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Yorodumi- EMDB-6774: Cryo-EM structure of human respiratory complex III (cytochrome bc... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-6774 | |||||||||
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Title | Cryo-EM structure of human respiratory complex III (cytochrome bc1 complex) | |||||||||
Map data | This map was obtained by sub-region refinement. | |||||||||
Sample |
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Function / homology | Function and homology information subthalamus development / pons development / cerebellar Purkinje cell layer development / pyramidal neuron development / response to mercury ion / mitochondrial respiratory chain complex III assembly / thalamus development / response to cobalamin / Mitochondrial protein import / : ...subthalamus development / pons development / cerebellar Purkinje cell layer development / pyramidal neuron development / response to mercury ion / mitochondrial respiratory chain complex III assembly / thalamus development / response to cobalamin / Mitochondrial protein import / : / : / response to alkaloid / : / oxidative phosphorylation / quinol-cytochrome-c reductase / response to copper ion / response to glucagon / cellular respiration / ubiquinol-cytochrome-c reductase activity / midbrain development / hypothalamus development / mitochondrial electron transport, ubiquinol to cytochrome c / response to hyperoxia / generation of precursor metabolites and energy / animal organ regeneration / electron transport coupled proton transport / Respiratory electron transport / response to cadmium ion / respiratory electron transport chain / response to activity / Mitochondrial protein degradation / hippocampus development / response to calcium ion / aerobic respiration / response to toxic substance / metalloendopeptidase activity / 2 iron, 2 sulfur cluster binding / response to ethanol / oxidoreductase activity / response to hypoxia / electron transfer activity / mitochondrial inner membrane / response to xenobiotic stimulus / ubiquitin protein ligase binding / heme binding / protein-containing complex binding / mitochondrion / proteolysis / nucleoplasm / membrane / nucleus / metal ion binding Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.4 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_6774.map.gz | 22.1 MB | EMDB map data format | |
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Header (meta data) | emd-6774-v30.xml emd-6774.xml | 10 KB 10 KB | Display Display | EMDB header |
Images | emd_6774.png | 18.2 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-6774 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-6774 | HTTPS FTP |
-Validation report
Summary document | emd_6774_validation.pdf.gz | 312.8 KB | Display | EMDB validaton report |
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Full document | emd_6774_full_validation.pdf.gz | 312.3 KB | Display | |
Data in XML | emd_6774_validation.xml.gz | 7.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-6774 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-6774 | HTTPS FTP |
-Related structure data
Related structure data | 5xteMC 6771C 6772C 6773C 6775C 6776C 5xtbC 5xtcC 5xtdC 5xthC 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_6774.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | This map was obtained by sub-region refinement. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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 complex III
Entire | Name: Human respiratory complex III |
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Components |
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-Supramolecule #1: Human respiratory complex III
Supramolecule | Name: Human respiratory complex III / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#11 / Details: Human cytochrome bc1 complex |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Experimental: 500 KDa |
-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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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: 3.4 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) |