6O97
| Crystal structure of the Thermus thermophilus 70S ribosome in complex with propylamycin and bound to mRNA and A-, P-, and E-site tRNAs at 2.75A resolution | Descriptor: | (1R,2R,3S,4R,6S)-4,6-diamino-2-{[3-O-(2,6-diamino-2,6-dideoxy-beta-L-idopyranosyl)-beta-D-ribofuranosyl]oxy}-3-hydroxyc yclohexyl 2-amino-2,4-dideoxy-4-propyl-alpha-D-glucopyranoside, 16S Ribosomal RNA, 23S Ribosomal RNA, ... | Authors: | Matsushita, T, Sati, G.C, Kondasinghe, N, Pirrone, M.G, Kato, T, Waduge, P, Kumar, H.S, Sanchon, A.C, Dobosz-Bartoszek, M, Shcherbakov, D, Juhas, M, Hobbie, S.N, Schrepfer, T, Chow, C.S, Polikanov, Y.S, Schacht, J, Vasella, A, Bottger, E.C, Crich, D. | Deposit date: | 2019-03-13 | Release date: | 2019-04-17 | Last modified: | 2023-11-15 | Method: | X-RAY DIFFRACTION (2.75 Å) | Cite: | Design, Multigram Synthesis, and in Vitro and in Vivo Evaluation of Propylamycin: A Semisynthetic 4,5-Deoxystreptamine Class Aminoglycoside for the Treatment of Drug-Resistant Enterobacteriaceae and Other Gram-Negative Pathogens. J. Am. Chem. Soc., 141, 2019
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8UVS
| Crystal structure of the wild-type Thermus thermophilus 70S ribosome in complex with spectinomycin derivative 2694, mRNA, deacylated A- and E-site tRNAphe, and deacylated P-site tRNAmet at 2.75A resolution | Descriptor: | (2R,4R,4aS,5aR,6S,7S,8R,9S,9aR,10aS)-2-methyl-6,8-bis(methylamino)-4-({[2-(oxan-4-yl)ethyl]amino}methyl)octahydro-2H-pyrano[2,3-b][1,4]benzodioxine-4,4a,7,9(10aH)-tetrol, 16S Ribosomal RNA, 23S Ribosomal RNA, ... | Authors: | Killam, B.Y, Phelps, G.A, Lee, R.E, Polikanov, Y.S. | Deposit date: | 2023-11-03 | Release date: | 2024-08-07 | Method: | X-RAY DIFFRACTION (2.75 Å) | Cite: | Development of 2nd generation aminomethyl spectinomycins that overcome native efflux in Mycobacterium abscessus. Proc.Natl.Acad.Sci.USA, 121, 2024
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2UUB
| Structure of the Thermus thermophilus 30S ribosomal subunit complexed with a Valine-ASL with cmo5U in position 34 bound to an mRNA with a GUU-codon in the A-site and paromomycin. | Descriptor: | 16S Ribosomal RNA, 30S RIBOSOMAL PROTEIN S10, 30S RIBOSOMAL PROTEIN S11, ... | Authors: | Weixlbaumer, A, Murphy, F.V, Dziergowska, A, Malkiewicz, A, Vendeix, F.A.P, Agris, P.F, Ramakrishnan, V. | Deposit date: | 2007-03-01 | Release date: | 2007-05-15 | Last modified: | 2023-12-13 | Method: | X-RAY DIFFRACTION (2.8 Å) | Cite: | Mechanism for Expanding the Decoding Capacity of Transfer Rnas by Modification of Uridines Nat.Struct.Mol.Biol., 14, 2007
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6CFJ
| Crystal structure of the Thermus thermophilus 70S ribosome in complex with histidyl-CAM and bound to mRNA and A-, P-, and E-site tRNAs at 2.8A resolution | Descriptor: | 16S Ribosomal RNA, 23S Ribosomal RNA, 30S ribosomal protein S10, ... | Authors: | Tereshchenkov, A.G, Dobosz-Bartoszek, M, Osterman, I.A, Marks, J, Sergeeva, V.A, Kasatsky, P, Komarova, E.S, Stavrianidi, A.N, Rodin, I.A, Konevega, A.L, Sergiev, P.V, Sumbatyan, N.V, Mankin, A.S, Bogdanov, A.A, Polikanov, Y.S. | Deposit date: | 2018-02-15 | Release date: | 2018-03-07 | Last modified: | 2023-11-15 | Method: | X-RAY DIFFRACTION (2.8 Å) | Cite: | Binding and Action of Amino Acid Analogs of Chloramphenicol upon the Bacterial Ribosome. J. Mol. Biol., 430, 2018
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5VP2
| Crystal structure of the Thermus thermophilus 70S ribosome in complex with madumycin II and bound to mRNA and A-, P- and E-site tRNAs at 2.8A resolution | Descriptor: | 16S ribosomal RNA, 23S Ribosomal RNA, 30S ribosomal protein S10, ... | Authors: | Osterman, I.A, Khabibullina, N.F, Komarova, E.S, Kasatsky, P, Kartsev, V.G, Bogdanov, A.A, Dontsova, O.A, Konevega, A.L, Sergiev, P.V, Polikanov, Y.S. | Deposit date: | 2017-05-04 | Release date: | 2017-06-28 | Last modified: | 2024-04-24 | Method: | X-RAY DIFFRACTION (2.8 Å) | Cite: | Madumycin II inhibits peptide bond formation by forcing the peptidyl transferase center into an inactive state. Nucleic Acids Res., 45, 2017
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3T1Y
| Structure of the Thermus thermophilus 30S ribosomal subunit complexed with a human anti-codon stem loop (HASL) of transfer RNA Lysine 3 (TRNALYS3) bound to an mRNA with an AAG-codon in the A-site and paromomycin | Descriptor: | 16S rRNA, 30S ribosomal protein S10, 30S ribosomal protein S11, ... | Authors: | Murphy, F.V, Vendeix, F.A.P, Cantara, W, Leszczynska, G, Gustilo, E.M, Sproat, B, Malkiewicz, A.A.P, Agris, P.F. | Deposit date: | 2011-07-22 | Release date: | 2012-01-25 | Last modified: | 2023-09-13 | Method: | X-RAY DIFFRACTION (2.8 Å) | Cite: | Human tRNA(Lys3)(UUU) Is Pre-Structured by Natural Modifications for Cognate and Wobble Codon Binding through Keto-Enol Tautomerism. J.Mol.Biol., 416, 2012
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9B00
| Crystal structure of the wild-type Thermus thermophilus 70S ribosome in complex with berberine analog of chloramphenicol CAM-BER, mRNA, deacylated A- and E-site tRNAphe, and deacylated P-site tRNAmet at 2.80A resolution | Descriptor: | 13-(2-{[(1R,2R)-1,3-dihydroxy-1-(4-nitrophenyl)propan-2-yl]amino}-2-oxoethyl)-9,10-dimethoxy-5,6-dihydro-2H-[1,3]dioxolo[4,5-g]isoquinolino[3,2-a]isoquinolin-7-ium, 16S Ribosomal RNA, 23S Ribosomal RNA, ... | Authors: | Batool, Z, Pavlova, J.A, Paranjpe, M.N, Tereshchenkov, A.G, Lukianov, D.A, Osterman, I.A, Bogdanov, A.A, Sumbatyan, N.V, Polikanov, Y.S. | Deposit date: | 2024-03-11 | Release date: | 2024-08-07 | Last modified: | 2024-09-18 | Method: | X-RAY DIFFRACTION (2.8 Å) | Cite: | Berberine analog of chloramphenicol exhibits a distinct mode of action and unveils ribosome plasticity. Structure, 32, 2024
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6XQD
| Crystal structure of the Thermus thermophilus 70S ribosome in complex with sarecycline, UUC-mRNA, and deacylated P-site tRNA at 2.80A resolution | Descriptor: | 16S Ribosomal RNA, 23S Ribosomal RNA, 30S ribosomal protein S10, ... | Authors: | Batool, Z, Lomakin, I.B, Bunick, C.G, Polikanov, Y.S. | Deposit date: | 2020-07-09 | Release date: | 2020-08-05 | Last modified: | 2023-11-15 | Method: | X-RAY DIFFRACTION (2.8 Å) | Cite: | Sarecycline interferes with tRNA accommodation and tethers mRNA to the 70S ribosome. Proc.Natl.Acad.Sci.USA, 117, 2020
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6OF1
| Crystal structure of the Thermus thermophilus 70S ribosome in complex with dirithromycin and bound to mRNA and A-, P-, and E-site tRNAs at 2.80A resolution | Descriptor: | 16S Ribosomal RNA, 23S Ribosomal RNA, 30S ribosomal protein S10, ... | Authors: | Khabibullina, N.F, Tereshchenkov, A.G, Komarova, E.S, Syroegin, E.A, Shiriaev, D.I, Paleskava, A, Kartsev, V.G, Bogdanov, A.A, Konevega, A.L, Dontsova, O.A, Sergiev, P.V, Osterman, I.A, Polikanov, Y.S. | Deposit date: | 2019-03-28 | Release date: | 2019-04-17 | Last modified: | 2023-11-15 | Method: | X-RAY DIFFRACTION (2.8 Å) | Cite: | Structure of Dirithromycin Bound to the Bacterial Ribosome Suggests New Ways for Rational Improvement of Macrolides. Antimicrob.Agents Chemother., 63, 2019
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7MD7
| Crystal structure of the Thermus thermophilus 70S ribosome in complex with triphenylphosphonium analog of chloramphenicol CAM-C4-TPP and protein Y (YfiA) at 2.80A resolution | Descriptor: | (4S)-2-METHYL-2,4-PENTANEDIOL, 16S Ribosomal RNA, 23S Ribosomal RNA, ... | Authors: | Chen, C.-W, Pavlova, J.A, Lukianov, D.A, Tereshchenkov, A.G, Makarov, G.I, Khairullina, Z.Z, Tashlitsky, V.N, Paleskava, A, Konevega, A.L, Bogdanov, A.A, Osterman, I.A, Sumbatyan, N.V, Polikanov, Y.S. | Deposit date: | 2021-04-03 | Release date: | 2021-04-21 | Last modified: | 2023-11-15 | Method: | X-RAY DIFFRACTION (2.8 Å) | Cite: | Binding and Action of Triphenylphosphonium Analog of Chloramphenicol upon the Bacterial Ribosome. Antibiotics, 10, 2021
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6ND6
| Crystal structure of the Thermus thermophilus 70S ribosome in complex with erythromycin and bound to mRNA and A-, P-, and E-site tRNAs at 2.85A resolution | Descriptor: | 16S Ribosomal RNA, 23S Ribosomal RNA, 30S ribosomal protein S10, ... | Authors: | Svetlov, M.S, Plessa, E, Chen, C.-W, Bougas, A, Krokidis, M.G, Dinos, G.P, Polikanov, Y.S. | Deposit date: | 2018-12-13 | Release date: | 2019-02-20 | Last modified: | 2023-11-15 | Method: | X-RAY DIFFRACTION (2.85 Å) | Cite: | High-resolution crystal structures of ribosome-bound chloramphenicol and erythromycin provide the ultimate basis for their competition. RNA, 25, 2019
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8EV7
| Crystal structure of the Thermus thermophilus 70S ribosome in complex with kanamycin, mRNA, and A-, P-, and E-site tRNAs | Descriptor: | 16S Ribosomal RNA, 23S Ribosomal RNA, 30S ribosomal protein S10, ... | Authors: | Seely, S.M, Gagnon, M.G. | Deposit date: | 2022-10-19 | Release date: | 2023-08-09 | Last modified: | 2023-11-15 | Method: | X-RAY DIFFRACTION (2.89 Å) | Cite: | Molecular basis of the pleiotropic effects by the antibiotic amikacin on the ribosome. Nat Commun, 14, 2023
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2UUA
| Structure of the Thermus thermophilus 30S ribosomal subunit complexed with a Valine-ASL with cmo5U in position 34 bound to an mRNA with a GUC-codon in the A-site and paromomycin. | Descriptor: | 16S RRNA, 30S RIBOSOMAL PROTEIN S10, 30S RIBOSOMAL PROTEIN S11, ... | Authors: | Weixlbaumer, A, Murphy, F.V, Dziergowska, A, Malkiewicz, A, Vendeix, F.A.P, Agris, P.F, Ramakrishnan, V. | Deposit date: | 2007-03-01 | Release date: | 2007-05-15 | Last modified: | 2023-12-13 | Method: | X-RAY DIFFRACTION (2.9 Å) | Cite: | Mechanism for expanding the decoding capacity of transfer RNAs by modification of uridines. Nat. Struct. Mol. Biol., 14, 2007
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4B3M
| Crystal structure of the 30S ribosome in complex with compound 1 | Descriptor: | (1R,2R,3S,4R,6S)-4,6-diamino-2-{[3-O-(2,6-diamino-2,6-dideoxy-beta-L-idopyranosyl)-beta-D-ribofuranosyl]oxy}-3-hydroxycyclohexyl 2-amino-4,6-O-benzylidene-2-deoxy-alpha-D-glucopyranoside, 16S RIBOSOMAL RNA, 30S RIBOSOMAL PROTEIN S10, ... | Authors: | Ng, C.L, Lang, K, Shcherbakov, D, Matt, T, Perez-Fernandez, D, Patak, R, Meyer, M, Duscha, S, Akbergenov, R, Boukari, H, Freihofer, P, Kudyba, I, Reddy, M.S.K, Nandurikar, R.S, Ramakrishnan, V, Vasella, A, Bottger, E.C. | Deposit date: | 2012-07-25 | Release date: | 2013-08-07 | Last modified: | 2023-12-20 | Method: | X-RAY DIFFRACTION (2.9 Å) | Cite: | 4'-O-Substitutions Determine Selectivity of Aminoglycoside Antibiotics Nat.Commun., 5, 2014
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2VQF
| Modified uridines with C5-methylene substituents at the first position of the tRNA anticodon stabilize U-G wobble pairing during decoding | Descriptor: | 16S RRNA, 30S RIBOSOMAL PROTEIN S10, 30S RIBOSOMAL PROTEIN S11, ... | Authors: | Kurata, S, Weixlbaumer, A, Ohtsuki, T, Shimazaki, T, Wada, T, Kirino, Y, Takai, K, Watanabe, K, Ramakrishnan, V, Suzuki, T. | Deposit date: | 2008-03-14 | Release date: | 2008-04-29 | Last modified: | 2023-12-13 | Method: | X-RAY DIFFRACTION (2.9 Å) | Cite: | Modified Uridines with C5-Methylene Substituents at the First Position of the tRNA Anticodon Stabilize U.G Wobble Pairing During Decoding. J.Biol.Chem., 283, 2008
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2UXC
| Crystal structure of an extended tRNA anticodon stem loop in complex with its cognate mRNA UCGU in the context of the Thermus thermophilus 30S subunit. | Descriptor: | 16S RIBOSOMAL RNA, A-SITE MESSENGER RNA FRAGMENT CGGG, ANTICODON STEM-LOOP OF TRANSFER RNA WITH ANTICODON ACGA, ... | Authors: | Dunham, C.M, Selmer, M, Phelps, S.S, Kelley, A.C, Suzuki, T, Joseph, S, Ramakrishnan, V. | Deposit date: | 2007-03-28 | Release date: | 2007-05-08 | Last modified: | 2024-05-08 | Method: | X-RAY DIFFRACTION (2.9 Å) | Cite: | Structures of Trnas with an Expanded Anticodon Loop in the Decoding Center of the 30S Ribosomal Subunit. RNA, 13, 2007
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8EV6
| Crystal structure of the Thermus thermophilus 70S ribosome in complex with amikacin, mRNA, and A-, P-, and E-site tRNAs | Descriptor: | (2S)-N-[(1R,2S,3S,4R,5S)-4-[(2R,3R,4S,5S,6R)-6-(aminomethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-5-azanyl-2-[(2S,3R,4S,5S ,6R)-4-azanyl-6-(hydroxymethyl)-3,5-bis(oxidanyl)oxan-2-yl]oxy-3-oxidanyl-cyclohexyl]-4-azanyl-2-oxidanyl-butanamide, 16S Ribosomal RNA, 23S Ribosomal RNA, ... | Authors: | Seely, S.M, Gagnon, M.G. | Deposit date: | 2022-10-19 | Release date: | 2023-08-09 | Last modified: | 2023-11-15 | Method: | X-RAY DIFFRACTION (2.946 Å) | Cite: | Molecular basis of the pleiotropic effects by the antibiotic amikacin on the ribosome. Nat Commun, 14, 2023
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5E81
| Structure of T. thermophilus 70S ribosome complex with mRNA and tRNALys in the A-site with wobble pair | Descriptor: | 16S ribosomal RNA, 23S ribosomal RNA, 30S ribosomal protein S10, ... | Authors: | Rozov, A, Demeshkina, N, Khusainov, I, Yusupov, M, Yusupova, G. | Deposit date: | 2015-10-13 | Release date: | 2016-01-27 | Last modified: | 2024-01-10 | Method: | X-RAY DIFFRACTION (2.95 Å) | Cite: | Novel base-pairing interactions at the tRNA wobble position crucial for accurate reading of the genetic code. Nat Commun, 7, 2016
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5NDK
| Crystal structure of aminoglycoside TC007 co-crystallized with 70S ribosome from Thermus thermophilus, three tRNAs and mRNA | Descriptor: | 16S ribosomal RNA, 23S ribosomal RNA, 30S ribosomal protein S10, ... | Authors: | Prokhorova, I, Djumagulov, M, Urzhumtsev, A, Yusupov, M, Yusupova, G. | Deposit date: | 2017-03-08 | Release date: | 2017-12-13 | Last modified: | 2024-05-08 | Method: | X-RAY DIFFRACTION (2.95 Å) | Cite: | Aminoglycoside interactions and impacts on the eukaryotic ribosome. Proc. Natl. Acad. Sci. U.S.A., 114, 2017
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6UO1
| Crystal structure of the Thermus thermophilus 70S ribosome in complex with mRNA (containing pseudouridine at the first position of the codon) and deacylated A-, P-, and E-site tRNAs at 2.95A resolution | Descriptor: | 16S Ribosomal RNA, 23S Ribosomal RNA, 30S ribosomal protein S10, ... | Authors: | Batool, Z, Dobosz-Bartoszek, M, Polikanov, Y.S. | Deposit date: | 2019-10-14 | Release date: | 2019-11-27 | Last modified: | 2023-11-15 | Method: | X-RAY DIFFRACTION (2.95 Å) | Cite: | Pseudouridinylation of mRNA coding sequences alters translation. Proc.Natl.Acad.Sci.USA, 116, 2019
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6GSJ
| Structure of T. thermophilus 70S ribosome complex with mRNA, tRNAfMet and cognate tRNAThr in the A-site | Descriptor: | 16S ribosomal RNA, 23S ribosomal RNA, 30S ribosomal protein S10, ... | Authors: | Rozov, A, Yusupov, M, Yusupova, G. | Deposit date: | 2018-06-14 | Release date: | 2018-07-04 | Last modified: | 2024-01-17 | Method: | X-RAY DIFFRACTION (2.96 Å) | Cite: | Tautomeric G•U pairs within the molecular ribosomal grip and fidelity of decoding in bacteria. Nucleic Acids Res., 46, 2018
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4V67
| Crystal structure of a translation termination complex formed with release factor RF2. | Descriptor: | 16S RRNA, 23S RRNA, 30S ribosomal protein S10, ... | Authors: | Korostelev, A, Asahara, H, Lancaster, L, Laurberg, M, Hirschi, A, Noller, H.F. | Deposit date: | 2008-10-27 | Release date: | 2014-07-09 | Last modified: | 2023-09-20 | Method: | X-RAY DIFFRACTION (3 Å) | Cite: | Crystal structure of a translation termination complex formed with release factor RF2. Proc.Natl.Acad.Sci.USA, 105, 2008
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1N32
| Structure of the Thermus thermophilus 30S ribosomal subunit bound to codon and near-cognate transfer RNA anticodon stem-loop mismatched at the first codon position at the a site with paromomycin | Descriptor: | 16S RIBOSOMAL RNA, 30S RIBOSOMAL PROTEIN S10, 30S RIBOSOMAL PROTEIN S11, ... | Authors: | Ogle, J.M, Murphy IV, F.V, Tarry, M.J, Ramakrishnan, V. | Deposit date: | 2002-10-25 | Release date: | 2002-11-29 | Last modified: | 2019-11-20 | Method: | X-RAY DIFFRACTION (3 Å) | Cite: | Selection of tRNA by the Ribosome Requires a Transition from an Open to a Closed Form Cell(Cambridge,Mass.), 111, 2002
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4B3R
| Crystal structure of the 30S ribosome in complex with compound 30 | Descriptor: | (1R,2R,3S,4R,6S)-4,6-diamino-2-{[3-O-(2,6-diamino-2,6-dideoxy-beta-L-idopyranosyl)-beta-D-ribofuranosyl]oxy}-3-hydroxycyclohexyl 2-amino-2-deoxy-4,6-O-[(1R)-3-phenylpropylidene]-alpha-D-glucopyranoside, 16S RIBOSOMAL RNA, 30S RIBOSOMAL PROTEIN S10, ... | Authors: | Ng, C.L, Lang, K, Shcherbakov, D, Matt, T, Perez-Fernandez, D, Patak, R, Meyer, M, Duscha, S, Akbergenov, R, Boukari, H, Freihofer, P, Kudyba, I, Reddy, M.S.K, Nandurikar, R.S, Ramakrishnan, V, Vasella, A, Bottger, E.C. | Deposit date: | 2012-07-26 | Release date: | 2013-08-07 | Last modified: | 2023-12-20 | Method: | X-RAY DIFFRACTION (3 Å) | Cite: | 4'-O-Substitutions Determine Selectivity of Aminoglycoside Antibiotics Nat.Commun., 5, 2014
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4B3T
| Crystal structure of the 30S ribosome in complex with compound 39 | Descriptor: | (2S,3S,4R,5R,6R)-2-(aminomethyl)-5-azanyl-6-[(2R,3S,4R,5S)-5-[(1R,2R,3S,5R,6S)-3,5-bis(azanyl)-2-[(2S,3R,4R,5S,6R)-3-azanyl-5-[(4-chlorophenyl)methoxy]-6-(hydroxymethyl)-4-oxidanyl-oxan-2-yl]oxy-6-oxidanyl-cyclohexyl]oxy-2-(hydroxymethyl)-4-oxidanyl-oxolan-3-yl]oxy-oxane-3,4-diol, 16S RIBOSOMAL RNA, 30S RIBOSOMAL PROTEIN S10, ... | Authors: | Ng, C.L, Lang, K, Shcherbakov, D, Matt, T, Perez-Fernandez, D, Patak, R, Meyer, M, Duscha, S, Akbergenov, R, Boukari, H, Freihofer, P, Kudyba, I, Reddy, M.S.K, Nandurikar, R.S, Ramakrishnan, V, Vasella, A, Bottger, E.C. | Deposit date: | 2012-07-26 | Release date: | 2013-08-07 | Last modified: | 2023-12-20 | Method: | X-RAY DIFFRACTION (3 Å) | Cite: | 4'-O-Substitutions Determine Selectivity of Aminoglycoside Antibiotics Nat.Commun., 5, 2014
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