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Yorodumi- EMDB-6772: Cryo-EM structure of human respiratory complex I transmembrane arm -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-6772 | |||||||||
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Title | Cryo-EM structure of human respiratory complex I transmembrane arm | |||||||||
Map data | This map was obtained by sub-region refinement. | |||||||||
Sample |
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Function / homology | Function and homology information protein insertion into mitochondrial inner membrane / protein lipoylation / Mitochondrial Fatty Acid Beta-Oxidation / Protein lipoylation / cellular response to oxygen levels / iron-sulfur cluster assembly complex / response to light intensity / Mitochondrial protein import / mitochondrial large ribosomal subunit binding / gliogenesis ...protein insertion into mitochondrial inner membrane / protein lipoylation / Mitochondrial Fatty Acid Beta-Oxidation / Protein lipoylation / cellular response to oxygen levels / iron-sulfur cluster assembly complex / response to light intensity / Mitochondrial protein import / mitochondrial large ribosomal subunit binding / gliogenesis / neural precursor cell proliferation / : / [2Fe-2S] cluster assembly / oxygen sensor activity / cellular response to glucocorticoid stimulus / respiratory chain complex I / iron-sulfur cluster assembly / azurophil granule membrane / NADH dehydrogenase activity / NADH:ubiquinone reductase (H+-translocating) / positive regulation of execution phase of apoptosis / endopeptidase activator activity / acyl binding / ubiquinone binding / Complex I biogenesis / acyl carrier activity / cellular response to interferon-beta / quinone binding / electron transport coupled proton transport / neurogenesis / Respiratory electron transport / : / ATP synthesis coupled electron transport / negative regulation of intrinsic apoptotic signaling pathway / cellular response to retinoic acid / extrinsic apoptotic signaling pathway / mitochondrial ATP synthesis coupled electron transport / mitochondrial respiratory chain complex I assembly / : / ionotropic glutamate receptor binding / reactive oxygen species metabolic process / cerebellum development / : / mitochondrial electron transport, NADH to ubiquinone / response to cocaine / proton motive force-driven mitochondrial ATP synthesis / Mitochondrial protein degradation / fatty acid binding / NADH dehydrogenase (ubiquinone) activity / apoptotic signaling pathway / sensory perception of sound / response to nicotine / response to hydrogen peroxide / mitochondrial membrane / aerobic respiration / mitochondrial intermembrane space / negative regulation of cell growth / fatty acid biosynthetic process / positive regulation of protein catabolic process / NAD binding / 4 iron, 4 sulfur cluster binding / response to ethanol / in utero embryonic development / response to oxidative stress / response to hypoxia / electron transfer activity / mitochondrial inner membrane / nuclear speck / mitochondrial matrix / negative regulation of DNA-templated transcription / ubiquitin protein ligase binding / calcium ion binding / Neutrophil degranulation / protein-containing complex binding / protein kinase binding / endoplasmic reticulum / mitochondrion / nucleoplasm / ATP binding / metal ion binding / plasma membrane / cytoplasm Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.7 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_6772.map.gz | 22.8 MB | EMDB map data format | |
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Header (meta data) | emd-6772-v30.xml emd-6772.xml | 12.4 KB 12.4 KB | Display Display | EMDB header |
Images | emd_6772.png | 20.8 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-6772 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-6772 | HTTPS FTP |
-Validation report
Summary document | emd_6772_validation.pdf.gz | 310.3 KB | Display | EMDB validaton report |
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Full document | emd_6772_full_validation.pdf.gz | 309.9 KB | Display | |
Data in XML | emd_6772_validation.xml.gz | 7.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-6772 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-6772 | HTTPS FTP |
-Related structure data
Related structure data | 5xtcMC 6771C 6773C 6774C 6775C 6776C 5xtbC 5xtdC 5xteC 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_6772.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 I transmembrane arm
Entire | Name: Human respiratory complex I transmembrane arm |
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Components |
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-Supramolecule #1: Human respiratory complex I transmembrane arm
Supramolecule | Name: Human respiratory complex I transmembrane arm / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#29 |
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Source (natural) | Organism: Homo sapiens (human) |
-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 / Chamber humidity: 100 % |
-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: 3.7 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) |