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	Structural conservation of antibiotic interaction with ribosomes.
Journal, issue, pages	Nat Struct Mol Biol, Vol. 30, Issue 9, Page 1380-1392, Year 2023
Publish date	Aug 7, 2023
Authors	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 Abstract	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.
External links	Nat Struct Mol Biol / PubMed:37550453 / PubMed Central
Methods	EM (single particle)
Resolution	1.64 - 2.2 Å
Structure data	16520 8ca7 EMDB-16520, PDB-8ca7: Omadacycline and spectinomycin bound to the 30S ribosomal subunit head Method: EM (single particle) / Resolution: 2.06 Å 16526 8cai EMDB-16526, PDB-8cai: Streptomycin and Hygromycin B bound to the 30S body Method: EM (single particle) / Resolution: 2.08 Å 16530 8cam EMDB-16530, PDB-8cam: Evernimicin bound to the 50S subunit Method: EM (single particle) / Resolution: 1.86 Å 16536 8caz EMDB-16536, PDB-8caz: empty 30S head Method: EM (single particle) / Resolution: 2.11 Å 16612 8cep EMDB-16612, PDB-8cep: Kasugamycin bound to the 30S body Method: EM (single particle) / Resolution: 2.04 Å 16613 8ceu EMDB-16613, PDB-8ceu: Retapamulin and Capreomycin bound to the 50S subunit Method: EM (single particle) / Resolution: 1.83 Å 16615 8cf1 EMDB-16615, PDB-8cf1: Tetracycline bound to the 30S head Method: EM (single particle) / Resolution: 1.82 Å 16620 8cf8 EMDB-16620, PDB-8cf8: Eravacycline bound to the 30S head Method: EM (single particle) / Resolution: 2.2 Å 16641 8cgd EMDB-16641, PDB-8cgd: Clindamycin bound to the 50S subunit Method: EM (single particle) / Resolution: 1.98 Å 16644 8cgi EMDB-16644, PDB-8cgi: Pentacycline TP038 bound to the 30S head Method: EM (single particle) / Resolution: 1.89 Å 16645 8cgj EMDB-16645, PDB-8cgj: Streptomycin bound to the 30S body Method: EM (single particle) / Resolution: 1.79 Å 16646 8cgk EMDB-16646, PDB-8cgk: Lincomycin and Avilamycin bound to the 50S subunit Method: EM (single particle) / Resolution: 1.64 Å 16650 8cgr EMDB-16650, PDB-8cgr: Apramycin bound to the 30S body Method: EM (single particle) / Resolution: 2.12 Å 16651 8cgu EMDB-16651, PDB-8cgu: Gentamicin bound to the 30S body Method: EM (single particle) / Resolution: 1.89 Å 16652 8cgv EMDB-16652, PDB-8cgv: Tiamulin bound to the 50S subunit Method: EM (single particle) / Resolution: 1.66 Å
Chemicals	ChemComp-K: Unknown entry ChemComp-U3B: Omadacycline ChemComp-SCM: SPECTINOMYCIN / antibioticYM / Spectinomycin ChemComp-MG: Unknown entry ChemComp-HOH: WATER / 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 / Acetate ChemComp-6O1: Evernimicin ChemComp-KSG: (1S,2R,3S,4R,5S,6S)-2,3,4,5,6-PENTAHYDROXYCYCLOHEXYL / antibioticYM / Kasugamycin ChemComp-G34: Retapamulin / antibioticYM / Retapamulin ChemComp-TAC: TETRACYCLINE / medication, antibioticYM / Tetracycline ChemComp-YQM: Eravacycline / antibioticYM / Eravacycline ChemComp-CLY: CLINDAMYCIN / medication, antibioticYM / Clindamycin ChemComp-AM2: APRAMYCIN / antibioticYM / Apramycin ChemComp-P8F: Pentacycline ChemComp-3QB: LINCOMYCIN / antibioticYM / Lincomycin 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 ChemComp-MUL: TIAMULIN / antibiotic, Antimicrobial*YM / Tiamulin
Source	escherichia coli bw25113 (bacteria) streptomyces californicus (bacteria)
Keywords	RIBOSOME / antibiotics / spectinomycin / omadacycline / Antibiotic