2020-12-02RELPDBePDBePDBe2020-02-032020-07-222020-07-222020-12-02Russian Science Foundation17-14-01416Russian FederationNational Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R21-AI137584United StatesNational Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01-GM132302United StatesRussian Science Foundation18-44-04005Russian FederationRussian Foundation for Basic Research17-00-00366Russian FederationE. coli 50S ribosomal subunit in complex with dirithromycin, fMet-Phe-tRNA(Phe) and deacylated tRNA(iMet).Pichkur EBPolikanov YSMyasnikov AGKonevega ALPichkur EBPaleskava ATereshchenkov AGKasatsky PKomarova ESShiriaev DIBogdanov AADontsova OAOsterman IASergiev PVPolikanov YSMyasnikov AGKonevega ALInsights into the improved macrolide inhibitory activity from the high-resolution cryo-EM structure of dirithromycin bound to theE. coli70S ribosome.RnaUK26715723202032144191doi:10.1261/rna.073817.1191469-90012122RNARFUEMD-10655associated EM volumeE. coli 50S ribosomal subunit in complex with dirithromycin, fMet-Phe-tRNA(Phe) and deacylated tRNA(iMet).6xz7FULLOVERLAPE. coli 50S ribosomal subunit in complex with dirithromycin, fMet-Phe-tRNA(Phe) and deacylated tRNA(iMet).E. coli 50S ribosomal subunit in complex with dirithromycin, fMet-Phe-tRNA(Phe) and deacylated tRNA(iMet).0123456789101112131415161718192021222324252627282930313233Escherichia coli (strain K12)2.7E. coli 50S ribosomal subunit11234567891011121314151617181920212223242526272829303132Escherichia coli (strain K12)fMet-Phe-tRNA(Phe)133Saccharomyces cerevisiae23S rRNAEscherichia coli (strain K12)0.939609251GGUUAAGCGACUAAGCGUACACGGUGGAUGCCCUGGCAGUCAGAGGCGAUGAAGGACGUGCUAAUCUGCGAUAAGCGUCG
GUAAGGUGAUAUGAACCGUUAUAACCGGCGAUUUCCGAAUGGGGAAACCCAGUGUGUUUCGACACACUAUCAUUAACUGA
AUCCAUAGGUUAAUGAGGCGAACCGGGGGAACUGAAACAUCUAAGUACCCCGAGGAAAAGAAAUCAACCGAGAUUCCCCC
AGUAGCGGCGAGCGAACGGGGAGCAGCCCAGAGCCUGAAUCAGUGUGUGUGUUAGUGGAAGCGUCUGGAAAGGCGCGCGA
UACAGGGUGACAGCCCCGUACACAAAAAUGCACAUGCUGUGAGCUCGAUGAGUAGGGCGGGACACGUGGUAUCCUGUCUG
AAUAUGGGGGGACCAUCCUCCAAGGCUAAAUACUCCUGACUGACCGAUAGUGAACCAGUACCGUGAGGGAAAGGCGAAAA
GAACCCCGGCGAGGGGAGUGAAAAAGAACCUGAAACCGUGUACGUACAAGCAGUGGGAGCACGCUUAGGCGUGUGACUGC
GUACCUUUUGUAUAAUGGGUCAGCGACUUAUAUUCUGUAGCAAGGUUAACCGAAUAGGGGAGCCGAAGGGAAACCGAGUC
UUAACUGGGCGUUAAGUUGCAGGGUAUAGACCCGAAACCCGGUGAUCUAGCCAUGGGCAGGUUGAAGGUUGGGUAACACU
AACUGGAGGACCGAACCGACUAAU(1MG)(PSU)(5MU)GAAAAAUUAGCGGAUGACUUGUGGCUGGGGGUGAAAGGCCA
AUCAAACCGGGAGAUAGCUGGUUCUCCCCGAAAGCUAUUUAGGUAGCGCCUCGUGAAUUCAUCUCCGGGGGUAGAGCACU
GUUUCGGCAAGGGGGUCACUUACCAACCCGAUGCAAACUGCGAAUACCGGAGAAUGUUAUCACGGGAGACACACGGCGGG
(PSU)GCUAACGUCCGUCGUGAAGAGGGAAACAACCCAGACCGCCAGCUAAGGUCCCAAAGUCAUGGUUAAGUGGGAAAC
GAUGUGGGAAGGCCCAGACAGCCAGGAUGUUGGCUUAGAAGCAGCCAUCAUUUAAAGAAAGCGUAAUAGCUCACUGGUCG
AGUCGGCCUGCGCGGAAGAUGUAACGGGGCUAAACCAUGCACCGAAGCUGCGGCAGCGACGCUUAUGCGUUGUUGGGUAG
GGGAGCGUUCUGUAAGCCUGCGAAGGUGUGCUGUGAGGCAUGCUGGAGGUAUCAGAAGUGCGAAUGCUGACAUAAGUAAC
GAUAAAGCGGGUGAAAAGCCCGCUCGCCGGAAGACCAAGGGUUCCUGUCCAACGUUAAUCGGGGCAGGGUGAGUCGACCC
CUAAGGCGAGGCCGAAAGGCGUAGUCGAUGGGAAACAGGUUAAUAUUCCUGUACUUGGUGUUACUGCGAAGGGGGGACGG
AGAAGGCUAUGUUGGCCGGGCGACGGUUGUCCCGGUUUAAGCGUGUAGGCUGGUUUUCCAGGCAAAUCCGGAAAAUCAAG
GCUGAGGCGUGAUGACGAGGCACUACGGUGCUGAAGCAACAAAUGCCCUGCUUCCAGGAAAAGCCUCUAAGCAUCAGGUA
ACAUCAAAUCGUACCCCAAACCGACAC(6MZ)GGUGGUCAGGUAGAGAAUACCAAGGCGCUUGAGAGAACUCGGGUGAAG
GAACUAGGCAAAAUGGUGCCGUAACUUCGGGAGAAGGCACGCUGAUAUGUAGGUGAGGUCCCUCGCGGAUGGAGCUGAAA
UCAGUCGAAGAUACCAGCUGGCUGCAACUGUUUAUUAAAAACACAGCACUGUGCAAACACGAAAGUGGACGUAUACGGUG
UGACGCCU(2MG)CCCGGUGCCGGAAGGUUAAUUGAUGGGGUUAGCGCAAGCGAAGCUCUUGAUCGAAGCCCCGGUAAAC
GGCGGCCG(PSU)AAC(3TD)A(PSU)AACGGUCCUAAGGUAGCGAAA(5MU)UCCUUGUCGGGUAAGUUCCGAC(5MC)
UGCACGAAUGGCGUAAUGAUGGCCAGGCUGUCUCCACCCGAGACUCAGUGAAAUUGAACUCGCUGUG(6MZ)AGAUGCAG
UGUACCCGCGGCAAGACGGAAAGACCCCGU(G7M)AACCUUUACUAUAGCUUGACACUGAACAUUGAGCCUUGAUGUGUA
GGAUAGGUGGGAGGCUUUGAAGUGUGGACGCCAGUCUGCAUGGAGCCGACCUUGAAAUACCACCCUUUAAUGUUUGAUGU
UCUAACGUUGACCCGUAAUCCGGGUUGCGGACAGUGUCUGGUGGGUAGUUUGACUG(OMG)GGCGGUCUCCUCCUAAAGA
GUAACGGAGGAGCACGAAGGUUGGCUAAUCCUGGUCGGACAUCAGGAGGUUAGUGCAAUGGCAUAAGCCAGCUUGACUGC
GAGCGUGACGGCGCGAGCAGGUGCGAAAGCAGGUCAUAGUGAUCCGGUGGUUCUGAAUGGAAGGGCCAUCGCUCAACGGA
UAAAAGGUACUCCG(2MG)GGA(H2U)AACAGGC(PSU)GAUACCGCCCAAGAGUUCAUAUCGACGGCGGUGUUUGGCA
(OMC)CUCG(2MA)(PSU)GUCGGCUCAUCACAUCCUGGGGCUGAAGUAGGUCCCAAGGGUAUGGC(OMU)GUUCGCCAU
UUAAAGUGGUACGCGAGC(PSU)GGGUUUAGAACGUCGUGAGACAG(PSU)(PSU)CGGUCCCUAUCUGCCGUGGGCGCU
GGAGAACUGAGGGGGGCUGCUCCUAGUACGAGAGGACCGGAGUGGACGCAUCACUGGUGUUCGGGUUGUCAUGCCAAUGG
CACUGCCCGGUAGCUAAAUGCGGAAGAGAUAAGUGCUGAAAGCAUCUAAGCACGAAACUUGCCCCGAGAUGAGUUCUCCC
UGACCCUUUAAGGGUCCUGAAGGAACGUUGAAGACGACGACGUUGAUAGGCCGGGUGUGUAAGCGCAGCGAUGCGUUGAG
CUAACCGGUACUAAUGAACCGUGAGGCUUAACCU5S rRNAEscherichia coli (strain K12)0.038790091UGCCUGGCGGCCGUAGCGCGGUGGUCCCACCUGACCCCAUGCCGAACUCAGAAGUGAAACGCCGUAGCGCCGAUGGUAGU
GUGGGGUCUCCCCAUGCGAGAGUAGGGAACUGCCAGGCAU50S ribosomal protein L2Escherichia coli (strain K12)0.0296632441LEVOAVVKCKPTSPGRRHVVKVVNPELHKGKPFAPLLEKNSKSGGRNNNGRITTRHIGGGHKQAYRIVDFKRNKDGIPAVVERL
EYDPNRSANIALVLYKDGERRYILAPKGLKAGDQIQSGVDAAIKPGNTLPMRNIPVGSTVHNVEMKPGKGGQLARSAGTY
VQIVARDGAYVTLRLRSGEMRKVEADCRATLGEVGNAEHMLRVLGKAGAARWRGVRPTVRGTAMNPVDHPHGGGEGRNFG
KHPVTPWGVQTKGKKTRSNKRTDKFIVRRRS50S ribosomal protein L3Escherichia coli (strain K12)0.0222915621LEVOMIGLVGKKVGMTRIFTEDGVSIPVTVIEVEANRVTQVKDLANDGYRAIQVTTGAKKANRVTKPEAGHFAKAGVEAGRGLW
EFRLAEGEEFTVGQSISVELFADVKKVDVTGTSKGKGFAGTVKRWNFRTQDATHGNSLSHRVPGSIGQN(MEQ)TPGKVF
KGKKMAGQMGNERVTVQSLDVVRVDAERNLLLVKGAVPGATGSDLIVKPAVKA50S ribosomal protein L4Escherichia coli (strain K12)0.0221215661LEVOMELVLKDAQSALTVSETTFGRDFNEALVHQVVVAYAAGARQGTRAQKTRAEVTGSGKKPWRQKGTGRARSGSIKSPIWRS
GGVTFAARPQDHSQKVNKKMYRGALKSILSELVRQDRLIVVEKFSVEAPKTKLLAQKLKDMALEDVLIITGELDENLFLA
ARNLHKVDVRDATGIDPVSLIAFDKVVMTADAVKQVEEMLA50S ribosomal protein L5Escherichia coli (strain K12)0.0200732341LEVOAKLHDYYKDEVVKKLMTEFNYNSVMQVPRVEKITLNMGVGEAIADKKLLDNAAADLAAISGQKPLITKARKSVAGFKIRQ
GYPIGCKVTLRGERMWEFFERLITIAVPRIRDFRGLSAKSFDGRGNYSMGVREQIIFPEIDYDKVDRVRGLDITITTTAK
SDEEGRALLAAFDFPFR50S ribosomal protein L6Escherichia coli (strain K12)0.0188015981LEVOSRVAKAPVVVPAGVDVKINGQVITIKGKNGELTRTLNDAVEVKHADNTLTFGPRDGYADGWAQAGTARALLNSMVIGVTE
GFTKKLQLVGVGYRAAVKGNVINLSLGFSHPVDHQLPAGITAECPTQTEIVLKGADKQVIGQVAADLRAYRRPEPYKGKG
VRYADEVVRTKEAKKK50S ribosomal protein L10Escherichia coli (strain K12)0.0145687481LEVOALNLQDKQAIVAEVSEVAKGALSAVVADSRGVTVDKMTELRKAGREAGVYMRVVRNTLLRRAVEGTPFECLKDAFVGPTL
IAYVTEHPGAAARLFKEFAKANAKFEVKAAAFEGELIPASQIDRLATLPTYEEAI50S ribosomal protein L11Escherichia coli (strain K12)0.0140203031LEVOYVKLQVAAGMANPSPPVGPALGQQGVNIMEFCKAFNAKTDSIEKGLPIPVVITVYADRSFTFVTKTPPAAVLLKKAAGIK
SGSGKPNKDKVGKISRAQLQEIAQTKAADMTGADIEAMTRSIEGTARSMGLVVE50S ribosomal protein L13Escherichia coli (strain K12)0.0160506061LEVOMKTFTAKPETVKRDWYVVDATGKTLGRLATELARRLRGKHKAEYTPHVDTGDYIIVLNADKVAVTGNKRTDKVYYHHTGH
IGGIKQATFEEMIARRPERVIEIAVKGMLPKGPLGRAMFRKLKVYAGNEHNHAAQQPQVLDI50S ribosomal protein L14Escherichia coli (strain K12)0.0135650671LEVOMIQEQTMLNVADNSGARRVMCIKVLGGSHRRYAGVGDIIKITIKEAIPRGKVKKGDVLKAVVVRTKKGVRRPDGSVIRFD
GNACVLLNNNSEQPIGTRIFGPVTRELRSEKFMKIISLAPEVL50S ribosomal protein L15Escherichia coli (strain K12)0.0150084711LEVOMRLNTLSPAEGSKKAGKRLGRGIGSGLGKTGGRGHKGQKSRSGGGVRRGFEGGQMPLYRRLPKFGFTSRKAAITAEIRLS
DLAKVEGGVVDLNTLKAANIIGIQIEFAKVILAGEVTTPVTVRGLRVTKGARAAIEAAGGKIEE50S ribosomal protein L16Escherichia coli (strain K12)0.0153272611LEVOMLQPKRTKFRKMHKGRNRGLAQGTDVSFGSFGLKAVGRGRLTARQIEAARRAMTRAVKRQGKIWIRVFPDKPITEKPLAV
(4D4)MGKGKGNVEYWVALIQPGKVLYEMDGVPEELAREAFKLAAAKLPIKTTFVTKTVM50S ribosomal protein L17Escherichia coli (strain K12)0.0141934651LEVOMRHRKSGRQLNRNSSHRQAMFRNMAGSLVRHEIIKTTLPKAKELRRVVEPLITLAKTDSVANRRLAFARTRDNEIVAKLF
NELGPRFASRAGGYTRILKCGFRAGDNAPMAYIELVDRSEKAEAA50S ribosomal protein L18Escherichia coli (strain K12)0.0127946681LEVOMDKKSARIRRATRARRKLQELGATRLVVHRTPRHIYAQVIAPNGSEVLVAASTVEKAIAEQLKYTGNKDAAAAVGKAVAE
RALEKGIKDVSFDRSGFQYHGRVQALADAAREAGLQF50S ribosomal protein L19Escherichia coli (strain K12)0.0130280821LEVOSNIIKQLEQEQMKQDVPSFRPGDTVEVKVWVVEGSKKRLQAFEGVVIAIRNRGLHSAFTVRKISNGEGVERVFQTHSPVV
DSISVKRRGAVRKAKLYYLRERTGKAARIKERLN50S ribosomal protein L20Escherichia coli (strain K12)0.0133968281LEVOARVKRGVIARARHKKILKQAKGYYGARSRVYRVAFQAVIKAGQYAYRDRRQRKRQFRQLWIARINAAARQNGISYSKFIN
GLKKASVEIDRKILADIAVFDKVAFTALVEKAKAALA50S ribosomal protein L21Escherichia coli (strain K12)0.0115863741LEVOMYAVFQSGGKQHRVSEGQTVRLEKLDIATGETVEFAEVLMIANGEEVKIGVPFVDGGVIKAEVVAHGRGEKVKIVKFRRR
KHYRKQQGHRQWFTDVKITGISA50S ribosomal protein L22Escherichia coli (strain K12)0.0122533591LEVOMETIAKHRHARSSAQKVRLVADLIRGKKVSQALDILTYTNKKAAVLVKKVLESAIANAEHNDGADIDDLKVTKIFVDEGP
SMKRIMPRAKGRADRILKRTSHITVVVSDR50S ribosomal protein L23Escherichia coli (strain K12)0.0105464721LEVOMIREERLLKVLRAPHVSEKASTAMEKSNTIVLKVAKDATKAEIKAAVQKLFEVEVEVVNTLVVKGKVKRHGQRIGRRSDW
KKAYVTLKEGQNL50S ribosomal protein L24Escherichia coli (strain K12)0.0110788741LEVOAAKIRRDDEVIVLTGKDKGKRGKVKNVLSSGKVIVEGINLVKKHQKPVPALNQPGGIVEKEAAIQVSNVAIFNAATGKAD
RVGFRFEDGKKVRFFKSNSETI50S ribosomal protein L25Escherichia coli (strain K12)0.0107134651LEVOMFTINAEVRKEQGKGASRRLRAANKFPAIIYGGKEAPLAIELDHDKVMNMQAKAEFYSEVLTIVVDGKEIKVKAQDVQRH
PYKPKLQHIDFVRA50S ribosomal protein L27Escherichia coli (strain K12)0.0082754981LEVOTRNGRDSEAKRLGVKRFGGESVLAGSIIVRQRGTKFHAGANVGCGRDHTLFAKADGKVKFEVKGPKNRKFISIEAE50S ribosomal protein L28Escherichia coli (strain K12)0.0088963541LEVOSRVCQVTGKRPVTGNNRSHALNATKRRFLPNLHSHRFWVESEKRFVTLRVSAKGMRVIDKKGIDTVLAELRARGEKY50S ribosomal protein L29Escherichia coli (strain K12)0.0071552671LEVOKAKELREKSVEELNTELLNLLREQFNLRMQAASGQLQQSHLLKQVRRDVARVKTLLNEKAGA50S ribosomal protein L30Escherichia coli (strain K12)0.0064236251LEVOAKTIKITQTRSAIGRLPKHKATLLGLGLRRIGHTVEREDTPAIRGMINAVSFMVKVEE50S ribosomal protein L32Escherichia coli (strain K12)0.0063322491LEVOAVQQNKPTRSKRGMRRSHDALTAVTSLSVDKTSGEKHLRHHITADGYYRGRKVIAK50S ribosomal protein L33Escherichia coli (strain K12)0.0059281LEVOGIREKIKLVSSAGTGHFYTTTKNKRTKPEKLELKKFDPVVRQHVIYKEAKI50S ribosomal protein L34Escherichia coli (strain K12)0.0053974631LEVOMKRTFQPSVLKRNRSHGFRARMATKNGRQVLARRRAKGRARLTVSK50S ribosomal protein L35Escherichia coli (strain K12)0.0071818351LEVOPKIKTVRGAAKRFKKTGKGGFKHKHANLRHILTKKATKRKRHLRPKAMVSKGDLGLVIACLPYA50S ribosomal protein L36Escherichia coli (strain K12)0.004377391LEVOMKVRASVKKLCRNCKIVKRDGVIRVICSAEPKHKQRQGDeacylated tRNAi(Met)Escherichia coli (strain K12)0.0245417191GCGGGG(4SU)GGAGCAGCCUGGUAGCUCGUCGGG(5MC)UCAUAACCCGAAGGUCGUCGG(5MU)(PSU)CAAAUCCGG
CCCCCGCAACCAfMet-Phe-tRNA(Phe)baker's yeast0.0251675061GCGGAUUUA(2MG)CUCAG(H2U)(H2U)GGGAGAGC(M2G)CCAGA(OMC)U(OMG)AA(YYG)A(PSU)(5MC)UGGA
G(7MG)UC(5MC)UGUG(5MU)(PSU)CG(1MA)UCCACAGAAUUCGCACC(31M)MAGNESIUM ION2.4305e-05178MGDirithromycin0.0008350741DI0water1.8015e-05528HOHsingleParticleparticle7.5Quantifoil R2/2COPPER/RHODIUM300CARBONCONTINUOUS10.0GLOW DISCHARGEAIRETHANEFEI TITAN KRIOSSPOT SCANBRIGHT FIELDFIELD EMISSION GUN300100.00.10.30.32.22.275000.0NITROGENFEI FALCON II (4k x 4k)INTEGRATING2-271.480.01973000GctfC12.1FSC 0.143 CUT-OFFRELION3.1beta401905OTHERMAXIMUM LIKELIHOODRELION3.14YBBOTHERREALemd_10655_msk_1.mapemd_10655_additional_1.map.gz1IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
512
512512
0
00512512512440.32440.32440.3290.090.090.0XYZ-35.80509694.27171-0.0217046161.9370510.860.860.86A map calculated and sharpened in CisTEM before high-order aberrations correction in Relion 3.1.emd_10655_half_map_2.map.gz1IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
512
512512
0
00512512512440.32440.32440.3290.090.090.0XYZ-0.054602210.153558450.000002369690.0047248630.860.860.86Half #1emd_10655_half_map_1.map.gz1IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)