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Yorodumi- PDB-7rjd: Complex III2 from Candida albicans, inhibitor free, Rieske head d... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7rjd | ||||||||||||||||||
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Title | Complex III2 from Candida albicans, inhibitor free, Rieske head domain in c position | ||||||||||||||||||
Components |
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Keywords | MEMBRANE PROTEIN / Candida albicans / mitochondrial complex III2 / indazole-derivative inhibitor / Rieske head domain | ||||||||||||||||||
Function / homology | Function and homology information regulation of filamentous growth / 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 / heterochromatin ...regulation of filamentous growth / 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 / heterochromatin / aerobic respiration / metalloendopeptidase activity / 2 iron, 2 sulfur cluster binding / oxidoreductase activity / electron transfer activity / heme binding / mitochondrion / membrane / metal ion binding / plasma membrane Similarity search - Function | ||||||||||||||||||
Biological species | Candida albicans (yeast) | ||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å | ||||||||||||||||||
Authors | Di Trani, J.M. / Rubinstein, J.L. | ||||||||||||||||||
Funding support | Canada, Sweden, 5items
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Citation | Journal: Structure / Year: 2022 Title: Rieske head domain dynamics and indazole-derivative inhibition of Candida albicans complex III. Authors: Justin M Di Trani / Zhongle Liu / Luke Whitesell / Peter Brzezinski / Leah E Cowen / John L Rubinstein / Abstract: Electron transfer between respiratory complexes drives transmembrane proton translocation, which powers ATP synthesis and membrane transport. The homodimeric respiratory complex III (CIII) oxidizes ...Electron transfer between respiratory complexes drives transmembrane proton translocation, which powers ATP synthesis and membrane transport. The homodimeric respiratory complex III (CIII) oxidizes ubiquinol to ubiquinone, transferring electrons to cytochrome c and translocating protons through a mechanism known as the Q cycle. The Q cycle involves ubiquinol oxidation and ubiquinone reduction at two different sites within each CIII monomer, as well as movement of the head domain of the Rieske subunit. We determined structures of Candida albicans CIII by cryoelectron microscopy (cryo-EM), revealing endogenous ubiquinone and visualizing the continuum of Rieske head domain conformations. Analysis of these conformations does not indicate cooperativity in the Rieske head domain position or ligand binding in the two CIIIs of the CIII dimer. Cryo-EM with the indazole derivative Inz-5, which inhibits fungal CIII and is fungicidal when administered with fungistatic azole drugs, showed that Inz-5 inhibition alters the equilibrium of Rieske head domain positions. | ||||||||||||||||||
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 | 7rjd.cif.gz | 602.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7rjd.ent.gz | 509.5 KB | Display | PDB format |
PDBx/mmJSON format | 7rjd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7rjd_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 7rjd_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 7rjd_validation.xml.gz | 62.4 KB | Display | |
Data in CIF | 7rjd_validation.cif.gz | 92.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rj/7rjd ftp://data.pdbj.org/pub/pdb/validation_reports/rj/7rjd | HTTPS FTP |
-Related structure data
Related structure data | 24485MC 7rjaC 7rjbC 7rjcC 7rjeC 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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1 |
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-Components
-Cytochrome b-c1 complex subunit ... , 3 types, 4 molecules EMGB
#1: Protein | Mass: 23233.385 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) Candida albicans (strain SC5314 / ATCC MYA-2876) (yeast) Strain: SC5314 / ATCC MYA-2876 References: UniProt: A0A1D8PJX3, quinol-cytochrome-c reductase #5: Protein | | Mass: 14440.710 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Candida albicans (strain SC5314 / ATCC MYA-2876) (yeast) Strain: SC5314 / ATCC MYA-2876 / References: UniProt: Q5ABS1 #9: Protein | | Mass: 39593.352 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Candida albicans (strain SC5314 / ATCC MYA-2876) (yeast) Strain: SC5314 / ATCC MYA-2876 / References: UniProt: P83782 |
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-Ubiquinol--cytochrome-c reductase ... , 5 types, 5 molecules ADFHI
#2: Protein | Mass: 48004.805 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Candida albicans (strain SC5314 / ATCC MYA-2876) (yeast) Strain: SC5314 / ATCC MYA-2876 / References: UniProt: A0A1D8PP59 |
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#4: Protein | Mass: 32261.389 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Candida albicans (strain SC5314 / ATCC MYA-2876) (yeast) Strain: SC5314 / ATCC MYA-2876 / References: UniProt: A0A1D8PHA3 |
#6: Protein | Mass: 11125.672 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Candida albicans (strain SC5314 / ATCC MYA-2876) (yeast) Strain: SC5314 / ATCC MYA-2876 / References: UniProt: A0A1D8PHA2 |
#7: Protein | Mass: 16042.014 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Candida albicans (strain SC5314 / ATCC MYA-2876) (yeast) Strain: SC5314 / ATCC MYA-2876 / References: UniProt: A0A1D8PJT8 |
#8: Protein | Mass: 7518.448 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Candida albicans (strain SC5314 / ATCC MYA-2876) (yeast) Strain: SC5314 / ATCC MYA-2876 / References: UniProt: A0A1D8PLP3 |
-Protein , 1 types, 1 molecules K
#3: Protein | Mass: 43738.457 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Candida albicans (strain SC5314 / ATCC MYA-2876) (yeast) Strain: SC5314 / ATCC MYA-2876 / References: UniProt: P0C8L0 |
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-Non-polymers , 4 types, 6 molecules
#10: Chemical | ChemComp-FES / | ||||
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#11: Chemical | #12: Chemical | #13: Chemical | ChemComp-HEC / | |
-Details
Has ligand of interest | N |
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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: Respiratory complex III2 from Candida albicans / Type: COMPLEX / Entity ID: #1-#9 / Source: NATURAL |
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Source (natural) | Organism: Candida albicans SC5314 (yeast) |
Buffer solution | pH: 7.4 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE-PROPANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: TFS KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 42 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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3D reconstruction | Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 78331 / Symmetry type: POINT |