+Open data
-Basic information
Entry | Database: PDB / ID: 5gpn | |||||||||
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Title | Architecture of mammalian respirasome | |||||||||
Components |
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Keywords | ELECTRON TRANSPORT / OXIDOREDUCTASE / Respiratory / Respirasome / Mammalian | |||||||||
Function / homology | Function and homology information TP53 Regulates Metabolic Genes / Cytoprotection by HMOX1 / mitochondrial respirasome assembly / respiratory chain complex IV / Complex I biogenesis / cellular response to oxygen levels / Respiratory electron transport / : / regulation of oxidative phosphorylation / Respiratory electron transport ...TP53 Regulates Metabolic Genes / Cytoprotection by HMOX1 / mitochondrial respirasome assembly / respiratory chain complex IV / Complex I biogenesis / cellular response to oxygen levels / Respiratory electron transport / : / regulation of oxidative phosphorylation / Respiratory electron transport / gliogenesis / anterograde axonal transport / Mitochondrial protein degradation / : / neural precursor cell proliferation / cytochrome-c oxidase / : / oxidative phosphorylation / oxygen sensor activity / quinol-cytochrome-c reductase / ubiquinone-6 biosynthetic process / ubiquinol-cytochrome-c reductase activity / mitochondrial electron transport, cytochrome c to oxygen / cytochrome-c oxidase activity / NADH dehydrogenase activity / mitochondrial electron transport, ubiquinol to cytochrome c / Mitochondrial protein degradation / NADH:ubiquinone reductase (H+-translocating) / acyl binding / ubiquinone binding / acyl carrier activity / quinone binding / electron transport coupled proton transport / : / enzyme regulator activity / ATP synthesis coupled electron transport / mitochondrial respiratory chain complex I assembly / axon cytoplasm / respiratory electron transport chain / reactive oxygen species metabolic process / : / mitochondrial electron transport, NADH to ubiquinone / central nervous system development / NADH dehydrogenase (ubiquinone) activity / electron transport chain / mitochondrial membrane / aerobic respiration / mitochondrial intermembrane space / metalloendopeptidase activity / 2 iron, 2 sulfur cluster binding / NAD binding / FMN binding / 4 iron, 4 sulfur cluster binding / response to oxidative stress / oxidoreductase activity / mitochondrial inner membrane / mitochondrial matrix / copper ion binding / ubiquitin protein ligase binding / heme binding / protein-containing complex binding / mitochondrion / proteolysis / nucleoplasm / membrane / metal ion binding / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Bos taurus (cattle) Sus scrofa (pig) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 5.4 Å | |||||||||
Authors | Gu, J. / Wu, M. / Guo, R. / Yang, M. | |||||||||
Funding support | China, 2items
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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 | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 5gpn.cif.gz | 2 MB | Display | PDBx/mmCIF format |
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PDB format | pdb5gpn.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 5gpn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5gpn_validation.pdf.gz | 2.2 MB | Display | wwPDB validaton report |
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Full document | 5gpn_full_validation.pdf.gz | 2.3 MB | Display | |
Data in XML | 5gpn_validation.xml.gz | 275.8 KB | Display | |
Data in CIF | 5gpn_validation.cif.gz | 459.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gp/5gpn ftp://data.pdbj.org/pub/pdb/validation_reports/gp/5gpn | HTTPS FTP |
-Related structure data
Related structure data | 9534MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
+Cytochrome b-c1 complex subunit ... , 9 types, 18 molecules AMBNEQFRGSHTIUJLKV
+Protein , 5 types, 8 molecules CODPYtAaw
+NADH dehydrogenase [ubiquinone] iron-sulfur protein ... , 6 types, 6 molecules WZabox
+NADH dehydrogenase [ubiquinone] flavoprotein ... , 2 types, 2 molecules cd
+NADH-ubiquinone oxidoreductase chain ... , 7 types, 8 molecules efghijkl
+NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit ... , 10 types, 11 molecules mnpqvrAcAeAfAgAn
+NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit ... , 3 types, 4 molecules uAiAjAk
+Cytochrome c oxidase subunit ... , 13 types, 13 molecules 0123456789syz
+NADH dehydrogenase [ubiquinone] 1 unknown subunit ... , 6 types, 12 molecules AbAhAdAoApAvAqAsAwArAtAu
+NADH dehydrogenase [ubiquinone] 1 subunit ... , 2 types, 2 molecules AlAm
+Non-polymers , 10 types, 25 molecules
+Details
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Respirasome / Type: COMPLEX / Details: Mammalian, respirasome / Entity ID: all / Source: NATURAL |
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Molecular weight | Value: 1.7 MDa / Experimental value: YES |
Source (natural) | Organism: Sus scrofa (pig) |
Buffer solution | pH: 7.2 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R1.2/1.3 |
Vitrification | Cryogen name: NITROGEN |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: TUNGSTEN HAIRPIN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 1.7 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON II (4k x 4k) |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 5.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 139996 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Space: REAL |