EMDB/PDB/SASBDBから引用されている文献のデータベース

キーワード
構造解析手法	All X線回折 NMR 電子顕微鏡小角散乱中性子線回折線維回折粉末回折赤外分光 EPR FRET 理論モデルハイブリッド
著者・登録者
ジャーナル
IF	>30 >20 >10 >5 all

タイトル	Cryo-EM structures of cytochrome reveal bound phospholipids and ubiquinone-8 in a dynamic substrate binding site.
ジャーナル・号・ページ	Proc Natl Acad Sci U S A, Vol. 118, Issue 34, Year 2021
掲載日	2021年8月24日
著者	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 要旨	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.
リンク	Proc Natl Acad Sci U S A / PubMed:34417297 / PubMed Central
手法	EM (単粒子)
解像度	2.19 - 3.25 Å
構造データ	24265 7n9z EMDB-24265, PDB-7n9z: E. coli cytochrome bo3 in MSP nanodisc 手法: EM (単粒子) / 解像度: 2.19 Å 30471 7cub EMDB-30471, PDB-7cub: 2.55-Angstrom Cryo-EM structure of Cytochrome bo3 from Escherichia coli in Native Membrane 手法: EM (単粒子) / 解像度: 2.55 Å 30474 7cuq EMDB-30474, PDB-7cuq: 2.55-Angstrom Cryo-EM structure of Cytochrome bo3 from Escherichia coli in Native Membrane 手法: EM (単粒子) / 解像度: 2.64 Å 30475 7cuw EMDB-30475, PDB-7cuw: Ubiquinol Binding Site of Cytochrome bo3 from Escherichia coli 手法: EM (単粒子) / 解像度: 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 手法: EM (単粒子) / 解像度: 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 手法: EM (単粒子) / 解像度: 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 手法: EM (単粒子) / 解像度: 3.25 Å
化合物	ChemComp-HEM: PROTOPORPHYRIN IX CONTAINING FE / Heme B ChemComp-HEO: HEME O / Heme O ChemComp-CU: COPPER (II) ION / 銅 ChemComp-3PE: 1,2-Distearoyl-sn-glycerophosphoethanolamine / DSPE / リン脂質YM / ホスファチジルエタノールアミン ChemComp-UQ8: Ubiquinone-8 / ユビキノン8 ChemComp-HOH: WATER / 水 ChemComp-LHG: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / ジパルミトイルホスファチジルグリセロ-ル / リン脂質YM / Phosphatidylglycerol ChemComp-CDL: CARDIOLIPIN / リン脂質YM / Cardiolipin ChemComp-ZN*: Unknown entry
由来	escherichia coli (大腸菌) Escherichia coli 536 (大腸菌)
キーワード	OXIDOREDUCTASE (酸化還元酵素) / proton pump (プロトンポンプ) / ubiquinol / oxidase (酸化酵素) / protein pump / MEMBRANE PROTEIN (膜タンパク質) / Ubiquinone (ユビキノン) / Heme-copper Oxidoreductase / Electron transport (電子伝達系) / Bioenergetics