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Yorodumi- EMDB-35314: Respiratory complex Peripheral Arm of CI, focus-refined map of ty... -
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-Basic information
Entry | Database: EMDB / ID: EMD-35314 | |||||||||
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Title | Respiratory complex Peripheral Arm of CI, focus-refined map of type I, Wild type mouse under thermoneutral temperature | |||||||||
Map data | Focus-refined map, Peripheral Arm, Thermoneutral, Type I of Respiratory Supercomplex CI:CIII2 | |||||||||
Sample |
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Keywords | Respiratory complex / Respiratory supercomplex / ELECTRON TRANSPORT | |||||||||
Function / homology | Function and homology information response to injury involved in regulation of muscle adaptation / reproductive system development / Protein lipoylation / Mitochondrial Fatty Acid Beta-Oxidation / Complex I biogenesis / RHOG GTPase cycle / Respiratory electron transport / protein insertion into mitochondrial inner membrane / blastocyst hatching / circulatory system development ...response to injury involved in regulation of muscle adaptation / reproductive system development / Protein lipoylation / Mitochondrial Fatty Acid Beta-Oxidation / Complex I biogenesis / RHOG GTPase cycle / Respiratory electron transport / protein insertion into mitochondrial inner membrane / blastocyst hatching / circulatory system development / 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 / cellular response to glucocorticoid stimulus / neural precursor cell proliferation / cardiac muscle tissue development / : / [2Fe-2S] cluster assembly / adult walking behavior / oxygen sensor activity / response to hydroperoxide / cellular respiration / respiratory chain complex I / mitochondrial ribosome / iron-sulfur cluster assembly / adult behavior / mitochondrial translation / dopamine metabolic process / positive regulation of execution phase of apoptosis / NADH:ubiquinone reductase (H+-translocating) / proton motive force-driven mitochondrial ATP synthesis / NADH dehydrogenase activity / apoptotic mitochondrial changes / : / mitochondrial ATP synthesis coupled electron transport / mitochondrial electron transport, NADH to ubiquinone / mitochondrial respiratory chain complex I assembly / neuron development / electron transport coupled proton transport / acyl binding / cellular response to interferon-beta / acyl carrier activity / NADH dehydrogenase (ubiquinone) activity / 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 / neurogenesis / respiratory electron transport chain / reactive oxygen species metabolic process / kidney development / regulation of mitochondrial membrane potential / mitochondrion organization / cognition / synaptic membrane / fatty acid metabolic process / apoptotic signaling pathway / mitochondrial membrane / sensory perception of sound / brain development / regulation of protein phosphorylation / multicellular organism growth / 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 / nuclear body / response to hypoxia / mitochondrial matrix / structural constituent of ribosome / 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 | single particle reconstruction / cryo EM / Resolution: 3.2 Å | |||||||||
Authors | Shin Y-C / Liao M | |||||||||
Funding support | United States, 2 items
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Citation | Journal: To Be Published Title: Respiratory complex Peripheral Arm of CI, focus-refined map of type I, Wild type mouse under thermoneutral temperature Authors: Shin Y-C / Liao M | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_35314.map.gz | 197.5 MB | EMDB map data format | |
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Header (meta data) | emd-35314-v30.xml emd-35314.xml | 41.6 KB 41.6 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_35314_fsc.xml | 12.7 KB | Display | FSC data file |
Images | emd_35314.png | 31 KB | ||
Masks | emd_35314_msk_1.map | 216 MB | Mask map | |
Filedesc metadata | emd-35314.cif.gz | 10.1 KB | ||
Others | emd_35314_half_map_1.map.gz emd_35314_half_map_2.map.gz | 193.9 MB 193.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-35314 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-35314 | HTTPS FTP |
-Validation report
Summary document | emd_35314_validation.pdf.gz | 1 MB | Display | EMDB validaton report |
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Full document | emd_35314_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | emd_35314_validation.xml.gz | 21.4 KB | Display | |
Data in CIF | emd_35314_validation.cif.gz | 27.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-35314 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-35314 | HTTPS FTP |
-Related structure data
Related structure data | 8iapMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_35314.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | Focus-refined map, Peripheral Arm, Thermoneutral, Type I of Respiratory Supercomplex CI:CIII2 | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.1 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_35314_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Respiratory complex
+Supramolecule #1: Respiratory complex
+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 dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9, mit...
+Macromolecule #11: NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial
+Macromolecule #12: NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial
+Macromolecule #13: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2
+Macromolecule #14: Acyl carrier protein, mitochondrial
+Macromolecule #15: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5
+Macromolecule #16: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6
+Macromolecule #17: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8
+Macromolecule #18: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13
+Macromolecule #19: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1
+Macromolecule #20: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3
+Macromolecule #21: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12
+Macromolecule #22: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7
+Macromolecule #23: NADH dehydrogenase [ubiquinone] flavoprotein 3, mitochondrial
+Macromolecule #24: 1,2-Distearoyl-sn-glycerophosphoethanolamine
+Macromolecule #25: IRON/SULFUR CLUSTER
+Macromolecule #26: UBIQUINONE-1
+Macromolecule #27: FE2/S2 (INORGANIC) CLUSTER
+Macromolecule #28: FLAVIN MONONUCLEOTIDE
+Macromolecule #29: Ubiquinone-9
+Macromolecule #30: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE
+Macromolecule #31: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
+Macromolecule #32: ZINC ION
+Macromolecule #33: ~{S}-[2-[3-[[(2~{R})-3,3-dimethyl-2-oxidanyl-4-phosphonooxy-butan...
+Macromolecule #34: CARDIOLIPIN
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.33 mg/mL |
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Buffer | pH: 8 |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TALOS ARCTICA |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 46.6 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: OTHER / Imaging mode: OTHER / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.0 µm |
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |