[English] 日本語
Yorodumi- PDB-8abe: Complex III2 from Yarrowia lipolytica, oxidised with ferricyanide... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8abe | ||||||
---|---|---|---|---|---|---|---|
Title | Complex III2 from Yarrowia lipolytica, oxidised with ferricyanide, b-position | ||||||
Components |
| ||||||
Keywords | MEMBRANE PROTEIN / oxidoreductase / electron transport chain | ||||||
Function / homology | Function and homology information mitochondrial processing peptidase complex / mitochondrial processing peptidase / matrix side of mitochondrial inner membrane / protein processing involved in protein targeting to mitochondrion / mitochondrial respiratory chain complex III assembly / : / quinol-cytochrome-c reductase / ubiquinol-cytochrome-c reductase activity / mitochondrial electron transport, ubiquinol to cytochrome c / mitochondrial crista ...mitochondrial processing peptidase complex / mitochondrial processing peptidase / matrix side of mitochondrial inner membrane / protein processing involved in protein targeting to mitochondrion / mitochondrial respiratory chain complex III assembly / : / quinol-cytochrome-c reductase / ubiquinol-cytochrome-c reductase activity / mitochondrial electron transport, ubiquinol to cytochrome c / mitochondrial crista / nuclear periphery / mitochondrial intermembrane space / metalloendopeptidase activity / 2 iron, 2 sulfur cluster binding / oxidoreductase activity / heme binding / mitochondrion / proteolysis / membrane / metal ion binding Similarity search - Function | ||||||
Biological species | Yarrowia lipolytica (yeast) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.3 Å | ||||||
Authors | Wieferig, J.P. / Kuhlbrandt, W. | ||||||
Funding support | Germany, 1items
| ||||||
Citation | Journal: IUCrJ / Year: 2023 Title: Analysis of the conformational heterogeneity of the Rieske iron-sulfur protein in complex III by cryo-EM. Authors: Jan Philip Wieferig / Werner Kühlbrandt / Abstract: Movement of the Rieske domain of the iron-sulfur protein is essential for intramolecular electron transfer within complex III (CIII) of the respiratory chain as it bridges a gap in the cofactor chain ...Movement of the Rieske domain of the iron-sulfur protein is essential for intramolecular electron transfer within complex III (CIII) of the respiratory chain as it bridges a gap in the cofactor chain towards the electron acceptor cytochrome c. We present cryo-EM structures of CIII from Yarrowia lipolytica at resolutions up to 2.0 Å under different conditions, with different redox states of the cofactors of the high-potential chain. All possible permutations of three primary positions were observed, indicating that the two halves of the dimeric complex act independently. Addition of the substrate analogue decylubiquinone to CIII with a reduced high-potential chain increased the occupancy of the Q site. The extent of Rieske domain interactions through hydrogen bonds to the cytochrome b and cytochrome c subunits varied depending on the redox state and substrate. In the absence of quinols, the reduced Rieske domain interacted more closely with cytochrome b and cytochrome c than in the oxidized state. Upon addition of the inhibitor antimycin A, the heterogeneity of the cd-helix and ef-loop increased, which may be indicative of a long-range effect on the Rieske domain. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 8abe.cif.gz | 818.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb8abe.ent.gz | 660.8 KB | Display | PDB format |
PDBx/mmJSON format | 8abe.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8abe_validation.pdf.gz | 2.7 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 8abe_full_validation.pdf.gz | 2.7 MB | Display | |
Data in XML | 8abe_validation.xml.gz | 126.8 KB | Display | |
Data in CIF | 8abe_validation.cif.gz | 185.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ab/8abe ftp://data.pdbj.org/pub/pdb/validation_reports/ab/8abe | HTTPS FTP |
-Related structure data
Related structure data | 15318MC 8ab6C 8ab7C 8ab8C 8ab9C 8abaC 8abbC 8abfC 8abgC 8abhC 8abiC 8abjC 8abkC 8ablC 8abmC 8ac3C 8ac4C 8ac5C M: map data used to model this data C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
|
-Components
-Protein , 6 types, 12 molecules CNFQALDOITJU
#1: Protein | Mass: 43409.406 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast) / Strain: CLIB 122 / E 150 / References: UniProt: Q9B6D0 #4: Protein | Mass: 15789.444 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast) / Strain: CLIB 122 / E 150 / References: UniProt: Q6C0H4 #5: Protein | Mass: 52846.945 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast) / Strain: CLIB 122 / E 150 / References: UniProt: Q6CGY9 #7: Protein | Mass: 36555.605 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast) / Strain: CLIB 122 / E 150 / References: UniProt: Q6CGP7 #9: Protein | Mass: 8038.856 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast) / Strain: CLIB 122 / E 150 / References: UniProt: Q6CG23 #10: Protein | Mass: 9114.678 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast) / Strain: CLIB 122 / E 150 / References: UniProt: Q6CC60 |
---|
-Cytochrome b-c1 complex subunit ... , 4 types, 8 molecules PEGRBMHS
#2: Protein | Mass: 24563.213 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast) / Strain: CLIB 122 / E 150 / References: UniProt: Q6CI02, quinol-cytochrome-c reductase #3: Protein | Mass: 14675.995 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast) / Strain: CLIB 122 / E 150 / References: UniProt: Q6C3K7 #6: Protein | Mass: 44277.840 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast) / Strain: CLIB 122 / E 150 / References: UniProt: Q6C2E3 #8: Protein | Mass: 10463.970 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast) / Strain: CLIB 122 / E 150 / References: UniProt: Q6C387 |
---|
-Sugars , 1 types, 4 molecules
#15: Sugar | ChemComp-LMT / |
---|
-Non-polymers , 7 types, 27 molecules
#11: Chemical | ChemComp-HEM / #12: Chemical | ChemComp-PC1 / #13: Chemical | ChemComp-PTY / #14: Chemical | ChemComp-CDL / #16: Chemical | ChemComp-FES / | #17: Chemical | #18: Chemical | |
---|
-Details
Has ligand of interest | Y |
---|
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Complex III2, oxidised with ferricyanide, b-position / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: #1-#10 / Source: NATURAL |
---|---|
Molecular weight | Experimental value: NO |
Source (natural) | Organism: Yarrowia lipolytica (yeast) |
Buffer solution | pH: 8 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid type: UltrAuFoil R1.2/1.3 |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
---|---|
Microscopy | Model: TFS KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 800 nm |
Specimen holder | Cryogen: NITROGEN |
Image recording | Electron dose: 55 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
-Processing
Software | Name: REFMAC / Version: 5.8.0258 / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
EM software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 2.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 112357 / Symmetry type: POINT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | Resolution: 2.3→162.38 Å / Cor.coef. Fo:Fc: 0.936 / SU B: 5.965 / SU ML: 0.132 / ESU R: 0.2 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: PARAMETERS FOR MASK CACLULATION | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 58.761 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Total: 32540 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|