Database of articles cited by EMDB/PDB/SASBDB data

Keywords
Structure methods	All X-ray diffraction NMR electron microscopy small angle scattering neutron diffraction fiber diffraction powder diffraction infrared spectroscopy EPR fluorescence transfer theoretical model Hybrid
Author
Journal
IF	>30 >20 >10 >5 all

Title	Analysis of the conformational heterogeneity of the Rieske iron-sulfur protein in complex III by cryo-EM.
Journal, issue, pages	IUCrJ, Vol. 10, Issue Pt 1, Page 27-37, Year 2023
Publish date	Jan 1, 2023
Authors	Jan Philip Wieferig / Werner Kühlbrandt /
PubMed 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.
External links	IUCrJ / PubMed:36598500 / PubMed Central
Methods	EM (single particle)
Resolution	2.0 - 3.7 Å
Structure data	15312 8ab6 EMDB-15312, PDB-8ab6: Complex III2 from Yarrowia lipolytica, combined datasets, consensus refinement Method: EM (single particle) / Resolution: 2.0 Å 15313 8ab7 EMDB-15313, PDB-8ab7: Complex III2 from Yarrowia lipolytica, atovaquone and antimycin A bound Method: EM (single particle) / Resolution: 3.3 Å 15314 8ab8 EMDB-15314, PDB-8ab8: Complex III2, b-position, with decylubiquinone and ascorbate-reduced Method: EM (single particle) / Resolution: 2.6 Å 15315 8ab9 EMDB-15315, PDB-8ab9: Complex III2 from Yarrowia lipolytica, ascorbate-reduced, b-position Method: EM (single particle) / Resolution: 3.3 Å 15316 8aba EMDB-15316, PDB-8aba: Complex III2 from Yarrowia lipolytica, ascorbate-reduced, int-position Method: EM (single particle) / Resolution: 3.2 Å 15317 8abb EMDB-15317, PDB-8abb: Complex III2 from Yarrowia lipolytica, ascorbate-reduced, c-position Method: EM (single particle) / Resolution: 3.2 Å 15318 8abe EMDB-15318, PDB-8abe: Complex III2 from Yarrowia lipolytica, oxidised with ferricyanide, b-position Method: EM (single particle) / Resolution: 2.3 Å 15319 8abf EMDB-15319, PDB-8abf: Complex III2 from Yarrowia lipolytica, oxidised with ferricyanide, int-position Method: EM (single particle) / Resolution: 2.3 Å 15320 8abg EMDB-15320, PDB-8abg: Complex III2 from Yarrowia lipolytica, oxidised with ferricyanide, c-position Method: EM (single particle) / Resolution: 2.3 Å 15321 8abh EMDB-15321, PDB-8abh: Complex III2 from Yarrowia lipolytica, antimycin A bound, b-position Method: EM (single particle) / Resolution: 3.0 Å 15322 8abi EMDB-15322, PDB-8abi: Complex III2 from Yarrowia lipolytica,antimycin A bound, int-position Method: EM (single particle) / Resolution: 3.0 Å 15323 8abj EMDB-15323, PDB-8abj: Complex III2 from Yarrowia lipolytica, antimycin A bound, c-position Method: EM (single particle) / Resolution: 3.7 Å 15324 8abk EMDB-15324, PDB-8abk: Complex III2 from Yarrowia lipolytica, decylubiquinol bound, b-position Method: EM (single particle) / Resolution: 2.5 Å 15325 8abl EMDB-15325, PDB-8abl: Complex III2 from Yarrowia lipolytica, with decylubiquinol and antimycin A, consensus refinement Method: EM (single particle) / Resolution: 2.1 Å 15326 8abm EMDB-15326, PDB-8abm: Complex III2 from Yarrowia lipolytica, apo, b-position Method: EM (single particle) / Resolution: 2.8 Å 15332 8ac3 EMDB-15332, PDB-8ac3: Complex III2 from Yarrowia lipolytica, apo, int-position Method: EM (single particle) / Resolution: 2.8 Å 15333 8ac4 EMDB-15333, PDB-8ac4: Complex III2 from Yarrowia lipolytica, apo, c-position Method: EM (single particle) / Resolution: 2.7 Å 15334 8ac5 EMDB-15334, PDB-8ac5: Complex III2 from Yarrowia lipolytica, with decylubiquinol, oxidised, b-position Method: EM (single particle) / Resolution: 3.1 Å
Chemicals	ChemComp-HEM: PROTOPORPHYRIN IX CONTAINING FE ChemComp-PC1: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / phospholipidYM ChemComp-PTY: PHOSPHATIDYLETHANOLAMINE / phospholipidYM ChemComp-CDL: CARDIOLIPIN / phospholipidYM ChemComp-LMT: DODECYL-BETA-D-MALTOSIDE / detergentYM ChemComp-XP4: 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHATE / DMPA, phospholipidYM ChemComp-HEC: HEME C ChemComp-HOH: WATER ChemComp-AWB: [(2R,3S,6S,7R,8R)-3-[(3-formamido-2-oxidanyl-phenyl)carbonylamino]-8-hexyl-2,6-dimethyl-4,9-bis(oxidanylidene)-1,5-dioxonan-7-yl] 3-methylbutanoate ChemComp-AOQ: 2-[trans-4-(4-chlorophenyl)cyclohexyl]-3-hydroxynaphthalene-1,4-dione / medication, AntimicrobialYM ChemComp-FES: FE2/S2 (INORGANIC) CLUSTER ChemComp-DCQ: 2-decyl-5,6-dimethoxy-3-methylcyclohexa-2,5-diene-1,4-dione
Source	yarrowia lipolytica (yeast)
Keywords	MEMBRANE PROTEIN / oxidoreductase / electron transport chain / inhibitor