+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-6775 | |||||||||
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Title | Cryo-EM structure of human respiratory supercomplex I1III2IV1 | |||||||||
Map data | ||||||||||
Sample |
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Function / homology | Function and homology information subthalamus development / pons development / cerebellar Purkinje cell layer development / protein insertion into mitochondrial inner membrane / blastocyst hatching / protein lipoylation / pyramidal neuron development / TP53 Regulates Metabolic Genes / response to mercury ion / Mitochondrial Fatty Acid Beta-Oxidation ...subthalamus development / pons development / cerebellar Purkinje cell layer development / protein insertion into mitochondrial inner membrane / blastocyst hatching / protein lipoylation / pyramidal neuron development / TP53 Regulates Metabolic Genes / response to mercury ion / Mitochondrial Fatty Acid Beta-Oxidation / Protein lipoylation / mitochondrial respiratory chain complex III assembly / Cytoprotection by HMOX1 / respiratory chain complex IV assembly / thalamus development / mitochondrial respirasome assembly / response to cobalamin / respiratory chain complex IV / respiratory gaseous exchange by respiratory system / cellular response to oxygen levels / iron-sulfur cluster assembly complex / Mitochondrial protein import / : / mitochondrial large ribosomal subunit binding / regulation of oxidative phosphorylation / Respiratory electron transport / gliogenesis / : / response to alkaloid / neural precursor cell proliferation / cardiac muscle tissue development / cytochrome-c oxidase / : / [2Fe-2S] cluster assembly / oxidative phosphorylation / oxygen sensor activity / oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor / quinol-cytochrome-c reductase / response to copper ion / ubiquinone-6 biosynthetic process / response to glucagon / respiratory chain complex I / cellular respiration / ubiquinol-cytochrome-c reductase activity / mitochondrial electron transport, cytochrome c to oxygen / cytochrome-c oxidase activity / iron-sulfur cluster assembly / azurophil granule membrane / NADH dehydrogenase activity / midbrain development / mitochondrial ribosome / hypothalamus development / mitochondrial electron transport, ubiquinol to cytochrome c / sodium ion transport / mitochondrial translation / Mitochondrial protein degradation / NADH:ubiquinone reductase (H+-translocating) / positive regulation of execution phase of apoptosis / apoptotic mitochondrial changes / RHOG GTPase cycle / endopeptidase activator activity / acyl binding / ubiquinone binding / Complex I biogenesis / acyl carrier activity / response to hyperoxia / cellular response to interferon-beta / generation of precursor metabolites and energy / quinone binding / animal organ regeneration / electron transport coupled proton transport / neurogenesis / Respiratory electron transport / : / enzyme regulator activity / ATP synthesis coupled electron transport / response to cadmium ion / negative regulation of intrinsic apoptotic signaling pathway / ATP metabolic process / cellular response to retinoic acid / extrinsic apoptotic signaling pathway / mitochondrial ATP synthesis coupled electron transport / mitochondrial respiratory chain complex I assembly / response to cAMP / : / substantia nigra development / ionotropic glutamate receptor binding / respiratory electron transport chain / reactive oxygen species metabolic process / cerebellum development / regulation of mitochondrial membrane potential / : / mitochondrial electron transport, NADH to ubiquinone / response to activity / synaptic membrane / proton motive force-driven mitochondrial ATP synthesis / Mitochondrial protein degradation / central nervous system development / fatty acid binding / NADH dehydrogenase (ubiquinone) activity Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.9 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_6775.map.gz | 30.3 MB | EMDB map data format | |
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Header (meta data) | emd-6775-v30.xml emd-6775.xml | 17.5 KB 17.5 KB | Display Display | EMDB header |
Images | emd_6775.png | 25.5 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-6775 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-6775 | HTTPS FTP |
-Validation report
Summary document | emd_6775_validation.pdf.gz | 325 KB | Display | EMDB validaton report |
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Full document | emd_6775_full_validation.pdf.gz | 324.6 KB | Display | |
Data in XML | emd_6775_validation.xml.gz | 7.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-6775 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-6775 | HTTPS FTP |
-Related structure data
Related structure data | 5xthMC 6771C 6772C 6773C 6774C 6776C 5xtbC 5xtcC 5xtdC 5xteC 5xtiC 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_6775.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 supercomplex I1III2IV1
Entire | Name: Human respiratory supercomplex I1III2IV1 |
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Components |
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-Supramolecule #1: Human respiratory supercomplex I1III2IV1
Supramolecule | Name: Human respiratory supercomplex I1III2IV1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#68 |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Experimental: 1.7 MDa |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.2 mg/mL |
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Buffer | pH: 7.4 |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON II (4k x 4k) / Average electron dose: 1.25 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: OTHER / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
CTF correction | Software - Name: CTFFIND (ver. 3.0) |
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Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 1.4) / Number images used: 167761 |
Initial angle assignment | Type: RANDOM ASSIGNMENT / Software - Name: RELION (ver. 1.4) |
Final angle assignment | Type: RANDOM ASSIGNMENT / Software - Name: RELION (ver. 1.4) |