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	Cryo-EM structures of cytochrome reveal bound phospholipids and ubiquinone-8 in a dynamic substrate binding site.
Journal, issue, pages	Proc Natl Acad Sci U S A, Vol. 118, Issue 34, Year 2021
Publish date	Aug 24, 2021
Authors	Jiao Li / Long Han / Francesca Vallese / Ziqiao Ding / Sylvia K Choi / Sangjin Hong / Yanmei Luo / Bin Liu / Chun Kit Chan / Emad Tajkhorshid / Jiapeng Zhu / Oliver Clarke / Kai Zhang / Robert Gennis /
PubMed Abstract	Two independent structures of the proton-pumping, respiratory cytochrome ubiquinol oxidase (cyt ) have been determined by cryogenic electron microscopy (cryo-EM) in styrene-maleic acid (SMA) ...Two independent structures of the proton-pumping, respiratory cytochrome ubiquinol oxidase (cyt ) have been determined by cryogenic electron microscopy (cryo-EM) in styrene-maleic acid (SMA) copolymer nanodiscs and in membrane scaffold protein (MSP) nanodiscs to 2.55- and 2.19-Å resolution, respectively. The structures include the metal redox centers (heme , heme , and Cu), the redox-active cross-linked histidine-tyrosine cofactor, and the internal water molecules in the proton-conducting D channel. Each structure also contains one equivalent of ubiquinone-8 (UQ8) in the substrate binding site as well as several phospholipid molecules. The isoprene side chain of UQ8 is clamped within a hydrophobic groove in subunit I by transmembrane helix TM0, which is only present in quinol oxidases and not in the closely related cytochrome oxidases. Both structures show carbonyl O1 of the UQ8 headgroup hydrogen bonded to D75 and R71 In both structures, residue H98 occupies two conformations. In conformation 1, H98 forms a hydrogen bond with carbonyl O4 of the UQ8 headgroup, but in conformation 2, the imidazole side chain of H98 has flipped to form a hydrogen bond with E14 at the N-terminal end of TM0. We propose that H98 dynamics facilitate proton transfer from ubiquinol to the periplasmic aqueous phase during oxidation of the substrate. Computational studies show that TM0 creates a channel, allowing access of water to the ubiquinol headgroup and to H98.
External links	Proc Natl Acad Sci U S A / PubMed:34417297 / PubMed Central
Methods	EM (single particle)
Resolution	2.19 - 3.25 Å
Structure data	24265 7n9z EMDB-24265, PDB-7n9z: E. coli cytochrome bo3 in MSP nanodisc Method: EM (single particle) / Resolution: 2.19 Å 30471 7cub EMDB-30471, PDB-7cub: 2.55-Angstrom Cryo-EM structure of Cytochrome bo3 from Escherichia coli in Native Membrane Method: EM (single particle) / Resolution: 2.55 Å 30474 7cuq EMDB-30474, PDB-7cuq: 2.55-Angstrom Cryo-EM structure of Cytochrome bo3 from Escherichia coli in Native Membrane Method: EM (single particle) / Resolution: 2.64 Å 30475 7cuw EMDB-30475, PDB-7cuw: Ubiquinol Binding Site of Cytochrome bo3 from Escherichia coli Method: EM (single particle) / Resolution: 2.63 Å EMDB-30817: High Resolution Cryo-EM Structure of Cytochrome bo3 from E. Coli Reveals High Affinity Quinol Binding Site and Interactions of Protein with Lipids Method: EM (single particle) / Resolution: 3.03 Å EMDB-30818: High Resolution Cryo-EM Structure of Cytochrome bo3 from E. Coli Reveals High Affinity Quinol Binding Site and Interactions of Protein with Lipids Method: EM (single particle) / Resolution: 3.19 Å EMDB-30819: High Resolution Cryo-EM Structure of Cytochrome bo3 from E. Coli Reveals High Affinity Quinol Binding Site and Interactions of Protein with Lipids Method: EM (single particle) / Resolution: 3.25 Å
Chemicals	ChemComp-HEM: PROTOPORPHYRIN IX CONTAINING FE ChemComp-HEO: HEME O ChemComp-CU: COPPER (II) ION ChemComp-3PE: 1,2-Distearoyl-sn-glycerophosphoethanolamine / phospholipidYM ChemComp-UQ8: Ubiquinone-8 ChemComp-HOH: WATER ChemComp-LHG: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / phospholipidYM ChemComp-CDL: CARDIOLIPIN / phospholipidYM ChemComp-ZN*: Unknown entry
Source	escherichia coli (E. coli) Escherichia coli 536 (bacteria)
Keywords	OXIDOREDUCTASE / proton pump / ubiquinol / oxidase / protein pump / MEMBRANE PROTEIN / Ubiquinone / Heme-copper Oxidoreductase / Electron transport / Bioenergetics