United States, 1 items
Citation






















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FIELD EMISSION GUN
