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	Structural conservation of antibiotic interaction with ribosomes.
ジャーナル・号・ページ	Nat Struct Mol Biol, Vol. 30, Issue 9, Page 1380-1392, Year 2023
掲載日	2023年8月7日
著者	Helge Paternoga / Caillan Crowe-McAuliffe / Lars V Bock / Timm O Koller / Martino Morici / Bertrand Beckert / Alexander G Myasnikov / Helmut Grubmüller / Jiří Nováček / Daniel N Wilson /
PubMed 要旨	The ribosome is a major target for clinically used antibiotics, but multidrug resistant pathogenic bacteria are making our current arsenal of antimicrobials obsolete. Here we present cryo-electron- ...The ribosome is a major target for clinically used antibiotics, but multidrug resistant pathogenic bacteria are making our current arsenal of antimicrobials obsolete. Here we present cryo-electron-microscopy structures of 17 distinct compounds from six different antibiotic classes bound to the bacterial ribosome at resolutions ranging from 1.6 to 2.2 Å. The improved resolution enables a precise description of antibiotic-ribosome interactions, encompassing solvent networks that mediate multiple additional interactions between the drugs and their target. Our results reveal a high structural conservation in the binding mode between antibiotics with the same scaffold, including ordered water molecules. Water molecules are visualized within the antibiotic binding sites that are preordered, become ordered in the presence of the drug and that are physically displaced on drug binding. Insight into RNA-ligand interactions will facilitate development of new antimicrobial agents, as well as other RNA-targeting therapies.
リンク	Nat Struct Mol Biol / PubMed:37550453 / PubMed Central
手法	EM (単粒子)
解像度	1.64 - 2.2 Å
構造データ	16520 8ca7 EMDB-16520, PDB-8ca7: Omadacycline and spectinomycin bound to the 30S ribosomal subunit head 手法: EM (単粒子) / 解像度: 2.06 Å 16526 8cai EMDB-16526, PDB-8cai: Streptomycin and Hygromycin B bound to the 30S body 手法: EM (単粒子) / 解像度: 2.08 Å 16530 8cam EMDB-16530, PDB-8cam: Evernimicin bound to the 50S subunit 手法: EM (単粒子) / 解像度: 1.86 Å 16536 8caz EMDB-16536, PDB-8caz: empty 30S head 手法: EM (単粒子) / 解像度: 2.11 Å 16612 8cep EMDB-16612, PDB-8cep: Kasugamycin bound to the 30S body 手法: EM (単粒子) / 解像度: 2.04 Å 16613 8ceu EMDB-16613, PDB-8ceu: Retapamulin and Capreomycin bound to the 50S subunit 手法: EM (単粒子) / 解像度: 1.83 Å 16615 8cf1 EMDB-16615, PDB-8cf1: Tetracycline bound to the 30S head 手法: EM (単粒子) / 解像度: 1.82 Å 16620 8cf8 EMDB-16620, PDB-8cf8: Eravacycline bound to the 30S head 手法: EM (単粒子) / 解像度: 2.2 Å 16641 8cgd EMDB-16641, PDB-8cgd: Clindamycin bound to the 50S subunit 手法: EM (単粒子) / 解像度: 1.98 Å 16644 8cgi EMDB-16644, PDB-8cgi: Pentacycline TP038 bound to the 30S head 手法: EM (単粒子) / 解像度: 1.89 Å 16645 8cgj EMDB-16645, PDB-8cgj: Streptomycin bound to the 30S body 手法: EM (単粒子) / 解像度: 1.79 Å 16646 8cgk EMDB-16646, PDB-8cgk: Lincomycin and Avilamycin bound to the 50S subunit 手法: EM (単粒子) / 解像度: 1.64 Å 16650 8cgr EMDB-16650, PDB-8cgr: Apramycin bound to the 30S body 手法: EM (単粒子) / 解像度: 2.12 Å 16651 8cgu EMDB-16651, PDB-8cgu: Gentamicin bound to the 30S body 手法: EM (単粒子) / 解像度: 1.89 Å 16652 8cgv EMDB-16652, PDB-8cgv: Tiamulin bound to the 50S subunit 手法: EM (単粒子) / 解像度: 1.66 Å
化合物	ChemComp-K: Unknown entry / カリウムカチオン ChemComp-U3B: Omadacycline ChemComp-SCM: SPECTINOMYCIN / スペクチノマイシン / 抗生剤YM ChemComp-MG: Unknown entry / マグネシウムジカチオン ChemComp-HOH: WATER ChemComp-HY0: HYGROMYCIN B VARIANT ChemComp-5I0: [(2~{S},3~{S},4~{S},5~{R},6~{S})-2-[(2~{R},3~{R},4~{R},5~{S})-2-[(1~{R},2~{S},3~{R},4~{R},5~{S},6~{R})-2,4-bis[[azaniumylidene(azanyl)methyl]amino]-3,5,6-tris(oxidanyl)cyclohexyl]oxy-4-[bis(oxidanyl)methyl]-5-methyl-4-oxidanyl-oxolan-3-yl]oxy-6-(hydroxymethyl)-4,5-bis(oxidanyl)oxan-3-yl]-methyl-azanium ChemComp-ZN: Unknown entry ChemComp-ACT: ACETATE ION / 酢酸イオン ChemComp-6O1: Evernimicin ChemComp-KSG: (1S,2R,3S,4R,5S,6S)-2,3,4,5,6-PENTAHYDROXYCYCLOHEXYL / カスガマイシン / 抗生剤YM ChemComp-G34: Retapamulin / レタパムリン / 抗生剤YM ChemComp-TAC: TETRACYCLINE / テトラサイクリン / 薬剤, 抗生剤YM ChemComp-YQM: Eravacycline / 抗生剤YM ChemComp-CLY: CLINDAMYCIN / クリンダマイシン / 薬剤, 抗生剤YM ChemComp-AM2: APRAMYCIN / 抗生剤YM ChemComp-P8F: Pentacycline ChemComp-3QB: LINCOMYCIN / リンコマイシン / 抗生剤YM ChemComp-6UQ: (2R,3S,4R,6S)-4-hydroxy-6-{[(2R,3aR,4R,4'R,5'S,6S,6'R,7aR)-4'-hydroxy-6-{[(2S,3R,4R,5S,6R)-3-hydroxy-2-{[(2R,3S,4S,5S,6S)-4-hydroxy-6-({(2R,3aS,3a'R,6S,6'R,7R,7'R,7aR,7a'R)-7'-hydroxy-7'-[(1S)-1-hydroxyethyl]-6'-methyl-7-[(2-methylpropanoyl)oxy]octahydro-4H-2,4'-spirobi[[1,3]dioxolo[4,5-c]pyran]-6-yl}oxy)-5-methoxy-2-(methoxymethyl)tetrahydro-2H-pyran-3-yl]oxy}-5-methoxy-6-methyltetrahydro-2H-pyran-4-yl]oxy}-4,6',7a-trimethyloctahydro-4H-spiro[1,3-dioxolo[4,5-c]pyran-2,2'-pyran]-5'-yl]oxy}-2-methyltetrahydro-2H-pyran-3-yl 3,5-dichloro-4-hydroxy-2-methoxy-6-methylbenzoate (non-preferred name) ChemComp-LLL: (2R,3R,4R,5R)-2-((1S,2S,3R,4S,6R)-4,6-DIAMINO-3-((2R,3R,6S)-3-AMINO-6-(AMINOMETHYL)-TETRAHYDRO-2H-PYRAN-2-YLOXY)-2-HYDR / ゲンタマイシンC_1a ChemComp-MUL: TIAMULIN / チアムリン / 抗生剤, Antimicrobial*YM
由来	escherichia coli bw25113 (大腸菌) streptomyces californicus (バクテリア)
キーワード	RIBOSOME / antibiotics / spectinomycin / omadacycline / Antibiotic