Crystal structure of kasugamycin bound to the 30S ribosomal subunit

(1S,2R,3S,4R,5S,6S)-2,3,4,5,6-PENTAHYDROXYCYCLOHEXYL 2-AMINO-4-{[CARBOXY(IMINO)METHYL]AMINO}-2,3,4,6-TETRADEOXY-ALPHA-D-ARABINO-HEXOPYRANOSIDE

The antibiotic kasugamycin mimics mRNA nucleotides to destabilize tRNA binding and inhibit canonical translation initiation.

UUUGUUGGAGAGUUUGAUCCUGGCUCAGGGUGAACGCUGGCGGCGUGCCUAAGACAUGCAAGUCGUGCGGGCCGCGGGGU
UUUACUCCGUGGUCAGCGGCGGACGGGUGAGUAACGCGUGGGUGACCUACCCGGAAGAGGGGGACAACCCGGGGAAACUC
GGGCUAAUCCCCCAUGUGGACCCGCCCCUUGGGGUGUGUCCAAAGGGCUUUGCCCGCUUCCGGAUGGGCCCGCGUCCCAU
CAGCUAGUUGGUGGGGUAAUGGCCCACCAAGGCGACGACGGGUAGCCGGUCUGAGAGGAUGGCCGGCCACAGGGGCACUG
AGACACGGGCCCCACUCCUACGGGAGGCAGCAGUUAGGAAUCUUCCGCAAUGGGCGCAAGCCUGACGGAGCGACGCCGCU
UGGAGGAAGAAGCCCUUCGGGGUGUAAACUCCUGAACCCGGGACGAAACCCCCGACGAGGGGACUGACGGUACCGGGGUA
AUAGCGCCGGCCAACUCCGUGCCAGCAGCCGCGGUAAUACGGAGGGCGCGAGCGUUACCCGGAUUCACUGGGCGUAAAGG
GCGUGUAGGCGGCCUGGGGCGUCCCAUGUGAAAGACCACGGCUCAACCGUGGGGGAGCGUGGGAUACGCUCAGGCUAGAC
GGUGGGAGAGGGUGGUGGAAUUCCCGGAGUAGCGGUGAAAUGCGCAGAUACCGGGAGGAACGCCGAUGGCGAAGGCAGCC
ACCUGGUCCACCCGUGACGCUGAGGCGCGAAAGCGUGGGGAGCAAACCGGAUUAGAUACCCGGGUAGUCCACGCCCUAAA
CGAUGCGCGCUAGGUCUCUGGGUCUCCUGGGGGCCGAAGCUAACGCGUUAAGCGCGCCGCCUGGGGAGUACGGCCGCAAG
GCUGAAACUCAAAGGAAUUGACGGGGGCCCGCACAAGCGGUGGAGCAUGUGGUUUAAUUCGAAGCAACGCGAAGAACCUU
ACCAGGCCUUGACAUGCUAGGGAACCCGGGUGAAAGCCUGGGGUGCCCCGCGAGGGGAGCCCUAGCACAGGUGCUGCAUG
GCCGUCGUCAGCUCGUGCCGUGAGGUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCCCGCCGUUAGUUGCCAGCGGUUC
GGCCGGGCACUCUAACGGGACUGCCCGCGAAAGCGGGAGGAAGGAGGGGACGACGUCUGGUCAGCAUGGCCCUUACGGCC
UGGGCGACACACGUGCUACAAUGCCCACUACAAAGCGAUGCCACCCGGCAACGGGGAGCUAAUCGCAAAAAGGUGGGCCC
AGUUCGGAUUGGGGUCUGCAACCCGACCCCAUGAAGCCGGAAUCGCUAGUAAUCGCGGAUCAGCCAUGCCGCGGUGAAUA
CGUUCCCGGGCCUUGUACACACCGCCCGUCACGCCAUGGGAGCGGGCUCUACCCGAAGUCGCCGGGAGCCUACGGGCAGG
CGCCGAGGGUAGGGCCCGUGACUGGGGCGAAGUCGUAACAAGGUAGCUGUACCGGAAGGUGCGGCUGGAUCACCUCCUUU
CU

MPVEITVKELLEAGVHFGHERKRWNPKFARYIYAERNGIHIIDLQKTMEELERTFRFIEDLAMRGGTILFVGTKKQAQDI
VRMEAERAGMPYVNQRWLGGMLTNFKTISQRVHRLEELEALFASPEIEERPKKEQVRLKHELERLQKYLSGFRLLKRLPD
AIFVVDPTKEAIAVREARKLFIPVIALADTDSDPDLVDYIIPGNDDAIRSIQLILSRAVDLIIQARGGVVEPSPSYALVQ
EAEATETPEGESEVEA

MGNKIHPIGFRLGITRDWESRWYAGKKQYRHLLLEDQRIRGLLEKELYSAGLARVDIERAADNVAVTVHVAKPGVVIGRG
GERIRVLREELAKLTGKNVALNVQEVQNPNLSAPLVAQRVAEQIERRFAVRRAIKQAVQRVMESGAKGAKVIVSGRIGGA
EQARTEWAAQGRVPLHTLRANIDYGFALARTTYGVLGVKAYIFLGEVIGGQKPKARPELPKAEERPRRRRPAVRVKKEE

MGRYIGPVCRLCRREGVKLYLKGERCYSPKCAMERRPYPPGQHGQKRARRPSDYAVRLREKQKLRRIYGISERQFRNLFE
EASKKKGVTGSVFLGLLESRLDNVVYRLGFAVSRRQARQLVRHGHITVNGRRVDLPSYRVRPGDEIAVAEKSRNLELIRQ
NLEAMKGRKVGPWLSLDVEGMKGKFLRLPDREDLALPVNEQLVIEFYSR

MPETDFEEKMILIRRTARMQAGGRRFRFGALVVVGDRQGRVGLGFGKAPEVPLAVQKAGYYARRNMVEVPLQNGTIPHEI
EVEFGASKIVLKPAAPGTGVIAGAVPRAILELAGVTDILTKELGSRNPINIAYATMEALRQLRTKADVERLRKGEAHAQA
QG

MRRYEVNIVLNPNLDQSQLALEKEIIQRALENYGARVEKVEELGLRRLAYPIAKDPQGYFLWYQVEMPEDRVNDLARELR
IRDNVRRVMVVKSQEPFLANA

MARRRRAEVRQLQPDLVYGDVLVTAFINKIMRDGKKNLAARIFYDACKIIQEKTGQEPLKVFKQAVENVKPRMEVRSRRV
GGANYQVPMEVSPRRQQSLALRWLVQAANQRPERRAAVRIAHELMDAAEGKGGAVKKKEDVERMAEANRAYAHYRW

MLTDPIADMLTRIRNATRVYKESTDVPASRFKEEILRILAREGFIKGYERVDVDGKPYLRVYLKYGPRRQGPDPRPEQVI
HHIRRISKPGRRVYVGVKEIPRVRRGLGIAILSTSKGVLTDREARKLGVGGELICEVW

MEQYYGTGRRKEAVARVFLRPGNGKVTVNGQDFNEYFQGLVRAVAALEPLRAVDALGRFDAYITVRGGGKSGQIDAIKLG
IARALVQYNPDYRAKLKPLGFLTRDARVVERKKYGKHKARRAPQYSKR

MPKIRIKLRGFDHKTLDASAQKIVEAARRSGAQVSGPIPLPTRVRRFTVIRGPFKHKDSREHFELRTHNRLVDIINPNRK
TIEQLMTLDLPTGVEIEIKTVGGGR

MAKKPSKKKVKRQVASGRAYIHASYNNTIVTITDPDGNPITWSSGGVIGYKGSRKGTPYAAQLAALDAAKKAMAYGMQSV
DVIVRGTGAGREQAIRALQASGLQVKSIVDDTPVPHNGCRPKKKFRKAS

MVALPTINQLVRKGREKVRKKSKVPALKGAPFRRGVCTVVRTVTPKKPNSALRKVAKVRLTSGYEVTAYIPGEGHNLQEH
SVVLIRGGRVKDLPGVRYHIVRGVYDAAGVKDRKKSRSKYGTKKPKEAAKTAAKK

MARIAGVEIPRNKRVDVALTYIYGIGKARAKEALEKTGINPATRVKDLTEAEVVRLREYVENTWKLEGELRAEVAANIKR
LMDIGCYRGLRHRRGLPVRGQRTRTNARTRKGPRKTVAGKKKAPRK

MPITKEEKQKVIQEFARFPGDTGSTEVQVALLTLRINRLSEHLKVHKKDHHSHRGLLMMVGQRRRLLRYLQREDPERYRA
LIEKLGIRG

MVKIRLARFGSKHNPHYRIVVTDARRKRDGKYIEKIGYYDPRKTTPDWLKVDVERARYWLSVGAQPTDTARRLLRQAGVF
RQEAREGA

MPKKVLTGVVVSDKMQKTVTVLVERQFPHPLYGKVIKRSKKYLAHDPEEKYKLGDVVEIIESRPISKRKRFRVLRLVESG
RMDLVEKYLIRRQNYQSLSKRGGKA

MSTKNAKPKKEAQRRPSRKAKVKATLGEFDLRDYRNVEVLKRFLSETGKILPRRRTGLSGKEQRILAKTIKRARILGLLP
FTEKLVRK

MPRSLKKGVFVDDHLLEKVLELNAKGEKRLIKTWSRRSTIVPEMVGHTIAVYNGKQHVPVYITENMVGHKLGEFAPTRTY
RGHGKEAKATKKK

MAQKKPKRNLSALKRHRQSLKRRLRNKAKKSAIKTLSKKAIQLAQEGKAEEALKIMRKAESLIDKAAKGSTLHKNAAARR
KSRLMRKVRQLLEAAGAPLIGGGLSA

MPD, MAGNESIUM CHLORIDE, POTASSIUM CHLORIDE, AMMONIUM CHLORIDE, MES-KOH, pH 6.50, VAPOR DIFFUSION, HANGING DROP, temperature 300K

MEQYYGTGRRKEAVARVFLRPGNGKVTVNGQDFNEYFQGLVRAVAALEPLRAVDALGHFDAYITVRGGGKSGQIDAIKLG
IARALVQYNPDYRAKLKPLGFLTRDARVVERKKYGKHKARRAPQYSKR

MPTINQLVRKGREKVRKKSKVPALKGAPFRRGVCTVVRTVTPKKPNSALRKVAKVRLTSGYEVTAYIPGEGHNLQEHSVV
LIRGGRVKDLPGVRYHIVRGVYDAAGVKDRKKSRSKYGTKKPKEAAKTAAKK