[English] 日本語
Yorodumi- PDB-6q9b: CI Membrane Arm focused refinement from Ovine respiratory SC I+III2 -
+Open data
-Basic information
Entry | Database: PDB / ID: 6q9b | ||||||
---|---|---|---|---|---|---|---|
Title | CI Membrane Arm focused refinement from Ovine respiratory SC I+III2 | ||||||
Components |
| ||||||
Keywords | ELECTRON TRANSPORT / complex I / membrane arm / cellular respiration / mitochondria | ||||||
Function / homology | Function and homology information oxidoreductase activity, acting on NAD(P)H / 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 ...oxidoreductase activity, acting on NAD(P)H / 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 / reactive oxygen species metabolic process / : / mitochondrial electron transport, NADH to ubiquinone / NADH dehydrogenase (ubiquinone) activity / electron transport chain / mitochondrial intermembrane space / NAD binding / 4 iron, 4 sulfur cluster binding / membrane => GO:0016020 / mitochondrial inner membrane / mitochondrial matrix 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 | 6q9b.cif.gz | 877.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6q9b.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 6q9b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6q9b_validation.pdf.gz | 1.9 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 6q9b_full_validation.pdf.gz | 2 MB | Display | |
Data in XML | 6q9b_validation.xml.gz | 142.5 KB | Display | |
Data in CIF | 6q9b_validation.cif.gz | 211.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q9/6q9b ftp://data.pdbj.org/pub/pdb/validation_reports/q9/6q9b | HTTPS FTP |
-Related structure data
Related structure data | 4479MC 4480C 4481C 4482C 4493C 4494C 4495C 4496C 4497C 4498C 4499C 4500C 4501C 4502C 4505C 4506C 4507C 6q9dC 6q9eC 6qa9C 6qbxC 6qc2C 6qc3C 6qc4C 6qc5C 6qc6C 6qc7C 6qc8C 6qc9C 6qcaC 6qcfC M: map data used to model this data C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
|
---|---|
1 |
|
-Components
-Protein , 2 types, 2 molecules S2AB
#1: Protein | Mass: 49193.273 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: Since this is a focused refinement only the N-terminal part of this subunit is present in the density.,Since this is a focused refinement only the N-terminal part of this subunit is present in the density. 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: W5PJ73 |
---|---|
#11: Protein | Mass: 10119.541 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: The first residue is disordered and therefore not modeled. 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-ubiquinone oxidoreductase chain ... , 7 types, 7 molecules D3D1D64LD5D4D2
#2: Protein | Mass: 13106.520 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: There is a disordered region in the protein that is not modeled. Source: (natural) Ovis aries (sheep) References: UniProt: O78753, NADH:ubiquinone reductase (H+-translocating) |
---|---|
#3: Protein | Mass: 35884.902 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: There is a disordered region in the protein that is not modeled. Source: (natural) Ovis aries (sheep) References: UniProt: O78747, NADH:ubiquinone reductase (H+-translocating) |
#4: Protein | Mass: 19126.619 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: There is a disordered region in the protein that was not modeled. 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: O78757, NADH:ubiquinone reductase (H+-translocating) |
#5: Protein | Mass: 10840.228 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: O78754, NADH:ubiquinone reductase (H+-translocating) |
#6: Protein | Mass: 68410.898 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: O78756, NADH:ubiquinone reductase (H+-translocating) |
#7: Protein | Mass: 52058.734 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: O78755, NADH:ubiquinone reductase (H+-translocating) |
#8: Protein | Mass: 39149.805 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: O78748, NADH:ubiquinone reductase (H+-translocating) |
-NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit ... , 5 types, 5 molecules AKA8AJAMA1
#9: Protein | Mass: 14610.776 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: W5PAR2 |
---|---|
#12: Protein | Mass: 20008.014 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: W5PYA5 |
#14: Protein | Mass: 36803.762 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: W5QBF5 |
#20: Protein | Mass: 16635.264 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: Because this is a focused refinement only the C-terminal part of this subunit is present in the density. Source: (natural) Ovis aries (sheep) / Organ: Heart Plasmid details: Ovis aries (sheep) hearts were purchased from C Humphreys & Sons (Chelmsford, UK). Tissue: Cardiac |
#29: Protein | Mass: 8211.519 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 ... , 9 types, 9 molecules B5BJS5A3B3B4B7B9B2
#10: Protein | Mass: 16714.369 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: First few residues are disordered and therefore not modeled. 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: W5QHN8 |
---|---|
#13: Protein | Mass: 20880.752 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: Some residues are disordered and therefore not modeled. Source: (natural) Ovis aries (sheep) / Organ: Heart Plasmid details: Ovis aries (sheep) hearts were purchased from C Humphreys & Sons (Chelmsford, UK). Tissue: Cardiac |
#15: Protein | Mass: 12474.397 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: W5QFF9 |
#16: Protein | Mass: 9194.655 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: The N-terminus is disordered and therefore not modeled. 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: W5NYM7 |
#17: Protein | Mass: 11015.482 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: The termini are disordered and therefore not modeled. 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: W5Q5T4 |
#19: Protein | Mass: 14975.999 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: W5QF73 |
#22: Protein | Mass: 16282.610 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: The C-terminus of this subunit was disordered and therefore not modeled 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: W5P5V3 |
#23: Protein | Mass: 21648.715 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: W5PGA3 |
#24: Protein | Mass: 8500.289 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: W5PVD7 |
-NADH dehydrogenase [ubiquinone] 1 subunit ... , 2 types, 2 molecules C2C1
#18: Protein | Mass: 14231.420 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: The N-terminal residue is disordered and therefore not modeled. 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: W5P9Q8 |
---|---|
#27: Protein/peptide | Mass: 5808.645 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 dehydrogenase [ubiquinone] 1 beta subcomplex subunit ... , 4 types, 4 molecules B6B8BKB1
#21: Protein | Mass: 15433.929 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: Disordered regions of this subunit were not modeled. 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: W5PZE3 |
---|---|
#25: Protein | Mass: 18818.070 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: W5Q1B0 |
#26: Protein | Mass: 14455.033 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: The N-terminus was disordered and therefore not modeled. 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: W5PWF1 |
#28: Protein | Mass: 6930.083 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: W5QG39 |
-Non-polymers , 4 types, 13 molecules
#30: Chemical | ChemComp-3PE / #31: Chemical | ChemComp-CDL / #32: Chemical | #33: Chemical | ChemComp-ZMP / | |
---|
-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 I membrane arm focused refinement from ovine respiratory SC I+III2 Entity ID: #1-#29 / 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 | ||||||||||||||||||||
Specimen support | Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R0.6/1 | ||||||||||||||||||||
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: 174334 / Algorithm: FOURIER SPACE / Num. of class averages: 2 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||
Atomic model building | B value: 90 / Protocol: OTHER / Space: REAL | ||||||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 1LNK |