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	Distinct ubiquinone binding at the oxidation and reduction sites of cytochrome bc.
Journal, issue, pages	Proc Natl Acad Sci U S A, Vol. 123, Issue 36, Page e2618242123, Year 2026
Publish date	Sep 8, 2026
Authors	Rafał Pietras / Anna Wójcik-Augustyn / Bohun Mielecki / Marcin Sarewicz / Marcin Jaciuk / Łukasz Koziej / Sebastian Glatt / Artur Osyczka /
PubMed Abstract	The function of cytochrome bc, a widespread energy-conserving enzyme, requires the coordinated activity of two quinone-binding sites (Q catalyzing oxidation of ubiquinol and Q catalyzing reduction of ...The function of cytochrome bc, a widespread energy-conserving enzyme, requires the coordinated activity of two quinone-binding sites (Q catalyzing oxidation of ubiquinol and Q catalyzing reduction of ubiquinone). The operation of Q, but not Q, involves large-scale movement of the head domain of iron-sulfur protein (ISP-HD). How the respective sites accommodate quinone molecules for efficient catalysis remains elusive. Here, we present high-resolution cryoelectron microscopy structures of bacterial cytochrome bc with native ubiquinone molecules in various states. They show that the quinone headgroup occupies a catalytically competent position in Q only when the ISP-HD interacts with cytochrome b. When the ISP-HD does not interact with this subunit, quinone is present in the hydrophobic groove, however its headgroup is prevented from reaching the catalytic cavity by steric hindrance. In this state, the position of quinone headgroup is clearly not fixed. In contrast, all structures show Q in the same state with a well-resolved and catalytically competent quinone headgroup, but with its tail not fixed. These distinctly different ubiquinone binding modes for Q and Q secure the smooth operation of cytochrome bc.
External links	Proc Natl Acad Sci U S A / PubMed:42679026
Methods	EM (single particle)
Resolution	2.16 - 2.74 Å
Structure data	57440 29xz EMDB-57440: Cytochrome bc1 complex from Rhodobacter capsulatus at 2.16 A resolution PDB-29xz: Cryo-EM structure of Rhodobacter capsulatus cytochrome bc1 dimer at 2.16 A resolution with water molecules and quinone in the quinone reduction site Method: EM (single particle) / Resolution: 2.16 Å 57441 29ya EMDB-57441: R. capsulatus cytochrome bc1 dimer with one Rieske protein in the c position and one in the b position PDB-29ya: Cryo-EM structure of Rhodobacter capsulatus cytochrome bc1 dimer with one Rieske protein in the c position and one in the b position and quinone in the quinone oxidation site Method: EM (single particle) / Resolution: 2.69 Å 57442 29yb EMDB-57442: R. capsulatus cytochrome bc1 dimer with both Rieske proteins in the b position PDB-29yb: Cryo-EM structure of Rhodobacter capsulatus cytochrome bc1 dimer with both Rieske proteins in the b position Method: EM (single particle) / Resolution: 2.74 Å 57443 29yc EMDB-57443: R. capsulatus cytochrome bc1 dimer with both Rieske proteins in the c position PDB-29yc: Cryo-EM structure of Rhodobacter capsulatus cytochrome bc1 dimer with both Rieske proteins in the c position Method: EM (single particle) / Resolution: 2.43 Å 57444 29yd EMDB-57444: R. capsulatus cytochrome bc1 dimer with one Rieske protein in the c position and one in an intermediate position PDB-29yd: Cryo-EM structure of Rhodobacter capsulatus cytochrome bc1 dimer with one Rieske protein in the c position and one in an intermediate position Method: EM (single particle) / Resolution: 2.73 Å 57445 29ye EMDB-57445: Rhodobacter capsulatus +2Ala insertion mutant of cytochrome bc1 dimer at 2.41 A PDB-29ye: Cryo-EM structure of +2Ala insertion mutant of Rhodobacter capsulatus cytochrome bc1 dimer at 2.41 A with quinone in quinone oxidation and reduction sites Method: EM (single particle) / Resolution: 2.41 Å
Chemicals	ChemComp-FES: FE2/S2 (INORGANIC) CLUSTER ChemComp-UMQ: UNDECYL-MALTOSIDE / detergentYM ChemComp-HEM: PROTOPORPHYRIN IX CONTAINING FE ChemComp-UQ1: UBIQUINONE-1 ChemComp-HEC: HEME C ChemComp-HOH: WATER ChemComp-U10: UBIQUINONE-10 ChemComp-LMT: DODECYL-BETA-D-MALTOSIDE / detergentYM
Source	rhodobacter capsulatus sb 1003 (bacteria)
Keywords	ELECTRON TRANSPORT / oxidoreductuse / proton pumping / quinol oxidation / respiration