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Yorodumi- EMDB-6776: Cryo-EM architecture of human respiratory chain megacomplex-I2III2IV2 -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-6776 | |||||||||
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Title | Cryo-EM architecture of human respiratory chain megacomplex-I2III2IV2 | |||||||||
Map data | ||||||||||
Sample |
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Function / homology | Function and homology information positive regulation of peptidase activity / subthalamus development / pons development / cerebellar Purkinje cell layer development / protein insertion into mitochondrial inner membrane / Complex I biogenesis / blastocyst hatching / pyramidal neuron development / TP53 Regulates Metabolic Genes / protein lipoylation ...positive regulation of peptidase activity / subthalamus development / pons development / cerebellar Purkinje cell layer development / protein insertion into mitochondrial inner membrane / Complex I biogenesis / blastocyst hatching / pyramidal neuron development / TP53 Regulates Metabolic Genes / protein lipoylation / Mitochondrial Fatty Acid Beta-Oxidation / respiratory chain complex IV assembly / response to mercury ion / ubiquinone-6 biosynthetic process / Cytoprotection by HMOX1 / thalamus development / mitochondrial respirasome assembly / respiratory chain complex IV / cellular response to oxygen levels / Respiratory electron transport / mitochondrial respiratory chain complex III assembly / respiratory gaseous exchange by respiratory system / iron-sulfur cluster assembly complex / mitochondrial large ribosomal subunit binding / Mitochondrial protein import / Respiratory electron transport / regulation of oxidative phosphorylation / gliogenesis / mitochondrial respiratory chain complex III / neural precursor cell proliferation / mitochondrial respiratory chain complex IV / [2Fe-2S] cluster assembly / Glyoxylate metabolism and glycine degradation / mitochondrial respirasome / NADH dehydrogenase activity / cardiac muscle tissue development / response to alkaloid / oxygen sensor activity / cytochrome-c oxidase / quinol-cytochrome-c reductase / cellular respiration / ubiquinol-cytochrome-c reductase activity / oxidative phosphorylation / ubiquinone binding / oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor / response to copper ion / acyl binding / response to glucagon / mitochondrial electron transport, cytochrome c to oxygen / mitochondrial ribosome / electron transport coupled proton transport / iron-sulfur cluster assembly / cytochrome-c oxidase activity / mitochondrial ATP synthesis coupled electron transport / mitochondrial electron transport, ubiquinol to cytochrome c / azurophil granule membrane / acyl carrier activity / hypothalamus development / mitochondrial translation / midbrain development / NADH:ubiquinone reductase (H+-translocating) / sodium ion transport / response to cobalamin / proton motive force-driven mitochondrial ATP synthesis / mitochondrial respiratory chain complex I / apoptotic mitochondrial changes / mitochondrial respiratory chain complex I assembly / mitochondrial electron transport, NADH to ubiquinone / positive regulation of cysteine-type endopeptidase activity involved in apoptotic process / NADH dehydrogenase (ubiquinone) activity / RHOG GTPase cycle / quinone binding / response to hyperoxia / ATP synthesis coupled electron transport / cellular response to interferon-beta / animal organ regeneration / negative regulation of intrinsic apoptotic signaling pathway / enzyme regulator activity / response to cadmium ion / respirasome / aerobic respiration / ATP metabolic process / cellular response to retinoic acid / extrinsic apoptotic signaling pathway / response to cAMP / response to organonitrogen compound / ionotropic glutamate receptor binding / substantia nigra development / reactive oxygen species metabolic process / respiratory electron transport chain / cerebellum development / neurogenesis / regulation of mitochondrial membrane potential / response to activity / response to nicotine / synaptic membrane / generation of precursor metabolites and energy / central nervous system development / fatty acid binding / apoptotic signaling pathway Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 17.4 Å | |||||||||
Authors | Gu J / Wu M / Yang M | |||||||||
Citation | Journal: Cell / Year: 2017 Title: Architecture of Human Mitochondrial Respiratory Megacomplex IIIIIV. Authors: Runyu Guo / Shuai Zong / Meng Wu / Jinke Gu / Maojun Yang / Abstract: The respiratory megacomplex represents the highest-order assembly of respiratory chain complexes, and it allows mitochondria to respond to energy-requiring conditions. To understand its architecture, ...The respiratory megacomplex represents the highest-order assembly of respiratory chain complexes, and it allows mitochondria to respond to energy-requiring conditions. To understand its architecture, we examined the human respiratory chain megacomplex-IIIIIV (MCIIIIIV) with 140 subunits and a subset of associated cofactors using cryo-electron microscopy. The MCIIIIIV forms a circular structure with the dimeric CIII located in the center, where it is surrounded by two copies each of CI and CIV. Two cytochrome c (Cyt.c) molecules are positioned to accept electrons on the surface of the c state CIII dimer. Analyses indicate that CII could insert into the gaps between CI and CIV to form a closed ring, which we termed the electron transport chain supercomplex. The structure not only reveals the precise assignment of individual subunits of human CI and CIII, but also enables future in-depth analysis of the electron transport chain as a whole. | |||||||||
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_6776.map.gz | 387.5 MB | EMDB map data format | |
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Header (meta data) | emd-6776-v30.xml emd-6776.xml | 17.7 KB 17.7 KB | Display Display | EMDB header |
Images | emd_6776.png | 20.7 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-6776 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-6776 | HTTPS FTP |
-Related structure data
Related structure data | 5xtiMC 6771C 6772C 6773C 6774C 6775C 5xtbC 5xtcC 5xtdC 5xteC 5xthC 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_6776.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 1.083 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 : Human respiratory chain megacomplex-I2III2IV2
Entire | Name: Human respiratory chain megacomplex-I2III2IV2 |
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Components |
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-Supramolecule #1: Human respiratory chain megacomplex-I2III2IV2
Supramolecule | Name: Human respiratory chain megacomplex-I2III2IV2 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#70 |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Experimental: 2.9 MDa |
-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 |
-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: 17.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 1.4) / Number images used: 8600 |