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Yorodumi- PDB-5gup: Cryo-EM structure of mammalian respiratory supercomplex I1III2IV1 -
+Open data
-Basic information
Entry | Database: PDB / ID: 5gup | ||||||||||||
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Title | Cryo-EM structure of mammalian respiratory supercomplex I1III2IV1 | ||||||||||||
Components |
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Keywords | ELECTRON TRANSPORT / Cryo-EM / Mammalian / Respiratory / Supercomplex | ||||||||||||
Function / homology | Function and homology information Cytoprotection by HMOX1 / TP53 Regulates Metabolic Genes / subthalamus development / pons development / cerebellar Purkinje cell layer development / pyramidal neuron development / Mitochondrial protein import / mitochondrial respiratory chain complex III assembly / thalamus development / Complex I biogenesis ...Cytoprotection by HMOX1 / TP53 Regulates Metabolic Genes / subthalamus development / pons development / cerebellar Purkinje cell layer development / pyramidal neuron development / Mitochondrial protein import / mitochondrial respiratory chain complex III assembly / thalamus development / Complex I biogenesis / cellular response to oxygen levels / Respiratory electron transport / : / gliogenesis / anterograde axonal transport / Mitochondrial protein degradation / : / neural precursor cell proliferation / oxygen sensor activity / ubiquinone-6 biosynthetic process / ubiquinol-cytochrome-c reductase activity / mitochondrial electron transport, cytochrome c to oxygen / NADH dehydrogenase activity / midbrain development / hypothalamus development / mitochondrial electron transport, ubiquinol to cytochrome c / NADH:ubiquinone reductase (H+-translocating) / acyl binding / ubiquinone binding / acyl carrier activity / quinone binding / electron transport coupled proton transport / : / 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 / NADH dehydrogenase (ubiquinone) activity / hippocampus development / electron transport chain / aerobic respiration / mitochondrial intermembrane space / 2 iron, 2 sulfur cluster binding / NAD binding / FMN binding / 4 iron, 4 sulfur cluster binding / response to oxidative stress / membrane => GO:0016020 / oxidoreductase activity / mitochondrial inner membrane / nuclear speck / mitochondrial matrix / ubiquitin protein ligase binding / protein-containing complex binding / endoplasmic reticulum / mitochondrion / nucleoplasm / membrane / metal ion binding / cytoplasm / cytosol Similarity search - Function | ||||||||||||
Biological species | Sus scrofa (pig) | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4 Å | ||||||||||||
Authors | Gu, J. / Wu, M. / Guo, R. / Yang, M. | ||||||||||||
Funding support | China, 3items
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Citation | Journal: Cell / Year: 2016 Title: Structure of Mammalian Respiratory Supercomplex IIIIIV. Authors: Meng Wu / Jinke Gu / Runyu Guo / Yushen Huang / Maojun Yang / Abstract: The mammalian respiratory chain complexes assemble into supercomplexes (SCs) and reside in the inner mitochondrial membrane to transfer electrons and establish the proton gradient for complex V to ...The mammalian respiratory chain complexes assemble into supercomplexes (SCs) and reside in the inner mitochondrial membrane to transfer electrons and establish the proton gradient for complex V to synthesize ATP. The precise arrangement of SCs is largely unknown. Here, we report a 4.0-Å cryo-electron microscopy (cryo-EM) structure of the major SC in porcine heart, the 1.7-MDa SCIIIIIV. The complex III (CIII) dimer and complex IV (CIV) bind at the same side of the L-shaped complex I (CI). Several accessory or supernumerary subunits of CI, such as NDUFA11, NDUFB4, NDUFB8, and NDUFB9, directly contribute to the oligomerization of CI, CIII, and CIV. COX7C and COX7A of CIV attach CIV to the concave surface formed by CIII and the distal end of membrane arm of CI. The structure suggests a possible mechanism by which electrons are transferred from NADH to cytochrome c and provides a platform for future functional dissection of respiration. | ||||||||||||
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 | 5gup.cif.gz | 2.5 MB | Display | PDBx/mmCIF format |
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PDB format | pdb5gup.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 5gup.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5gup_validation.pdf.gz | 2.9 MB | Display | wwPDB validaton report |
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Full document | 5gup_full_validation.pdf.gz | 3 MB | Display | |
Data in XML | 5gup_validation.xml.gz | 335.6 KB | Display | |
Data in CIF | 5gup_validation.cif.gz | 516.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gu/5gup ftp://data.pdbj.org/pub/pdb/validation_reports/gu/5gup | HTTPS FTP |
-Related structure data
Related structure data | 9539MC 6718C 6719C 6720C 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 c oxidase subunit ... , 13 types, 13 molecules AAgAhAiAjAkAlAmAnAoApAqAr
+NADH dehydrogenase [ubiquinone] flavoprotein ... , 2 types, 2 molecules BE
+NADH dehydrogenase [ubiquinone] iron-sulfur protein ... , 7 types, 7 molecules CDFHIJh
+Protein , 4 types, 7 molecules GOXw7x8
+NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit ... , 12 types, 13 molecules KRLMNPQSTUVWs
+NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit ... , 11 types, 11 molecules YZabcdenopt
+NADH dehydrogenase [ubiquinone] 1 subunit ... , 2 types, 2 molecules fg
+NADH-ubiquinone oxidoreductase chain ... , 7 types, 7 molecules ijklmqr
+Cytochrome b-c1 complex subunit ... , 9 types, 18 molecules u5v6y9zAa0Ab1Ac243AdAeAf
+Non-polymers , 14 types, 52 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: Respiratory supercomplex I1III2IV1 / Type: COMPLEX / Details: Supercomplex generated by complex I, III and IV. / Entity ID: #1-#67 / Source: NATURAL |
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Molecular weight | Value: 1.7 MDa / Experimental value: YES |
Source (natural) | Organism: Sus scrofa (pig) |
Buffer solution | pH: 7.4 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE / Humidity: 100 % |
-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: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 1.25 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k) |
-Processing
EM software |
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CTF correction | Type: NONE | ||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 161912 / Symmetry type: POINT |