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Yorodumi- PDB-6q9d: CI Peripheral Arm focused refinement from Ovine respiratory SC I+III2 -
+Open data
-Basic information
Entry | Database: PDB / ID: 6q9d | ||||||
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Title | CI Peripheral Arm focused refinement from Ovine respiratory SC I+III2 | ||||||
Components |
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Keywords | ELECTRON TRANSPORT / complex I / peripheral arm / cellular respiration / mitochondria | ||||||
Function / homology | Function and homology information NADH:ubiquinone reductase (H+-translocating) / NADH dehydrogenase activity / apoptotic mitochondrial changes / : / mitochondrial electron transport, NADH to ubiquinone / mitochondrial respiratory chain complex I assembly / acyl binding / acyl carrier activity / NADH dehydrogenase (ubiquinone) activity / : ...NADH:ubiquinone reductase (H+-translocating) / NADH dehydrogenase activity / apoptotic mitochondrial changes / : / mitochondrial electron transport, NADH to ubiquinone / mitochondrial respiratory chain complex I assembly / acyl binding / acyl carrier activity / NADH dehydrogenase (ubiquinone) activity / : / ATP metabolic process / respiratory electron transport chain / reactive oxygen species metabolic process / regulation of mitochondrial membrane potential / electron transport chain / mitochondrial intermembrane space / 2 iron, 2 sulfur cluster binding / circadian rhythm / NAD binding / FMN binding / 4 iron, 4 sulfur cluster binding / response to oxidative stress / mitochondrial inner membrane / mitochondrial matrix / protein-containing complex binding / metal ion binding Similarity search - Function | ||||||
Biological species | Ovis aries (sheep) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.8 Å | ||||||
Authors | Letts, J.A. / Sazanov, L.A. | ||||||
Funding support | Austria, 1items
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Citation | Journal: Mol Cell / Year: 2019 Title: Structures of Respiratory Supercomplex I+III Reveal Functional and Conformational Crosstalk. Authors: James A Letts / Karol Fiedorczuk / Gianluca Degliesposti / Mark Skehel / Leonid A Sazanov / Abstract: The mitochondrial electron transport chain complexes are organized into supercomplexes (SCs) of defined stoichiometry, which have been proposed to regulate electron flux via substrate channeling. We ...The mitochondrial electron transport chain complexes are organized into supercomplexes (SCs) of defined stoichiometry, which have been proposed to regulate electron flux via substrate channeling. We demonstrate that CoQ trapping in the isolated SC I+III limits complex (C)I turnover, arguing against channeling. The SC structure, resolved at up to 3.8 Å in four distinct states, suggests that CoQ oxidation may be rate limiting because of unequal access of CoQ to the active sites of CIII. CI shows a transition between "closed" and "open" conformations, accompanied by the striking rotation of a key transmembrane helix. Furthermore, the state of CI affects the conformational flexibility within CIII, demonstrating crosstalk between the enzymes. CoQ was identified at only three of the four binding sites in CIII, suggesting that interaction with CI disrupts CIII symmetry in a functionally relevant manner. Together, these observations indicate a more nuanced functional role for the SCs. | ||||||
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 | 6q9d.cif.gz | 646.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6q9d.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 6q9d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6q9d_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 6q9d_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 6q9d_validation.xml.gz | 106.6 KB | Display | |
Data in CIF | 6q9d_validation.cif.gz | 162.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q9/6q9d ftp://data.pdbj.org/pub/pdb/validation_reports/q9/6q9d | HTTPS FTP |
-Related structure data
Related structure data | 4480MC 4479C 4481C 4482C 4493C 4494C 4495C 4496C 4497C 4498C 4499C 4500C 4501C 4502C 4505C 4506C 4507C 6q9bC 6q9eC 6qa9C 6qbxC 6qc2C 6qc3C 6qc4C 6qc5C 6qc6C 6qc7C 6qc8C 6qc9C 6qcaC 6qcfC C: citing same article (ref.) M: map data used to model this data |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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-Components
-NADH dehydrogenase [ubiquinone] flavoprotein ... , 2 types, 2 molecules V1V2
#1: Protein | Mass: 48678.281 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: Heart Plasmid details: Ovis aries (sheep) hearts were purchased from C Humphreys & Sons (Chelmsford, UK). Tissue: Cardiac References: UniProt: W5PUX0, NADH dehydrogenase, NADH:ubiquinone reductase (H+-translocating) |
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#2: Protein | Mass: 23840.428 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: Heart Plasmid details: Ovis aries (sheep) hearts were purchased from C Humphreys & Sons (Chelmsford, UK). Tissue: Cardiac / References: UniProt: W5NRY1 |
-NADH:ubiquinone oxidoreductase core subunit ... , 5 types, 5 molecules S1S2S3S7S8
#3: Protein | Mass: 77031.156 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: Heart Plasmid details: Ovis aries (sheep) hearts were purchased from C Humphreys & Sons (Chelmsford, UK). Tissue: Cardiac / References: UniProt: W5QB34 |
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#4: Protein | Mass: 49193.273 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: Heart Plasmid details: Ovis aries (sheep) hearts were purchased from C Humphreys & Sons (Chelmsford, UK). Tissue: Cardiac |
#5: Protein | Mass: 26441.793 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: Heart Plasmid details: Ovis aries (sheep) hearts were purchased from C Humphreys & Sons (Chelmsford, UK). Tissue: Cardiac / References: UniProt: W5PB27 |
#6: Protein | Mass: 20104.531 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: Heart Plasmid details: Ovis aries (sheep) hearts were purchased from C Humphreys & Sons (Chelmsford, UK). Tissue: Cardiac |
#7: Protein | Mass: 20219.947 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: Heart Plasmid details: Ovis aries (sheep) hearts were purchased from C Humphreys & Sons (Chelmsford, UK). Tissue: Cardiac |
-NADH:ubiquinone oxidoreductase subunit ... , 4 types, 4 molecules V3S4A9A6
#8: Protein | Mass: 8423.314 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: Heart Plasmid details: Ovis aries (sheep) hearts were purchased from C Humphreys & Sons (Chelmsford, UK). Tissue: Cardiac |
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#10: Protein | Mass: 15375.300 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: Heart Plasmid details: Ovis aries (sheep) hearts were purchased from C Humphreys & Sons (Chelmsford, UK). Tissue: Cardiac / References: UniProt: W5PE07 |
#11: Protein | Mass: 38660.488 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: Heart Plasmid details: Ovis aries (sheep) hearts were purchased from C Humphreys & Sons (Chelmsford, UK). Tissue: Cardiac / References: UniProt: W5PI58 |
#14: Protein | Mass: 14923.245 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: Heart Plasmid details: Ovis aries (sheep) hearts were purchased from C Humphreys & Sons (Chelmsford, UK). Tissue: Cardiac / References: UniProt: W5QC06 |
-Protein , 2 types, 2 molecules S6AA
#9: Protein | Mass: 10651.796 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: Heart Plasmid details: Ovis aries (sheep) hearts were purchased from C Humphreys & Sons (Chelmsford, UK). Tissue: Cardiac |
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#17: Protein | Mass: 10119.541 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: Heart Plasmid details: Ovis aries (sheep) hearts were purchased from C Humphreys & Sons (Chelmsford, UK). Tissue: Cardiac / References: UniProt: W5NQT7 |
-NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit ... , 5 types, 5 molecules A2A5A7ALAM
#12: Protein | Mass: 10966.627 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: Heart Plasmid details: Ovis aries (sheep) hearts were purchased from C Humphreys & Sons (Chelmsford, UK). Tissue: Cardiac / References: UniProt: W5QAH8 |
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#13: Protein | Mass: 13156.311 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: Heart Plasmid details: Ovis aries (sheep) hearts were purchased from C Humphreys & Sons (Chelmsford, UK). Tissue: Cardiac / References: UniProt: W5PNX7 |
#15: Protein | Mass: 12399.201 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: Heart Plasmid details: Ovis aries (sheep) hearts were purchased from C Humphreys & Sons (Chelmsford, UK). Tissue: Cardiac / References: UniProt: W5P0I2 |
#16: Protein | Mass: 17115.508 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: Heart Plasmid details: Ovis aries (sheep) hearts were purchased from C Humphreys & Sons (Chelmsford, UK). Tissue: Cardiac / References: UniProt: B9VGZ9 |
#18: Protein | Mass: 16635.264 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: This is a focused refinement so only the N-terminal part of this subunit is present in the map. Source: (natural) Ovis aries (sheep) / Organ: Heart Plasmid details: Ovis aries (sheep) hearts were purchased from C Humphreys & Sons (Chelmsford, UK). Tissue: Cardiac |
-Non-polymers , 6 types, 12 molecules
#19: Chemical | ChemComp-SF4 / #20: Chemical | ChemComp-FMN / | #21: Chemical | #22: Chemical | ChemComp-ZN / | #23: Chemical | ChemComp-NDP / | #24: Chemical | ChemComp-ZMP / | |
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-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: Ovine mitochondrial SC I+III2 / Type: COMPLEX Details: Complex I membrane arm focused refinement from ovine respiratory SC I+III2 Entity ID: #1-#18 / Source: NATURAL | ||||||||||||||||||||
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Molecular weight | Value: 1.4 MDa / Experimental value: NO | ||||||||||||||||||||
Source (natural) | Organism: Ovis aries (sheep) / Cellular location: Mitochondrial inner membrane / Organ: Heart / Organelle: Mitochondria / Tissue: Cardiac | ||||||||||||||||||||
Buffer solution | pH: 7.4 / Details: 250 mM NaCl, 20 mM HEPES, pH 7.7, 0.02% Brij-35 | ||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: PROPANE / Humidity: 95 % / Chamber temperature: 277 K Details: blotting for 30 seconds at 4 degrees Celsius, 95% humidity and flash freezing |
-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 |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 2 sec. / Electron dose: 51 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 1854 |
Image scans | Movie frames/image: 34 |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 400000 | ||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 178121 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||
Atomic model building | B value: 90 / Protocol: OTHER / Space: REAL | ||||||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 1LNK |