{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,6]],"date-time":"2026-05-06T20:06:20Z","timestamp":1778097980900,"version":"3.51.4"},"publisher-location":"New York, NY","reference-count":43,"publisher":"Springer New York","isbn-type":[{"value":"9781493927623","type":"print"},{"value":"9781493927630","type":"electronic"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2016]]},"DOI":"10.1007\/978-1-4939-2763-0_20","type":"book-chapter","created":{"date-parts":[[2015,7,30]],"date-time":"2015-07-30T09:40:44Z","timestamp":1438249244000},"page":"315-327","source":"Crossref","is-referenced-by-count":5,"title":["Crystallographic Studies of the Ribosomal A-Site Molecular Switches by Using Model RNA Oligomers"],"prefix":"10.1007","author":[{"given":"Jiro","family":"Kondo","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","reference":[{"key":"20_CR1","doi-asserted-by":"publisher","first-page":"897","DOI":"10.1126\/science.1060612","volume":"292","author":"JM Ogle","year":"2001","unstructured":"Ogle JM, Brodersen DE, Clemons WM Jr, Tarry MJ, Carter AP, Ramakrishnan V (2001) Recognition of cognate transfer RNA by the 30S ribosomal subunit. Science 292:897\u2013902","journal-title":"Science"},{"key":"20_CR2","doi-asserted-by":"publisher","first-page":"259","DOI":"10.1016\/S0968-0004(03)00066-5","volume":"28","author":"JM Ogle","year":"2003","unstructured":"Ogle JM, Carter AP, Ramakrishnan V (2003) Insights into the decoding mechanism from recent ribosome structures. Trends Biochem Sci 28:259\u2013266","journal-title":"Trends Biochem Sci"},{"key":"20_CR3","doi-asserted-by":"publisher","first-page":"721","DOI":"10.1016\/S0092-8674(02)01086-3","volume":"111","author":"JM Ogle","year":"2002","unstructured":"Ogle JM, Murphy FV, Tarry MJ, Ramakrishnan V (2002) Selection of tRNA by the ribosome requires a transition from an open to a closed form. Cell 111:721\u2013732","journal-title":"Cell"},{"key":"20_CR4","doi-asserted-by":"publisher","first-page":"129","DOI":"10.1146\/annurev.biochem.74.061903.155440","volume":"74","author":"JM Ogle","year":"2005","unstructured":"Ogle JM, Ramakrishnan V (2005) Structural insights into translational fidelity. Annu Rev Biochem 74:129\u2013177","journal-title":"Annu Rev Biochem"},{"key":"20_CR5","doi-asserted-by":"crossref","first-page":"209","DOI":"10.1002\/9780470149676.ch6","volume-title":"Aminoglycoside antibiotics from chemical biology to drug discovery","author":"J Kondo","year":"2007","unstructured":"Kondo J, Westhof E (2007) Structural comparisons between prokaryotic and eukaryotic ribosomal decoding A sites free and complexed with aminoglycosides. In: Arya DP (ed) Aminoglycoside antibiotics from chemical biology to drug discovery. Wiley-Interscience, Hoboken, NJ, pp 209\u2013223"},{"key":"20_CR6","doi-asserted-by":"publisher","first-page":"340","DOI":"10.1038\/35030019","volume":"407","author":"AP Carter","year":"2000","unstructured":"Carter AP, Clemons WM, Brodersen DE, Morgan-Warren RJ, Wimberly BT, Ramakrishnan V (2000) Functional insights from the structure of the 30S ribosomal subunit and its interactions with antibiotics. Nature 407:340\u2013348","journal-title":"Nature"},{"key":"20_CR7","doi-asserted-by":"publisher","first-page":"579","DOI":"10.1128\/AAC.6.5.579","volume":"6","author":"JA Waitz","year":"1974","unstructured":"Waitz JA, Sabatelli F, Menzel F, Moss EL Jr (1974) Biological activity of antibiotic G-418, a new micromonospora-produced aminoglycoside with activity against protozoa and helminths. Antimicrob Agents Chemother 6:579\u2013581","journal-title":"Antimicrob Agents Chemother"},{"key":"20_CR8","doi-asserted-by":"publisher","first-page":"811","DOI":"10.1128\/AAC.7.6.811","volume":"7","author":"D Loebenberg","year":"1975","unstructured":"Loebenberg D, Counelis M, Waitz JA (1975) Antibiotic G-418, a new micromonospora-produced aminoglycoside with activity against protozoa and helminths: antiparasitic activity. Antimicrob Agents Chemother 7:811\u2013815","journal-title":"Antimicrob Agents Chemother"},{"key":"20_CR9","doi-asserted-by":"publisher","first-page":"156","DOI":"10.1016\/j.exppara.2006.12.004","volume":"116","author":"J El-On","year":"2007","unstructured":"El-On J, Bazarsky E, Sneir R (2007) Leishmania major: in vitro and in vivo anti-leishmanial activity of paromomycin ointment (Leshcutan) combined with the immunomodulator Imiquimod. Exp Parasitol 116:156\u2013162","journal-title":"Exp Parasitol"},{"key":"20_CR10","doi-asserted-by":"publisher","first-page":"6086","DOI":"10.1093\/nar\/gkm658","volume":"35","author":"SN Hobbie","year":"2007","unstructured":"Hobbie SN, Kalapala SK, Akshay S, Bruell C, Schmidt S, Dabow S, Vasella A, Sander P, B\u00f6ttger EC (2007) Engineering the rRNA decoding site of eukaryotic cytosolic ribosomes in bacteria. Nucleic Acids Res 35:6086\u20136093","journal-title":"Nucleic Acids Res"},{"key":"20_CR11","doi-asserted-by":"publisher","first-page":"20888","DOI":"10.1073\/pnas.0811258106","volume":"105","author":"SN Hobbie","year":"2008","unstructured":"Hobbie SN, Akshay S, Kalapala SK, Bruell CM, Shcherbakov D, B\u00f6ttger EC (2008) Genetic analysis of interactions with eukaryotic rRNA identify the mitoribosome as target in aminoglycoside ototoxicity. Proc Natl Acad Sci U S A 105:20888\u201320893","journal-title":"Proc Natl Acad Sci U S A"},{"key":"20_CR12","doi-asserted-by":"publisher","first-page":"91","DOI":"10.1016\/j.tox.2008.04.015","volume":"249","author":"OW Guthrie","year":"2008","unstructured":"Guthrie OW (2008) Aminoglycoside induced ototoxicity. Toxicology 249:91\u201396","journal-title":"Toxicology"},{"key":"20_CR13","doi-asserted-by":"publisher","first-page":"647","DOI":"10.1016\/S0969-2126(01)00629-3","volume":"9","author":"Q Vicens","year":"2001","unstructured":"Vicens Q, Westhof E (2001) Crystal structure of paromomycin docked into the eubacterial ribosomal decoding a site. Structure 9:647\u2013658","journal-title":"Structure"},{"key":"20_CR14","doi-asserted-by":"publisher","first-page":"747","DOI":"10.1016\/S1074-5521(02)00153-9","volume":"9","author":"Q Vicens","year":"2002","unstructured":"Vicens Q, Westhof E (2002) Crystal structure of a complex between the aminoglycoside tobramycin and an oligonucleotide containing the ribosomal decoding a site. Chem Biol 9:747\u2013755","journal-title":"Chem Biol"},{"key":"20_CR15","doi-asserted-by":"publisher","first-page":"1175","DOI":"10.1016\/S0022-2836(02)01435-3","volume":"326","author":"Q Vicens","year":"2003","unstructured":"Vicens Q, Westhof E (2003) Crystal structure of geneticin bound to a bacterial 16S ribosomal RNA A site oligonucleotide. J Mol Biol 326:1175\u20131188","journal-title":"J Mol Biol"},{"key":"20_CR16","doi-asserted-by":"publisher","first-page":"6735","DOI":"10.1002\/anie.200462092","volume":"43","author":"B Fran\u00e7ois","year":"2004","unstructured":"Fran\u00e7ois B, Szychowski J, Adhikari SS, Pachamuthu K, Swayze EE, Griffey RH, Migawa MT, Westhof E, Hanessian S (2004) Antibacterial aminoglycosides with a modified mode of binding to the ribosomal-RNA decoding site. Angew Chem Int Ed Engl 43:6735\u20136738","journal-title":"Angew Chem Int Ed Engl"},{"key":"20_CR17","doi-asserted-by":"publisher","first-page":"5677","DOI":"10.1093\/nar\/gki862","volume":"33","author":"B Fran\u00e7ois","year":"2005","unstructured":"Fran\u00e7ois B, Russell RJM, Murray JB, Aboul-ela F, Masquida B, Vicens Q, Westhof E (2005) Crystal structures of complexes between aminoglycosides and decoding A site oligonucleotides: role of the number of rings and positive charges in the specific binding leading to miscoding. Nucleic Acids Res 33:5677\u20135690","journal-title":"Nucleic Acids Res"},{"key":"20_CR18","doi-asserted-by":"publisher","first-page":"1027","DOI":"10.1016\/j.biochi.2006.05.017","volume":"88","author":"J Kondo","year":"2006","unstructured":"Kondo J, Fran\u00e7ois B, Russell RJ, Murray JB, Westhof E (2006) Crystal structure of the bacterial ribosomal decoding site complexed with amikacin containing the \u03b3-amino-\u03b1-hydroxybutyryl (haba) group. Biochimie 88:1027\u20131031","journal-title":"Biochimie"},{"key":"20_CR19","doi-asserted-by":"publisher","first-page":"2352","DOI":"10.1021\/jm061200+","volume":"50","author":"S Hanessian","year":"2007","unstructured":"Hanessian S, Szychowski J, Adhikari SS, Vasquez G, Kandasamy P, Swayze EE, Migawa MT, Ranken R, Fran\u00e7ois B, Wirmer-Bartoschek J, Kondo J, Westhof E (2007) Structure-based design, synthesis, and A-site rRNA cocrystal complexes of functionally novel aminoglycoside antibiotics: C2\u2033 ether analogues of paromomycin. J Med Chem 50:2352\u20132369","journal-title":"J Med Chem"},{"key":"20_CR20","doi-asserted-by":"publisher","first-page":"1631","DOI":"10.1002\/cmdc.200700113","volume":"2","author":"J Kondo","year":"2007","unstructured":"Kondo J, Pachamuthu K, Fran\u00e7ois B, Szychowski J, Hanessian S, Westhof E (2007) Crystal structure of the bacterial ribosomal decoding site complexed with a synthetic doubly functionalized paromomycin derivative: a new specific binding mode to an a-minor motif enhances in vitro antibacterial activity. Chem Med Chem 2:1631\u20131638","journal-title":"Chem Med Chem"},{"key":"20_CR21","doi-asserted-by":"publisher","first-page":"7097","DOI":"10.1016\/j.bmcl.2010.09.084","volume":"20","author":"S Hanessian","year":"2010","unstructured":"Hanessian S, Pachamuthu K, Szychowski J, Gigu\u00e8re A, Swayze EE, Migawa MT, Fran\u00e7ois B, Kondo J, Westhof E (2010) Structure-based design, synthesis and A-site rRNA co-crystal complexes of novel amphiphilic aminoglycoside antibiotics with new binding modes: a synergistic hydrophobic effect against resistant bacteria. Bioorg Med Chem Lett 20:7097\u20137101","journal-title":"Bioorg Med Chem Lett"},{"key":"20_CR22","doi-asserted-by":"publisher","first-page":"1961","DOI":"10.1002\/cmdc.201100346","volume":"6","author":"J Szychowski","year":"2011","unstructured":"Szychowski J, Kondo J, Zahr O, Auclair K, Westhof E, Hanessian S, Keillor JW (2011) Inhibition of aminoglycoside-deactivating enzymes APH(3\u2032)-IIIa and AAC(6\u2032)-Ii by amphiphilic paromomycin O2\u2033-ether analogues. Chem Med Chem 6:1961\u20131966","journal-title":"Chem Med Chem"},{"key":"20_CR23","doi-asserted-by":"publisher","first-page":"741","DOI":"10.1021\/ml300145y","volume":"3","author":"J Kondo","year":"2012","unstructured":"Kondo J, Koganei M, Kasahara T (2012) Crystal structure and specific binding mode of sisomicin to the bacterial ribosomal decoding site. ACS Med Chem Lett 3:741\u2013744","journal-title":"ACS Med Chem Lett"},{"key":"20_CR24","doi-asserted-by":"publisher","first-page":"676","DOI":"10.1093\/nar\/gkj467","volume":"34","author":"J Kondo","year":"2006","unstructured":"Kondo J, Urzhumtsev A, Westhof E (2006) Two conformational states in the crystal structure of the Homo sapiens cytoplasmic ribosomal decoding a site. Nucleic Acids Res 34:676\u2013685","journal-title":"Nucleic Acids Res"},{"key":"20_CR25","doi-asserted-by":"publisher","first-page":"3310","DOI":"10.1002\/anie.200600354","volume":"45","author":"J Kondo","year":"2006","unstructured":"Kondo J, Fran\u00e7ois B, Urzhumtsev A, Westhof E (2006) Crystal structure of the Homo sapiens cytoplasmic ribosomal decoding site complexed with apramycin. Angew Chem Int Ed Engl 45:3310\u20133314","journal-title":"Angew Chem Int Ed Engl"},{"key":"20_CR26","doi-asserted-by":"publisher","first-page":"1700","DOI":"10.1002\/cbic.200700271","volume":"8","author":"J Kondo","year":"2007","unstructured":"Kondo J, Hainrichson M, Nudelman I, Shallom-Shezifi D, Barbieri CM, Pilch DS, Westhof E, Baasov T (2007) Differential selectivity of natural and synthetic aminoglycosides towards the eukaryotic and prokaryotic decoding A sites. Chembiochem 8:1700\u20131709","journal-title":"Chembiochem"},{"key":"20_CR27","doi-asserted-by":"publisher","first-page":"465","DOI":"10.1002\/anie.201106084","volume":"51","author":"J Kondo","year":"2012","unstructured":"Kondo J (2012) A structural basis for the antibiotic resistance conferred by an A1408G mutation in 16S rRNA and for the antiprotozoal activity of aminoglycosides. Angew Chem Int Ed Engl 51:465\u2013468","journal-title":"Angew Chem Int Ed Engl"},{"key":"20_CR28","doi-asserted-by":"publisher","first-page":"733","DOI":"10.1002\/cmdc.201200579","volume":"8","author":"J Kondo","year":"2013","unstructured":"Kondo J, Koganei M, Maianti JP, Ly VL, Hanessian S (2013) Crystal structures of a bioactive 6\u2032-hydroxy variant of sisomicin bound to the bacterial and protozoal ribosomal decoding sites. ChemMedChem 8:733\u2013739","journal-title":"ChemMedChem"},{"issue":"33","key":"20_CR29","doi-asserted-by":"crossref","first-page":"13333","DOI":"10.1073\/pnas.1307365110","volume":"110","author":"M. Shalev","year":"2013","unstructured":"Shalev M, Kondo J, Kopelyanskiy D, Jaffe CL, Noam A, Baasov T (2013) Identification of the molecular attributes required for aminoglycoside activity against Leishmania. Proc Natl Acad Sci USA 110:13333\u201313338","journal-title":"Proceedings of the National Academy of Sciences"},{"key":"20_CR30","doi-asserted-by":"publisher","first-page":"389","DOI":"10.1038\/327389a0","volume":"327","author":"D Moazed","year":"1987","unstructured":"Moazed D, Noller HF (1987) Interaction of antibiotics with functional sites in 16S ribosomal RNA. Nature 327:389\u2013394","journal-title":"Nature"},{"key":"20_CR31","doi-asserted-by":"publisher","first-page":"659","DOI":"10.1038\/370659a0","volume":"370","author":"P Purohit","year":"1994","unstructured":"Purohit P, Stern S (1994) Interactions of a small RNA with antibiotic and RNA ligands of the 30S subunit. Nature 370:659\u2013662","journal-title":"Nature"},{"key":"20_CR32","doi-asserted-by":"publisher","first-page":"12577","DOI":"10.1021\/bi9904508","volume":"38","author":"AC Anderson","year":"1999","unstructured":"Anderson AC, O\u2019Neil RH, Filman DJ, Frederick CA (1999) Crystal structure of a brominated RNA helix with four mismatched base pairs: an investigation into RNA conformational variability. Biochemistry 38:12577\u201312585","journal-title":"Biochemistry"},{"key":"20_CR33","doi-asserted-by":"publisher","first-page":"1262","DOI":"10.1107\/S0907444902009526","volume":"58","author":"E Ennifar","year":"2002","unstructured":"Ennifar E, Carpentier P, Ferrer JL, Walter P, Dumas P (2002) X-ray-induced debromination of nucleic acids at the Br K absorption edge and implications for MAD phasing. Acta Crystallogr D Biol Crystallogr 58:1262\u20131268","journal-title":"Acta Crystallogr D Biol Crystallogr"},{"key":"20_CR34","doi-asserted-by":"publisher","first-page":"24","DOI":"10.1021\/ja0171097","volume":"124","author":"Q Du","year":"2002","unstructured":"Du Q, Carrasco N, Teplova M, Wilds CJ, Egli M, Huang Z (2002) Internal derivatization of oligonucleotides with selenium for X-ray crystallography using MAD. J Am Chem Soc 124:24\u201325","journal-title":"J Am Chem Soc"},{"key":"20_CR35","doi-asserted-by":"publisher","first-page":"707","DOI":"10.1261\/rna.1499309","volume":"15","author":"V Olieric","year":"2009","unstructured":"Olieric V, Rieder U, Lang K, Serganov A, Schulze-Briese C, Micura R, Dumas P, Ennifar E (2009) A fast selenium derivatization strategy for crystallization and phasing of RNA structures. RNA 15:707\u2013715","journal-title":"RNA"},{"key":"20_CR36","doi-asserted-by":"publisher","first-page":"1221","DOI":"10.1016\/S0969-2126(96)00129-3","volume":"4","author":"JH Cate","year":"1996","unstructured":"Cate JH, Doudna JA (1996) Metal-binding sites in the major groove of a large ribozyme domain. Structure 4:1221\u20131229","journal-title":"Structure"},{"key":"20_CR37","doi-asserted-by":"publisher","first-page":"761","DOI":"10.1016\/j.str.2007.06.003","volume":"15","author":"AY Keel","year":"2007","unstructured":"Keel AY, Rambo RP, Batey RT, Kieft JS (2007) A general strategy to solve the phase problem in RNA crystallography. Structure 15: 761\u2013772","journal-title":"Structure"},{"key":"20_CR38","doi-asserted-by":"publisher","first-page":"738","DOI":"10.1107\/S0907444908011578","volume":"64","author":"MP Robertson","year":"2008","unstructured":"Robertson MP, Scott WG (2008) A general method for phasing novel complex RNA crystal structures without heavy-atom derivatives. Acta Crystallogr D Biol Crystallogr 64:738\u2013744","journal-title":"Acta Crystallogr D Biol Crystallogr"},{"key":"20_CR39","doi-asserted-by":"publisher","first-page":"1078","DOI":"10.1107\/S090744490802595X","volume":"64","author":"J Kondo","year":"2008","unstructured":"Kondo J, Urzhumtseva L, Urzhumtsev A (2008) Patterson-guided ab initio analysis of structures with helical symmetry. Acta Crystallogr D Biol Crystallogr 64:1078\u20131091","journal-title":"Acta Crystallogr D Biol Crystallogr"},{"key":"20_CR40","doi-asserted-by":"publisher","first-page":"168","DOI":"10.1016\/j.ymeth.2010.06.011","volume":"52","author":"MP Robertson","year":"2010","unstructured":"Robertson MP, Chi YI, Scott WG (2010) Solving novel RNA structures using only secondary structural fragments. Methods 52:168\u2013172","journal-title":"Methods"},{"issue":"3","key":"20_CR41","doi-asserted-by":"crossref","first-page":"465","DOI":"10.1107\/S0907444995013564","volume":"52","author":"I. Berger","year":"1996","unstructured":"Berger I, Kang CH, Sinha N, Wolters M, Rich A (1996) A highly effic ient 24-condition matrix for the crystallization of nucleic acid fragments. Acta Crystallogr D Biol Crystallogr 52:465\u2013468","journal-title":"Acta Crystallographica Section D Biological Crystallography"},{"key":"20_CR42","first-page":"767","volume":"54","author":"MC Vaney","year":"2001","unstructured":"Vaney MC, Broutin I, Retailleau P, Douangamath A, Lafont S, Hamiaux C, Prang\u00e9 T, Ducruix A, Ri\u00e8s-Kautt M (2001) Structural effects of monovalent anions on polymorphic lysozyme crystals. Acta Crystallogr D Biol Crystallogr 54:767\u2013780","journal-title":"Acta Crystallogr D Biol Crystallogr"},{"key":"20_CR43","doi-asserted-by":"publisher","first-page":"349","DOI":"10.1107\/S0907444906000825","volume":"62","author":"C Brinkmann","year":"2006","unstructured":"Brinkmann C, Weiss MS, Weckert E (2006) The structure of the hexagonal crystal form of hen egg-white lysozyme. Acta Crystallogr D Biol Crystallogr 62:349\u2013355","journal-title":"Acta Crystallogr D Biol Crystallogr"}],"container-title":["Methods in Molecular Biology","Nucleic Acid Crystallography"],"original-title":[],"link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1007\/978-1-4939-2763-0_20","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2020,9,6]],"date-time":"2020-09-06T17:35:18Z","timestamp":1599413718000},"score":1,"resource":{"primary":{"URL":"http:\/\/link.springer.com\/10.1007\/978-1-4939-2763-0_20"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2016]]},"ISBN":["9781493927623","9781493927630"],"references-count":43,"URL":"https:\/\/doi.org\/10.1007\/978-1-4939-2763-0_20","relation":{},"ISSN":["1064-3745","1940-6029"],"issn-type":[{"value":"1064-3745","type":"print"},{"value":"1940-6029","type":"electronic"}],"subject":[],"published":{"date-parts":[[2016]]}}}