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Yorodumi- EMDB-35336: Respiratory complex CI:CIII2, type IB, Wild type mouse under cold... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-35336 | |||||||||
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Title | Respiratory complex CI:CIII2, type IB, Wild type mouse under cold temperature | |||||||||
Map data | Cold Acclimated, Type IB of Respiratory Supercomplex CI:CIII2 | |||||||||
Sample |
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Keywords | Respiratory complex / Respiratory supercomplex / ELECTRON TRANSPORT | |||||||||
Function / homology | Function and homology information Complex III assembly / subthalamus development / pons development / response to injury involved in regulation of muscle adaptation / Protein lipoylation / reproductive system development / Mitochondrial Fatty Acid Beta-Oxidation / Complex I biogenesis / Mitochondrial protein import / cerebellar Purkinje cell layer development ...Complex III assembly / subthalamus development / pons development / response to injury involved in regulation of muscle adaptation / Protein lipoylation / reproductive system development / Mitochondrial Fatty Acid Beta-Oxidation / Complex I biogenesis / Mitochondrial protein import / cerebellar Purkinje cell layer development / RHOG GTPase cycle / respiratory chain complex III / Respiratory electron transport / protein insertion into mitochondrial inner membrane / circulatory system development / blastocyst hatching / pyramidal neuron development / response to mercury ion / mitochondrial respiratory chain complex III assembly / thalamus 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 / : / response to alkaloid / neural precursor cell proliferation / cardiac muscle tissue development / : / negative regulation of non-canonical NF-kappaB signal transduction / [2Fe-2S] cluster assembly / quinol-cytochrome-c reductase / adult walking behavior / oxygen sensor activity / response to copper ion / response to glucagon / cellular response to glucocorticoid stimulus / response to hydroperoxide / positive regulation of mitochondrial membrane potential / ubiquinol-cytochrome-c reductase activity / cellular respiration / respiratory chain complex I / iron-sulfur cluster assembly / mitochondrial ribosome / midbrain development / hypothalamus development / mitochondrial electron transport, ubiquinol to cytochrome c / adult behavior / mitochondrial translation / positive regulation of ATP biosynthetic process / response to cobalamin / dopamine metabolic process / positive regulation of execution phase of apoptosis / NADH:ubiquinone reductase (H+-translocating) / ubiquinone binding / : / NADH dehydrogenase activity / apoptotic mitochondrial changes / : / 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 / response to hyperoxia / acyl carrier activity / cellular response to interferon-beta / NADH dehydrogenase (ubiquinone) activity / neuron development / animal organ regeneration / quinone binding / response to cadmium ion / ATP synthesis coupled electron transport / cellular response to retinoic acid / negative regulation of intrinsic apoptotic signaling pathway / muscle contraction / negative regulation of reactive oxygen species biosynthetic process / ATP metabolic process / extrinsic apoptotic signaling pathway / tricarboxylic acid cycle / visual perception / ionotropic glutamate receptor binding / aerobic respiration / response to hormone / Neutrophil degranulation / respiratory electron transport chain / reactive oxygen species metabolic process / neurogenesis / cerebellum development / regulation of mitochondrial membrane potential / response to activity / kidney development / mitochondrion organization Similarity search - Function | |||||||||
Biological species | Mus musculus (house mouse) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.3 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 CI:CIII2, 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_35336.map.gz | 178.9 MB | EMDB map data format | |
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Header (meta data) | emd-35336-v30.xml emd-35336.xml | 76.9 KB 76.9 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_35336_fsc.xml | 13.7 KB | Display | FSC data file |
Images | emd_35336.png | 189.6 KB | ||
Masks | emd_35336_msk_1.map | 216 MB | Mask map | |
Filedesc metadata | emd-35336.cif.gz | 15.7 KB | ||
Others | emd_35336_half_map_1.map.gz emd_35336_half_map_2.map.gz | 173.1 MB 173.1 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-35336 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-35336 | HTTPS FTP |
-Validation report
Summary document | emd_35336_validation.pdf.gz | 1.1 MB | Display | EMDB validaton report |
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Full document | emd_35336_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | emd_35336_validation.xml.gz | 20.9 KB | Display | |
Data in CIF | emd_35336_validation.cif.gz | 27.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-35336 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-35336 | HTTPS FTP |
-Related structure data
Related structure data | 8ib9MC 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_35336.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | Cold Acclimated, Type IB 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_35336_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-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: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11
+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: Cytochrome b-c1 complex subunit 1, mitochondrial
+Macromolecule #46: Cytochrome b-c1 complex subunit 2, mitochondrial
+Macromolecule #47: Cytochrome b
+Macromolecule #48: Cytochrome c1, heme protein, mitochondrial
+Macromolecule #49: Cytochrome b-c1 complex subunit Rieske, mitochondrial
+Macromolecule #50: Cytochrome b-c1 complex subunit 7
+Macromolecule #51: Cytochrome b-c1 complex subunit 8
+Macromolecule #52: Cytochrome b-c1 complex subunit 6, mitochondrial
+Macromolecule #53: Cytochrome b-c1 complex subunit 9
+Macromolecule #54: Cytochrome b-c1 complex subunit 10
+Macromolecule #55: IRON/SULFUR CLUSTER
+Macromolecule #56: UBIQUINONE-1
+Macromolecule #57: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE
+Macromolecule #58: 1,2-Distearoyl-sn-glycerophosphoethanolamine
+Macromolecule #59: FE2/S2 (INORGANIC) CLUSTER
+Macromolecule #60: FLAVIN MONONUCLEOTIDE
+Macromolecule #61: Ubiquinone-9
+Macromolecule #62: CARDIOLIPIN
+Macromolecule #63: ADENOSINE-5'-DIPHOSPHATE
+Macromolecule #64: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
+Macromolecule #65: ZINC ION
+Macromolecule #66: ~{S}-[2-[3-[[(2~{R})-3,3-dimethyl-2-oxidanyl-4-phosphonooxy-butan...
+Macromolecule #67: PROTOPORPHYRIN IX CONTAINING FE
+Macromolecule #68: UBIQUINONE-10
+Macromolecule #69: 5-(3,7,11,15,19,23-HEXAMETHYL-TETRACOSA-2,6,10,14,18,22-HEXAENYL)...
+Macromolecule #70: HEME C
-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 |