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Yorodumi- EMDB-35338: Respiratory complex Membrane domain of CI, focus-refined of type ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-35338 | |||||||||
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Title | Respiratory complex Membrane domain of CI, focus-refined of type IB, Wild type mouse under cold temperature | |||||||||
Map data | Focus-refined map, Membrane Domain, Cold Acclimated, Type IB of Respiratory Supercomplex | |||||||||
Sample |
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Keywords | Respiratory complex / Respiratory supercomplex / ELECTRON TRANSPORT | |||||||||
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 | single particle reconstruction / cryo EM / Resolution: 3.3 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 Membrane domain of CI, focus-refined of type IB, Wild type mouse under cold 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_35338.map.gz | 180.8 MB | EMDB map data format | |
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Header (meta data) | emd-35338-v30.xml emd-35338.xml | 40.4 KB 40.4 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_35338_fsc.xml | 12.7 KB | Display | FSC data file |
Images | emd_35338.png | 97.7 KB | ||
Masks | emd_35338_msk_1.map | 216 MB | Mask map | |
Filedesc metadata | emd-35338.cif.gz | 9.6 KB | ||
Others | emd_35338_half_map_1.map.gz emd_35338_half_map_2.map.gz | 177.3 MB 177.3 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-35338 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-35338 | HTTPS FTP |
-Validation report
Summary document | emd_35338_validation.pdf.gz | 1 MB | Display | EMDB validaton report |
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Full document | emd_35338_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | emd_35338_validation.xml.gz | 21.7 KB | Display | |
Data in CIF | emd_35338_validation.cif.gz | 28.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-35338 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-35338 | HTTPS FTP |
-Related structure data
Related structure data | 8ibbMC 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_35338.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | Focus-refined map, Membrane Domain, Cold Acclimated, Type IB of Respiratory Supercomplex | ||||||||||||||||||||||||||||||||||||
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_35338_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Respiratory Supercomplex CI:CIII2
+Supramolecule #1: Respiratory Supercomplex CI:CIII2
+Macromolecule #1: NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial
+Macromolecule #2: NADH-ubiquinone oxidoreductase chain 6
+Macromolecule #3: NADH-ubiquinone oxidoreductase chain 4L
+Macromolecule #4: NADH-ubiquinone oxidoreductase chain 5
+Macromolecule #5: NADH-ubiquinone oxidoreductase chain 4
+Macromolecule #6: NADH-ubiquinone oxidoreductase chain 2
+Macromolecule #7: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mi...
+Macromolecule #8: Acyl carrier protein, mitochondrial
+Macromolecule #9: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8
+Macromolecule #10: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11
+Macromolecule #11: NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrial
+Macromolecule #12: NADH dehydrogenase [ubiquinone] 1 subunit C2
+Macromolecule #13: NADH dehydrogenase [ubiquinone] iron-sulfur protein 5
+Macromolecule #14: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1
+Macromolecule #15: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 11, mit...
+Macromolecule #16: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 5, mito...
+Macromolecule #17: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6
+Macromolecule #18: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2, mito...
+Macromolecule #19: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3
+Macromolecule #20: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mito...
+Macromolecule #21: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4
+Macromolecule #22: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9
+Macromolecule #23: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7
+Macromolecule #24: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10
+Macromolecule #25: 1,2-Distearoyl-sn-glycerophosphoethanolamine
+Macromolecule #26: CARDIOLIPIN
+Macromolecule #27: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE
+Macromolecule #28: ADENOSINE-5'-DIPHOSPHATE
+Macromolecule #29: ~{S}-[2-[3-[[(2~{R})-3,3-dimethyl-2-oxidanyl-4-phosphonooxy-butan...
-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 | #0 - Image recording ID: 1 / #0 - Film or detector model: GATAN K3 (6k x 4k) / #0 - Average electron dose: 46.1 e/Å2 / #1 - Image recording ID: 2 / #1 - Film or detector model: GATAN K3 (6k x 4k) / #1 - Average electron dose: 45.9 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 |