+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-9534 | |||||||||
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Title | Architecture of mammalian respirasome | |||||||||
Map data | ||||||||||
Sample |
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Function / homology | Function and homology information ubiquinone-6 biosynthetic process / TP53 Regulates Metabolic Genes / mitochondrial respirasome assembly / Cytoprotection by HMOX1 / cellular response to oxygen levels / respiratory chain complex IV / Complex I biogenesis / Respiratory electron transport / mitochondrial respiratory chain complex III assembly / regulation of oxidative phosphorylation ...ubiquinone-6 biosynthetic process / TP53 Regulates Metabolic Genes / mitochondrial respirasome assembly / Cytoprotection by HMOX1 / cellular response to oxygen levels / respiratory chain complex IV / Complex I biogenesis / Respiratory electron transport / mitochondrial respiratory chain complex III assembly / regulation of oxidative phosphorylation / Respiratory electron transport / gliogenesis / mitochondrial respiratory chain complex III / neural precursor cell proliferation / anterograde axonal transport / mitochondrial respiratory chain complex IV / mitochondrial respirasome / NADH dehydrogenase activity / oxygen sensor activity / cytochrome-c oxidase / quinol-cytochrome-c reductase / ubiquinone binding / ubiquinol-cytochrome-c reductase activity / oxidative phosphorylation / 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 / 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 / enzyme regulator activity / respirasome / aerobic respiration / axon cytoplasm / reactive oxygen species metabolic process / respiratory electron transport chain / central nervous system development / mitochondrial membrane / mitochondrial intermembrane space / 2 iron, 2 sulfur cluster binding / metalloendopeptidase activity / NAD binding / FMN binding / 4 iron, 4 sulfur cluster binding / response to oxidative stress / mitochondrial inner membrane / oxidoreductase activity / mitochondrial matrix / copper ion binding / ubiquitin protein ligase binding / heme binding / protein-containing complex binding / mitochondrion / proteolysis / nucleoplasm / membrane / metal ion binding / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Sus scrofa (pig) / Bovine (cattle) / Pig (pig) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 5.4 Å | |||||||||
Authors | Gu J / Wu M / Guo R / Yang M | |||||||||
Citation | Journal: Nature / Year: 2016 Title: The architecture of the mammalian respirasome. Authors: Jinke Gu / Meng Wu / Runyu Guo / Kaige Yan / Jianlin Lei / Ning Gao / Maojun Yang / Abstract: The respiratory chain complexes I, III and IV (CI, CIII and CIV) are present in the bacterial membrane or the inner mitochondrial membrane and have a role of transferring electrons and establishing ...The respiratory chain complexes I, III and IV (CI, CIII and CIV) are present in the bacterial membrane or the inner mitochondrial membrane and have a role of transferring electrons and establishing the proton gradient for ATP synthesis by complex V. The respiratory chain complexes can assemble into supercomplexes (SCs), but their precise arrangement is unknown. Here we report a 5.4 Å cryo-electron microscopy structure of the major 1.7 megadalton SCI1III2IV1 respirasome purified from porcine heart. The CIII dimer and CIV bind at the same side of the L-shaped CI, with their transmembrane domains essentially aligned to form a transmembrane disk. Compared to free CI, the CI in the respirasome is more compact because of interactions with CIII and CIV. The NDUFA11 and NDUFB9 supernumerary subunits of CI contribute to the oligomerization of CI and CIII. The structure of the respirasome provides information on the precise arrangements of the respiratory chain complexes in mitochondria. | |||||||||
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_9534.map.gz | 26.2 MB | EMDB map data format | |
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Header (meta data) | emd-9534-v30.xml emd-9534.xml | 75.9 KB 75.9 KB | Display Display | EMDB header |
Images | emd_9534.png | 15.2 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-9534 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-9534 | HTTPS FTP |
-Related structure data
Related structure data | 5gpnMC 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_9534.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: 1.05296 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 : Respirasome
+Supramolecule #1: Respirasome
+Macromolecule #1: Cytochrome b-c1 complex subunit 1, mitochondrial
+Macromolecule #2: Cytochrome b-c1 complex subunit 2, mitochondrial
+Macromolecule #3: Cytochrome b
+Macromolecule #4: Cytochrome c1, heme protein, mitochondrial
+Macromolecule #5: Cytochrome b-c1 complex subunit Rieske, mitochondrial
+Macromolecule #6: Cytochrome b-c1 complex subunit 7
+Macromolecule #7: Cytochrome b-c1 complex subunit 8
+Macromolecule #8: Cytochrome b-c1 complex subunit 6, mitochondrial
+Macromolecule #9: Cytochrome b-c1 complex subunit Rieske, mitochondrial
+Macromolecule #10: Cytochrome b-c1 complex subunit 9
+Macromolecule #11: Cytochrome b-c1 complex subunit 10
+Macromolecule #12: NADH dehydrogenase [ubiquinone] iron-sulfur protein 3
+Macromolecule #13: NADH-ubiquinone oxidoreductase 75 kDa subunit
+Macromolecule #14: NADH dehydrogenase [ubiquinone] iron-sulfur protein 2
+Macromolecule #15: NADH dehydrogenase [ubiquinone] iron-sulfur protein 7
+Macromolecule #16: NADH dehydrogenase [ubiquinone] iron-sulfur protein 8
+Macromolecule #17: NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial
+Macromolecule #18: NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial
+Macromolecule #19: NADH-ubiquinone oxidoreductase chain 1
+Macromolecule #20: NADH-ubiquinone oxidoreductase chain 2
+Macromolecule #21: NADH-ubiquinone oxidoreductase chain 3
+Macromolecule #22: NADH-ubiquinone oxidoreductase chain 4
+Macromolecule #23: NADH-ubiquinone oxidoreductase chain 4L
+Macromolecule #24: NADH-ubiquinone oxidoreductase chain 5
+Macromolecule #25: NADH-ubiquinone oxidoreductase chain 6
+Macromolecule #26: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3
+Macromolecule #27: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2
+Macromolecule #28: NADH dehydrogenase [ubiquinone] iron-sulfur protein 5
+Macromolecule #29: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9
+Macromolecule #30: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mi...
+Macromolecule #31: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13
+Macromolecule #32: Acyl carrier protein
+Macromolecule #33: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 5
+Macromolecule #34: Mitochondrial NADH dehydrogenase Fe-S protein 4
+Macromolecule #35: NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial
+Macromolecule #36: Cytochrome c oxidase subunit 3
+Macromolecule #37: Cytochrome c oxidase subunit 4 isoform 1, mitochondrial
+Macromolecule #38: Cytochrome c oxidase subunit 5A, mitochondrial
+Macromolecule #39: Cytochrome c oxidase subunit 5B, mitochondrial
+Macromolecule #40: Cytochrome c oxidase subunit 6A2, mitochondrial
+Macromolecule #41: Cytochrome c oxidase subunit 6B1
+Macromolecule #42: Cytochrome c oxidase subunit 6C
+Macromolecule #43: Cytochrome c oxidase subunit 7A1, mitochondrial
+Macromolecule #44: Cytochrome c oxidase subunit 7B, mitochondrial
+Macromolecule #45: Cytochrome c oxidase subunit 7C, mitochondrial
+Macromolecule #46: Cytochrome c oxidase subunit 8B, mitochondrial
+Macromolecule #47: Cytochrome c oxidase subunit 1
+Macromolecule #48: Cytochrome c oxidase subunit 2
+Macromolecule #49: NADH dehydrogenase [ubiquinone] 1 unknown subunit fragment
+Macromolecule #50: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1
+Macromolecule #51: NADH dehydrogenase [ubiquinone] 1 unknown subunit fragment
+Macromolecule #52: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5
+Macromolecule #53: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6
+Macromolecule #54: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11
+Macromolecule #55: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10
+Macromolecule #56: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9
+Macromolecule #57: NADH dehydrogenase [ubiquinone] 1 subunit C2
+Macromolecule #58: NADH dehydrogenase [ubiquinone] 1 subunit C1
+Macromolecule #59: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8
+Macromolecule #60: NADH dehydrogenase [ubiquinone] 1 unknown subunit fragment
+Macromolecule #61: NADH dehydrogenase [ubiquinone] 1 unknown subunit fragment
+Macromolecule #62: NADH dehydrogenase [ubiquinone] 1 unknown subunit fragment
+Macromolecule #63: NADH dehydrogenase [ubiquinone] 1 unknown subunit fragment
+Macromolecule #64: PROTOPORPHYRIN IX CONTAINING FE
+Macromolecule #65: HEME C
+Macromolecule #66: FE2/S2 (INORGANIC) CLUSTER
+Macromolecule #67: IRON/SULFUR CLUSTER
+Macromolecule #68: FLAVIN MONONUCLEOTIDE
+Macromolecule #69: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
+Macromolecule #70: ZINC ION
+Macromolecule #71: HEME-A
+Macromolecule #72: COPPER (II) ION
+Macromolecule #73: MAGNESIUM ION
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.2 |
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Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 400 |
Vitrification | Cryogen name: NITROGEN |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: TUNGSTEN HAIRPIN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy |
Image recording | Film or detector model: FEI FALCON II (4k x 4k) / Detector mode: COUNTING / Average electron dose: 1.7 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
CTF correction | Software - Name: CTFFIND (ver. 3) |
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Initial angle assignment | Type: ANGULAR RECONSTITUTION / Software - Name: EMAN (ver. 2.1) |
Final 3D classification | Software - Name: EMAN (ver. 2.1) |
Final angle assignment | Type: ANGULAR RECONSTITUTION / Software - Name: EMAN (ver. 2.1) |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 5.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: EMAN (ver. 2.1) / Number images used: 139996 |
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: RIGID BODY FIT |
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Output model | PDB-5gpn: |