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Yorodumi- EMDB-9539: Cryo-EM structure of mammalian respiratory supercomplex I1III2IV1 -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-9539 | ||||||||||||
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Title | Cryo-EM structure of mammalian respiratory supercomplex I1III2IV1 | ||||||||||||
Map data | |||||||||||||
Sample |
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Function / homology | Function and homology information TP53 Regulates Metabolic Genes / subthalamus development / pons development / cerebellar Purkinje cell layer development / respiratory chain complex III / pyramidal neuron development / ubiquinone-6 biosynthetic process / thalamus development / Mitochondrial protein import / cellular response to oxygen levels ...TP53 Regulates Metabolic Genes / subthalamus development / pons development / cerebellar Purkinje cell layer development / respiratory chain complex III / pyramidal neuron development / ubiquinone-6 biosynthetic process / thalamus development / Mitochondrial protein import / cellular response to oxygen levels / Complex I biogenesis / Respiratory electron transport / mitochondrial respiratory chain complex III assembly / gliogenesis / mitochondrial respiratory chain complex III / neural precursor cell proliferation / anterograde axonal transport / mitochondrial respiratory chain complex IV / NADH dehydrogenase activity / oxygen sensor activity / ubiquinone binding / ubiquinol-cytochrome-c reductase activity / acyl binding / mitochondrial electron transport, cytochrome c to oxygen / electron transport coupled proton transport / cytochrome-c oxidase activity / mitochondrial electron transport, ubiquinol to cytochrome c / acyl carrier activity / hypothalamus development / midbrain development / NADH:ubiquinone reductase (H+-translocating) / mitochondrial respiratory chain complex I / mitochondrial respiratory chain complex I assembly / mitochondrial electron transport, NADH to ubiquinone / electron transport chain / NADH dehydrogenase (ubiquinone) activity / quinone binding / ATP synthesis coupled electron transport / respirasome / aerobic respiration / axon cytoplasm / reactive oxygen species metabolic process / respiratory electron transport chain / hippocampus development / mitochondrial intermembrane space / 2 iron, 2 sulfur cluster binding / NAD binding / FMN binding / 4 iron, 4 sulfur cluster binding / response to oxidative stress / mitochondrial inner membrane / membrane => GO:0016020 / oxidoreductase activity / mitochondrial matrix / nuclear speck / ubiquitin protein ligase binding / protein-containing complex binding / endoplasmic reticulum / mitochondrion / nucleoplasm / membrane / metal ion binding / cytosol / cytoplasm Similarity search - Function | ||||||||||||
Biological species | Sus scrofa (pig) / Pig (pig) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.0 Å | ||||||||||||
Authors | Gu J / Wu M / Guo R / Yang M | ||||||||||||
Funding support | China, 3 items
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Citation | Journal: Cell / Year: 2016 Title: Structure of Mammalian Respiratory Supercomplex IIIIIV. Authors: Meng Wu / Jinke Gu / Runyu Guo / Yushen Huang / Maojun Yang / Abstract: The mammalian respiratory chain complexes assemble into supercomplexes (SCs) and reside in the inner mitochondrial membrane to transfer electrons and establish the proton gradient for complex V to ...The mammalian respiratory chain complexes assemble into supercomplexes (SCs) and reside in the inner mitochondrial membrane to transfer electrons and establish the proton gradient for complex V to synthesize ATP. The precise arrangement of SCs is largely unknown. Here, we report a 4.0-Å cryo-electron microscopy (cryo-EM) structure of the major SC in porcine heart, the 1.7-MDa SCIIIIIV. The complex III (CIII) dimer and complex IV (CIV) bind at the same side of the L-shaped complex I (CI). Several accessory or supernumerary subunits of CI, such as NDUFA11, NDUFB4, NDUFB8, and NDUFB9, directly contribute to the oligomerization of CI, CIII, and CIV. COX7C and COX7A of CIV attach CIV to the concave surface formed by CIII and the distal end of membrane arm of CI. The structure suggests a possible mechanism by which electrons are transferred from NADH to cytochrome c and provides a platform for future functional dissection of respiration. | ||||||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_9539.map.gz | 29.6 MB | EMDB map data format | |
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Header (meta data) | emd-9539-v30.xml emd-9539.xml | 78.9 KB 78.9 KB | Display Display | EMDB header |
Images | emd_9539.png | 15.6 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-9539 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-9539 | HTTPS FTP |
-Related structure data
Related structure data | 5gupMC 6718C 6719C 6720C M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_9539.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.08 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
+Entire : Respiratory supercomplex I1III2IV1
+Supramolecule #1: Respiratory supercomplex I1III2IV1
+Macromolecule #1: Cytochrome c oxidase subunit 6C
+Macromolecule #2: NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial
+Macromolecule #3: NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial
+Macromolecule #4: NADH dehydrogenase [ubiquinone] iron-sulfur protein 3, mitochondrial
+Macromolecule #5: NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial
+Macromolecule #6: NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial
+Macromolecule #7: NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial
+Macromolecule #8: NADH dehydrogenase [ubiquinone] iron-sulfur protein 8, mitochondrial
+Macromolecule #9: NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial
+Macromolecule #10: NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial
+Macromolecule #11: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12
+Macromolecule #12: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9, mit...
+Macromolecule #13: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7
+Macromolecule #14: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5
+Macromolecule #15: Acyl carrier protein, mitochondrial
+Macromolecule #16: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2
+Macromolecule #17: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6
+Macromolecule #18: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1
+Macromolecule #19: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3
+Macromolecule #20: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mi...
+Macromolecule #21: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11
+Macromolecule #22: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13
+Macromolecule #23: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2, mito...
+Macromolecule #24: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3
+Macromolecule #25: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 5, mito...
+Macromolecule #26: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6
+Macromolecule #27: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mito...
+Macromolecule #28: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10
+Macromolecule #29: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 11, mit...
+Macromolecule #30: NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrial
+Macromolecule #31: NADH dehydrogenase [ubiquinone] 1 subunit C2
+Macromolecule #32: NADH dehydrogenase [ubiquinone] iron-sulfur protein 5
+Macromolecule #33: NADH-ubiquinone oxidoreductase chain 2
+Macromolecule #34: NADH-ubiquinone oxidoreductase chain 3
+Macromolecule #35: NADH-ubiquinone oxidoreductase chain 4L
+Macromolecule #36: NADH-ubiquinone oxidoreductase chain 5
+Macromolecule #37: NADH-ubiquinone oxidoreductase chain 6
+Macromolecule #38: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1
+Macromolecule #39: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4
+Macromolecule #40: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9
+Macromolecule #41: NADH-ubiquinone oxidoreductase chain 4
+Macromolecule #42: NADH-ubiquinone oxidoreductase chain 1
+Macromolecule #43: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8
+Macromolecule #44: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7
+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 7
+Macromolecule #50: Cytochrome b-c1 complex subunit 8
+Macromolecule #51: Cytochrome b-c1 complex subunit 6, mitochondrial
+Macromolecule #52: Cytochrome b-c1 complex subunit 9
+Macromolecule #53: Cytochrome b-c1 complex subunit Rieske, mitochondrial
+Macromolecule #54: Cytochrome b-c1 complex subunit 10
+Macromolecule #55: Cytochrome b-c1 complex subunit Rieske transit peptide, mitochondrial
+Macromolecule #56: Cytochrome c oxidase subunit 8B, mitochondrial
+Macromolecule #57: Cytochrome c oxidase subunit 7A1, mitochondrial
+Macromolecule #58: Cytochrome c oxidase subunit 7B, mitochondrial
+Macromolecule #59: Cytochrome c oxidase subunit 7C, mitochondrial
+Macromolecule #60: Cytochrome c oxidase subunit 1
+Macromolecule #61: Cytochrome c oxidase subunit 2
+Macromolecule #62: Cytochrome c oxidase subunit 3
+Macromolecule #63: Cytochrome c oxidase subunit 4 isoform 1, mitochondrial
+Macromolecule #64: Cytochrome c oxidase subunit 5A, mitochondrial
+Macromolecule #65: Cytochrome c oxidase subunit 5B, mitochondrial
+Macromolecule #66: Cytochrome c oxidase subunit 6A, mitochondrial
+Macromolecule #67: Cytochrome c oxidase subunit 6B1
+Macromolecule #68: IRON/SULFUR CLUSTER
+Macromolecule #69: FLAVIN MONONUCLEOTIDE
+Macromolecule #70: FE2/S2 (INORGANIC) CLUSTER
+Macromolecule #71: (9R,11S)-9-({[(1S)-1-HYDROXYHEXADECYL]OXY}METHYL)-2,2-DIMETHYL-5,...
+Macromolecule #72: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
+Macromolecule #73: S-[2-({N-[(2S)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-b...
+Macromolecule #74: CARDIOLIPIN
+Macromolecule #75: 1,2-Dioleoyl-sn-glycero-3-phosphoethanolamine
+Macromolecule #76: PROTOPORPHYRIN IX CONTAINING FE
+Macromolecule #77: HEME C
+Macromolecule #78: HEME-A
+Macromolecule #79: COPPER (II) ION
+Macromolecule #80: MAGNESIUM ION
+Macromolecule #81: ZINC ION
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 |
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Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: OTHER / Imaging mode: BRIGHT FIELDBright-field microscopy |
Image recording | Film or detector model: FEI FALCON II (4k x 4k) / Average electron dose: 1.25 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
CTF correction | Software - Name: CTFFIND (ver. 3.0) |
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Initial angle assignment | Type: RANDOM ASSIGNMENT / Software - Name: RELION (ver. 1.4) |
Final angle assignment | Type: RANDOM ASSIGNMENT / Software - Name: RELION (ver. 1.4) |
Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 1.4) / Number images used: 161912 |