[English] 日本語
Yorodumi- PDB-6q9e: Complex III2 focused refinement from Ovine respiratory supercompl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6q9e | ||||||
---|---|---|---|---|---|---|---|
Title | Complex III2 focused refinement from Ovine respiratory supercomplex I+III2 | ||||||
Components |
| ||||||
Keywords | ELECTRON TRANSPORT / complex III / cellular respiration / mitochondria | ||||||
Function / homology | Function and homology information : / : / quinol-cytochrome-c reductase / ubiquinol-cytochrome-c reductase activity / mitochondrial electron transport, ubiquinol to cytochrome c / : / metalloendopeptidase activity / 2 iron, 2 sulfur cluster binding / mitochondrial inner membrane / membrane => GO:0016020 ...: / : / quinol-cytochrome-c reductase / ubiquinol-cytochrome-c reductase activity / mitochondrial electron transport, ubiquinol to cytochrome c / : / metalloendopeptidase activity / 2 iron, 2 sulfur cluster binding / mitochondrial inner membrane / membrane => GO:0016020 / electron transfer activity / ubiquitin protein ligase binding / heme binding / proteolysis / nucleoplasm / metal ion binding Similarity search - Function | ||||||
Biological species | Ovis aries (sheep) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.9 Å | ||||||
Authors | Letts, J.A. / Sazanov, L.A. | ||||||
Funding support | Austria, 1items
| ||||||
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 |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6q9e.cif.gz | 730.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6q9e.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 6q9e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6q9e_validation.pdf.gz | 2.4 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 6q9e_full_validation.pdf.gz | 2.4 MB | Display | |
Data in XML | 6q9e_validation.xml.gz | 115.4 KB | Display | |
Data in CIF | 6q9e_validation.cif.gz | 175.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q9/6q9e ftp://data.pdbj.org/pub/pdb/validation_reports/q9/6q9e | HTTPS FTP |
-Related structure data
Related structure data | 4481MC 4479C 4480C 4482C 4493C 4494C 4495C 4496C 4497C 4498C 4499C 4500C 4501C 4502C 4505C 4506C 4507C 6q9bC 6q9dC 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 |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
|
---|---|
1 |
|
-Components
-Ubiquinol-cytochrome c ... , 4 types, 8 molecules a1a3a2a4q1q2i1i2
#1: Protein | Mass: 49385.414 Da / Num. of mol.: 2 / 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: W5Q5G6 #2: Protein | Mass: 46655.531 Da / Num. of mol.: 2 / 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: W5Q0F9 #7: Protein | Mass: 9606.067 Da / Num. of mol.: 2 / 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: W5PUP9 #10: Protein | Mass: 7310.372 Da / Num. of mol.: 2 / 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: W5P6B2 |
---|
-Protein , 2 types, 4 molecules b1b2c1c2
#3: Protein | Mass: 42877.840 Da / Num. of mol.: 2 / 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: P24959 #4: Protein | Mass: 27322.316 Da / Num. of mol.: 2 / 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: W5Q0A9 |
---|
-Cytochrome b-c1 complex subunit ... , 4 types, 8 molecules f1f2d1d2h1h2x1x2
#5: Protein | Mass: 21654.607 Da / Num. of mol.: 2 / 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: W5P2X9, quinol-cytochrome-c reductase #6: Protein | Mass: 13432.314 Da / Num. of mol.: 2 / 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: W5P642 #8: Protein | Mass: 9223.133 Da / Num. of mol.: 2 / 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: W5PZC9, UniProt: B9VH04*PLUS #9: Protein/peptide | Mass: 2826.475 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: Modeled as poly-alanine due to poor density. / 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, 20 molecules
#11: Chemical | ChemComp-HEM / #12: Chemical | ChemComp-3PE / #13: Chemical | ChemComp-CDL / #14: Chemical | #15: Chemical | #16: Chemical | |
---|
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Ovine mitochondrial SC I+III2 / Type: COMPLEX Details: Complex III2 focused refinement from ovine respiratory SC I+III2 Entity ID: #1-#10 / Source: NATURAL | ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 |
| ||||||||||||||||||||
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 |
---|---|
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 |
| ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 400000 | ||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 102314 / 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: 1PPJ |