Structure of the Bacterial Ribosome without hypoxia-induced rRNA modifications

2025-12-24 REL PDBj INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY STRUCTURE_SUMMARY chem_comp chem_comp_atom chem_comp_bond em_admin entity pdbx_modification_feature pdbx_validate_chiral _chem_comp.formula _chem_comp.formula_weight _chem_comp.mon_nstd_flag _chem_comp.pdbx_synonyms _em_admin.last_update _entity.formula_weight STRUCTURE_SUMMARY em_admin entity _chem_comp.pdbx_synonyms _em_admin.last_update _entity.formula_weight PDBj PDBj 2024-05-07 2025-11-12 2025-11-12 2025-12-24 Ministry of Education, Culture, Sports, Science and Technology (Japan) Japan Japan Society for the Promotion of Science (JSPS) 26113003, 26220205 and 18H05272 Japan Japan Science and Technology JPMJER2002 Japan Structure of the Bacterial Ribosome without hypoxia-induced rRNA modifications Ishiguro K Yokoyama T Shirouzu M Ito T Suzuki T rRNA modifications, translation, RIBOSOME Ishiguro K Midorikawa K Miyauchi K Kimura S Naoki S Yokoyama T Shirouzu M Liiv A Remme J Ito T Suzuki T Novel rRNA methylations regulate translational efficiency of the ribosomes in response to oxygen condition To Be Published 0353 8zff FULLOVERLAP EMDB EMD-60059 associated EM volume

The complex of E. coli 70S ribosome with mRNA and P- site tRNA The complex of E. coli 70S ribosome with mRNA and P- site tRNA 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54

E. coli 70S ribosome without hypoxia-induced rRNA modifications was incubated with mRNA and E.coli tRNA-fMet

E. coli 70S ribosome 1 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52

E. coli 70S ribosome was purified from anaerobically grown KO cells

Escherichia coli BW25113 mRNA and P- site tRNA 1 53 54 16S rRNA Escherichia coli BW25113 0.499873406 1 AAAUUGAAGAGUUUGAUCAUGGCUCAGAUUGAACGCUGGCGGCAGGCCUAACACAUGCAAGUCGAACGGUAACAGGAAGA AGCUUGCUUCUUUGCUGACGAGUGGCGGACGGGUGAGUAAUGUCUGGGAAACUGCCUGAUGGAGGGGGAUAACUACUGGA AACGGUAGCUAAUACCGCAUAACGUCGCAAGACCAAAGAGGGGGACCUUCGGGCCUCUUGCCAUCGGAUGUGCCCAGAUG GGAUUAGCUAGUAGGUGGGGUAACGGCUCACCUAGGCGACGAUCCCUAGCUGGUCUGAGAGGAUGACCAGCCACACUGGA ACUGAGACACGGUCCAGACUCCUACGGGAGGCAGCAGUGGGGAAUAUUGCACAAUGGGCGCAAGCCUGAUGCAGCCAUGC CGCGUGUAUGAAGAAGGCCUUCGGGUUGUAAAGUACUUUCAGCGGGGAGGAAGGGAGUAAAGUUAAUACCUUUGCUCAUU GACGUUACCCGCAGAAGAAGCACCGGCUAACUCCG(PSU)GCCAGCAGCC(G7M)CGGUAAUACGGAGGGUGCAAGCGUU AAUCGGAAUUACUGGGCGUAAAGCGCACGCAGGCGGUUUGUUAAGUCAGAUGUGAAAUCCCCGGGCUCAACCUGGGAACU GCAUCUGAUACUGGCAAGCUUGAGUCUCGUAGAGGGGGGUAGAAUUCCAGGUGUAGCGGUGAAAUGCGUAGAGAUCUGGA GGAAUACCGGUGGCGAAGGCGGCCCCCUGGACGAAGACUGACGCUCAGGUGCGAAAGCGUGGGGAGCAAACAGGAUUAGA UACCCUGGUAGUCCACGCCGUAAACGAUGUCGACUUGGAGGUUGUGCCCUUGAGGCGUGGCUUCCGGAGCUAACGCGUUA AGUCGACCGCCUGGGGAGUACGGCCGCAAGGUUAAAACUCAAAUGAAUUGACGGGGGCCCGCACAAGCGGUGGAGCAUGU GGUUUAAUUCGAU(2MG)(5MC)AACGCGAAGAACCUUACCUGGUCUUGACAUCCACGGAAGUUUUCAGAGAUGAGAAUG UGCCUUCGGGAACCGUGAGACAGGUGCUGCAUGGCUGUCGUCAGCUCGUGUUGUGAAAUGUUGGGUUAAGUCCCGCAACG AGCGCAACCCUUAUCCUUUGUUGCCAGCGGUCCGGCCGGGAACUCAAAGGAGACUGCCAGUGAUAAACUGGAGGAAGGUG GGGAUGACGUCAAGUCAUCAUG(2MG)CCCUUACGACCAGGGCUACACACGUGCUACAAUGGCGCAUACAAAGAGAAGCG ACCUCGCGAGAGCAAGCGGACCUCAUAAAGUGCGUCGUAGUCCGGAUUGGAGUCUGCAACUCGACUCCAUGAAGUCGGAA UCGCUAGUAAUCGUGGAUCAGAAUGCCACGGUGAAUACGUUCCCGGGCCUUGUACACACCG(4OC)CCGU(5MC)ACACC AUGGGAGUGGGUUGCAAAAGAAGUAGGUAGCUUAACCUUCGGGAGGGCGCUUACCACUUUGUGAUUCAUGACUGGGGUGA AGUCG(UR3)AACAAGGUAACCGUAGG(2MG)G(MA6)(MA6)CCUGCGGUUGGAUCACCUCCUUA CP047127.1 Small ribosomal subunit protein uS2 Escherichia coli BW25113 0.026781669999999997 1 LEVO MATVSMRDMLKAGVHFGHQTRYWNPKMKPFIFGARNKVHIINLEKTVPMFNEALAELNKIASRKGKILFVGTKRAASEAV KDAALSCDQFFVNHRWLGGMLTNWKTVRQSIKRLKDLETQSQDGTFDKLTKKEALMRTRELEKLENSLGGIKDMGGLPDA LFVIDADHEHIAIKEANNLGIPVFAIVDTNSDPDGVDFVIPGNDDAIRAVTLYLGAVAATVREGRSQDLASQAEESFVEA E P0A7V0 Small ribosomal subunit protein uS3 Escherichia coli BW25113 0.026031316 1 LEVO MGQKVHPNGIRLGIVKPWNSTWFANTKEFADNLDSDFKVRQYLTKELAKASVSRIVIERPAKSIRVTIHTARPGIVIGKK GEDVEKLRKVVADIAGVPAQINIAEVRKPELDAKLVADSITSQLERRVMFRRAMKRAVQNAMRLGAKGIKVEVSGRLGGA EIARTEWYREGRVPLHTLRADIDYNTSEAHTTYGVIGVKVWIFKGEILGGMAAVEQPEKPAAQPKKQQRKGRK P0A7V3 Small ribosomal subunit protein uS4 Escherichia coli BW25113 0.023514199 1 LEVO MARYLGPKLKLSRREGTDLFLKSGVRAIDTKCKIEQAPGQHGARKPRLSDYGVQLREKQKVRRIYGVLERQFRNYYKEAA RLKGNTGENLLALLEGRLDNVVYRMGFGATRAEARQLVSHKAIMVNGRVVNIASYQVSPNDVVSIREKAKKQSRVKAALE LAEQREKPTWLEVDAGKMEGTFKRKPERSDLSADINEHLIVELYSK P0A7V8 Small ribosomal subunit protein uS5 Escherichia coli BW25113 0.017629398 1 LEVO MAHIEKQAGELQEKLIAVNRVSKTVKGGRIFSFTALTVVGDGNGRVGFGYGKAREVPAAIQKAMEKARRNMINVALNNGT LQHPVKGVHTGSRVFMQPASEGTGIIAGGAMRAVLEVAGVHNVLAKAYGSTNPINVVRATIDGLENMNSPEMVAAKRGKS VEEILGK P0A7W1 Small ribosomal subunit protein bS6, fully modified isoform Escherichia coli BW25113 0.015727512 1 LEVO MRHYEIVFMVHPDQSEQVPGMIERYTAAITGAEGKIHRLEDWGRRQLAYPINKLHKAHYVLMNVEAPQEVIDELETTFRF NDAVIRSMVMRTKHAVTEASPMVKAKDERRERRDDFANETADDAEAGDSEEEEEE P02358 Small ribosomal subunit protein uS7 Escherichia coli BW25113 0.020055155999999998 1 LEVO MPRRRVIGQRKILPDPKFGSELLAKFVNILMVDGKKSTAESIVYSALETLAQRSGKSELEAFEVALENVRPTVEVKSRRV GGSTYQVPVEVRPVRRNALAMRWIVEAARKRGDKSMALRLANELSDAAENKGTAVKKREDVHRMAEANKAFAHYRWLSLR SFSHQAGASSKQPALGYLN P02359 Small ribosomal subunit protein uS8 Escherichia coli BW25113 0.014146557 1 LEVO MSMQDPIADMLTRIRNGQAANKAAVTMPSSKLKVAIANVLKEEGFIEDFKVEGDTKPELELTLKYFQGKAVVESIQRVSR PGLRIYKRKDELPKVMAGLGIAVVSTSKGVMTDRAARQAGLGGEIICYVA P0A7W7 Small ribosomal subunit protein uS9 Escherichia coli BW25113 0.01488627 1 LEVO MAENQYYGTGRRKSSAARVFIKPGNGKIVINQRSLEQYFGRETARMVVRQPLELVDMVEKLDLYITVKGGGISGQAGAIR HGITRALMEYDESLRSELRKAGFVTRDARQVERKKVGLRKARRRPQFSKR P0A7X3 Small ribosomal subunit protein uS10 Escherichia coli BW25113 0.011755597 1 LEVO MQNQRIRIRLKAFDHRLIDQATAEIVETAKRTGAQVRGPIPLPTRKERFTVLISPHVNKDARDQYEIRTHLRLVDIVEPT EKTVDALMRLDLAAGVDVQISLG P0A7R5 Small ribosomal subunit protein uS11 Escherichia coli BW25113 0.013871959 1 LEVO MAKAPIRARKRVRKQVSDGVAHIHASFNNTIVTITDRQGNALGWATAGGSGFRGSRKSTPFAAQVAAERCADAVKEYGIK NLEVMVKGPGPGRESTIRALNAAGFRITNITDVTPIPH(IAS)GCRPPKKRRV P0A7R9 Small ribosomal subunit protein uS12 Escherichia coli BW25113 0.013814248999999999 1 LEVO MATVNQLVRKPRARKVAKSNVPALEACPQKRGVCTRVYTTTPKKPNSALRKVCRVRLTNGFEVTSYIGGEGHNLQEHSVI LIRGGRVK(D2T)LPGVRYHTVRGALDCSGVKDRKQARSKYGVKRPKA P0A7S3 Small ribosomal subunit protein uS13 Escherichia coli BW25113 0.013128467 1 LEVO MARIAGINIPDHKHAVIALTSIYGVGKTRSKAILAAAGIAEDVKISELSEGQIDTLRDEVAKFVVEGDLRREISMSIKRL MDLGCYRGLRHRRGLPVRGQRTKTNARTRKGPRKPIKK P0A7S9 Small ribosomal subunit protein uS14 Escherichia coli BW25113 0.011606559999999998 1 LEVO MAKQSMKAREVKRVALADKYFAKRAELKAIISDVNASDEDRWNAVLKLQTLPRDSSPSRQRNRCRQTGRPHGFLRKFGLS RIKVREAAMRGEIPGLKKASW P0AG59 Small ribosomal subunit protein uS15 Escherichia coli BW25113 0.010290816 1 LEVO MSLSTEATAKIVSEFGRDANDTGSTEVQVALLTAQINHLQGHFAEHKKDHHSRRGLLRMVSQRRKLLDYLKRKDVARYTQ LIERLGLRR P0ADZ4 Small ribosomal subunit protein bS16 Escherichia coli BW25113 0.009207571999999999 1 LEVO MVTIRLARHGAKKRPFYQVVVADSRNARNGRFIERVGFFNPIASEKEEGTRLDLDRIAHWVGQGATISDRVAALIKEVNK AA P0A7T3 Small ribosomal subunit protein uS17 Escherichia coli BW25113 0.009724491 1 LEVO MTDKIRTLQGRVVSDKMEKSIVVAIERFVKHPIYGKFIKRTTKLHVHDENNECGIGDVVEIRECRPLSKTKSWTLVRVVE KAVL P0AG63 Small ribosomal subunit protein bS18 Escherichia coli BW25113 0.009005471999999999 1 LEVO MARYFRRRKFCRFTAEGVQEIDYKDIATLKNYITESGKIVPSRITGTRAKYQRQLARAIKRARYLSLLPYTDRHQ P0A7T7 Small ribosomal subunit protein uS19 Escherichia coli BW25113 0.010455355 1 LEVO MPRSLKKGPFIDLHLLKKVEKAVESGDKKPLRTWSRRSTIFPNMIGLTIAVHNGRQHVPVFVTDEMVGHKLGEFAPTRTY RGHAADKKAKKK P0A7U3 Small ribosomal subunit protein bS20 Escherichia coli BW25113 0.009708464 1 LEVO MANIKSAKKRAIQSEKARKHNASRRSMMRTFIKKVYAAIEAGDKAAAQKAFNEMQPIVDRQAAKGLIHKNKAARHKANLT AQINKLA P0A7U7 Small ribosomal subunit protein bS21 Escherichia coli BW25113 0.008524039 1 LEVO MPVIKVRENEPFDVALRRFKRSCEKAGVLAEVRRREFYEKPTTERKRAKASAVKRHAKKLARENARRTRLY P68679 23S rRNA Escherichia coli BW25113 0.941811562 1 GGUUAAGCGACUAAGCGUACACGGUGGAUGCCCUGGCAGUCAGAGGCGAUGAAGGACGUGCUAAUCUGCGAUAAGCGUCG GUAAGGUGAUAUGAACCGUUAUAACCGGCGAUUUCCGAAUGGGGAAACCCAGUGUGUUUCGACACACUAUCAUUAACUGA AUCCAUAGGUUAAUGAGGCGAACCGGGGGAACUGAAACAUCUAAGUACCCCGAGGAAAAGAAAUCAACCGAGAUUCCCCC AGUAGCGGCGAGCGAACGGGGAGCAGCCCAGAGCCUGAAUCAGUGUGUGUGUUAGUGGAAGCGUCUGGAAAGGCGCGCGA UACAGGGUGACAGCCCCGUACACAAAAAUGCACAUGCUGUGAGCUCGAUGAGUAGGGCGGGACACGUGGUAUCCUGUCUG AAUAUGGGGGGACCAUCCUCCAAGGCUAAAUACUCCUGACUGACCGAUAGUGAACCAGUACCGUGAGGGAAAGGCGAAAA GAACCCCGGCGAGGGGAGUGAAAAAGAACCUGAAACCGUGUACGUACAAGCAGUGGGAGCACGCUUAGGCGUGUGACUGC GUACCUUUUGUAUAAUGGGUCAGCGACUUAUAUUCUGUAGCAAGGUUAACCGAAUAGGGGAGCCGAAGGGAAACCGAGUC UUAACUGGGCGUUAAGUUGCAGGGUAUAGACCCGAAACCCGGUGAUCUAGCCAUGGGCAGGUUGAAGGUUGGGUAACACU AACUGGAGGACCGAACCGACUAAU(1MG)(PSU)(5MU)GAAAAAUUAGCGGAUGACUUGUGGCUGGGGGUGAAAGGCCA AUCAAACCGGGAGAUAGCUGGUUCUCCCCGAAAGCUAUUUAGGUAGCGCCUCGUGAAUUCAUCUCCGGGGGUAGAGCACU GUUUCGGCAAGGGGGUCAUCCCGACUUACCAACCCGAUGCAAACUGCGAAUACCGGAGAAUGUUAUCACGGGAGACACAC GGCGGG(PSU)GCUAACGUCCGUCGUGAAGAGGGAAACAACCCAGACCGCCAGCUAAGGUCCCAAAGUCAUGGUUAAGUG GGAAACGAUGUGGGAAGGCCCAGACAGCCAGGAUGUUGGCUUAGAAGCAGCCAUCAUUUAAAGAAAGCGUAAUAGCUCAC UGGUCGAGUCGGCCUGCGCGGAAGAUGUAACGGGGCUAAACCAUGCACCGAAGCUGCGGCAGCGACGCUUAUGCGUUGUU GGGUAGGGGAGCGUUCUGUAAGCCUGCGAAGGUGUGCUGUGAGGCAUGCUGGAGGUAUCAGAAGUGCGAAUGCUGACAUA AGUAACGAUAAAGCGGGUGAAAAGCCCGCUCGCCGGAAGACCAAGGGUUCCUGUCCAACGUUAAUCGGGGCAGGGUGAGU CGACCCCUAAGGCGAGGCCGAAAGGCGUAGUCGAUGGGAAACAGGUUAAUAUUCCUGUACUUGGUGUUACUGCGAAGGGG GGACGGAGAAGGCUAUGUUGGCCGGGCGACGGUUGUCCCGGUUUAAGCGUGUAGGCUGGUUUUCCAGGCAAAUCCGGAAA AUCAAGGCUGAGGCGUGAUGACGAGGCACUACGGUGCUGAAGCAACAAAUGCCCUGCUUCCAGGAAAAGCCUCUAAGCAU CAGGUAACAUCAAAUCGUACCCCAAACCGACAC(6MZ)GGUGGUCAGGUAGAGAAUACCAAGGCGCUUGAGAGAACUCGG GUGAAGGAACUAGGCAAAAUGGUGCCGUAACUUCGGGAGAAGGCACGCUGAUAUGUAGGUGAGGUCCCUCGCGGAUGGAG CUGAAAUCAGUCGAAGAUACCAGCUGGCUGCAACUGUUUAUUAAAAACACAGCACUGUGCAAACACGAAAGUGGACGUAU ACGGUGUGACGCCU(2MG)CCCGGUGCCGGAAGGUUAAUUGAUGGGGUUAGCGCAAGCGAAGCUCUUGAUCGAAGCCCCG GUAAACGGCGGCCG(PSU)AAC(3TD)A(PSU)AACGGUCCUAAGGUAGCGAAA(5MU)UCCUUGUCGGGUAAGUUCCGA C(5MC)UGCACGAAUGGCGUAAUGAUGGCCAGGCUGUCUCCACCCGAGACUCAGUGAAAUUGAACUCGCUGUG(6MZ)AG AUGCAGUGUACCCGCGGCAAGACGGAAAGACCCCGU(G7M)AACCUUUACUAUAGCUUGACACUGAACAUUGAGCCUUGA UGUGUAGGAUAGGUGGGAGGCUUUGAAGUGUGGACGCCAGUCUGCAUGGAGCCGACCUUGAAAUACCACCCUUUAAUGUU UGAUGUUCUAACGUUGACCCGUAAUCCGGGUUGCGGACAGUGUCUGGUGGGUAGUUUGACUG(OMG)GGCGGUCUCCUCC UAAAGAGUAACGGAGGAGCACGAAGGUUGGCUAAUCCUGGUCGGACAUCAGGAGGUUAGUGCAAUGGCAUAAGCCAGCUU GACUGCGAGCGUGACGGCGCGAGCAGGUGCGAAAGCAGGUCAUAGUGAUCCGGUGGUUCUGAAUGGAAGGGCCAUCGCUC AACGGAUAAAAGGUACUCCG(2MG)GGA(H2U)AACAGGC(PSU)GAUACCGCCCAAGAGUUCAUAUCGACGGCGGUGUU UGGCA(OMC)CUCG(2MA)(PSU)GUCGGCUCAUCACAUCCUGGGGCUGAAGUAGGUCCCAAGGGUAUGGC(OMU)GUUC GCCAUUUAAAGUGGUACGCGAGC(PSU)GGGUUUAGAACGUCGUGAGACAG(PSU)(PSU)CGGUCCCUAUCUGCCGUGG GCGCUGGAGAACUGAGGGGGGCUGCUCCUAGUACGAGAGGACCGGAGUGGACGCAUCACUGGUGUUCGGGUUGUCAUGCC AAUGGCACUGCCCGGUAGCUAAAUGCGGAAGAGAUAAGUGCUGAAAGCAUCUAAGCACGAAACUUGCCCCGAGAUGAGUU CUCCCUGACCCUUUAAGGGUCCUGAAGGAACGUUGAAGACGACGACGUUGAUAGGCCGGGUGUGUAAGCGCAGCGAUGCG UUGAGCUAACCGGUACUAAUGAACCGUGAGGCUUAACCUU 5S rRNA Escherichia coli BW25113 0.03879008999999999 1 UGCCUGGCGGCCGUAGCGCGGUGGUCCCACCUGACCCCAUGCCGAACUCAGAAGUGAAACGCCGUAGCGCCGAUGGUAGU GUGGGGUCUCCCCAUGCGAGAGUAGGGAACUGCCAGGCAU CP049050.1 Large ribosomal subunit protein uL2 Escherichia coli BW25113 0.029923619 1 LEVO MAVVKCKPTSPGRRHVVKVVNPELHKGKPFAPLLEKNSKSGGRNNNGRITTRHIGGGHKQAYRIVDFKRNKDGIPAVVER LEYDPNRSANIALVLYKDGERRYILAPKGLKAGDQIQSGVDAAIKPGNTLPMRNIPVGSTVHNVEMKPGKGGQLARSAGT YVQIVARDGAYVTLRLRSGEMRKVEADCRATLGEVGNAEHMLRVLGKAGAARWRGVRPTVRGTAMNPVDHPHGGGEGRNF GKHPVTPWGVQTKGKKTRSNKRTDKFIVRRRSK P60422 Large ribosomal subunit protein uL3 Escherichia coli BW25113 0.022291562 1 LEVO MIGLVGKKVGMTRIFTEDGVSIPVTVIEVEANRVTQVKDLANDGYRAIQVTTGAKKANRVTKPEAGHFAKAGVEAGRGLW EFRLAEGEEFTVGQSISVELFADVKKVDVTGTSKGKGFAGTVKRWNFRTQDATHGNSLSHRVPGSIGQN(MEQ)TPGKVF KGKKMAGQMGNERVTVQSLDVVRVDAERNLLLVKGAVPGATGSDLIVKPAVKA P60438 Large ribosomal subunit protein uL4 Escherichia coli BW25113 0.022121566 1 LEVO MELVLKDAQSALTVSETTFGRDFNEALVHQVVVAYAAGARQGTRAQKTRAEVTGSGKKPWRQKGTGRARSGSIKSPIWRS GGVTFAARPQDHSQKVNKKMYRGALKSILSELVRQDRLIVVEKFSVEAPKTKLLAQKLKDMALEDVLIITGELDENLFLA ARNLHKVDVRDATGIDPVSLIAFDKVVMTADAVKQVEEMLA P60723 Large ribosomal subunit protein uL5 Escherichia coli BW25113 0.020333611 1 LEVO MAKLHDYYKDEVVKKLMTEFNYNSVMQVPRVEKITLNMGVGEAIADKKLLDNAAADLAAISGQKPLITKARKSVAGFKIR QGYPIGCKVTLRGERMWEFFERLITIAVPRIRDFRGLSAKSFDGRGNYSMGVREQIIFPEIDYDKVDRVRGLDITITTTA KSDEEGRALLAAFDFPFRK P62399 Large ribosomal subunit protein uL6 Escherichia coli BW25113 0.018932791 1 LEVO MSRVAKAPVVVPAGVDVKINGQVITIKGKNGELTRTLNDAVEVKHADNTLTFGPRDGYADGWAQAGTARALLNSMVIGVT EGFTKKLQLVGVGYRAAVKGNVINLSLGFSHPVDHQLPAGITAECPTQTEIVLKGADKQVIGQVAADLRAYRRPEPYKGK GVRYADEVVRTKEAKKK P0AG55 Large ribosomal subunit protein bL9 Escherichia coli BW25113 0.01578902 1 LEVO MQVILLDKVANLGSLGDQVNVKAGYARNFLVPQGKAVPATKKNIEFFEARRAELEAKLAEVLAAANARAEKINALETVTI ASKAGDEGKLFGSIGTRDIADAVTAAGVEVAKSEVRLPNGVLRTTGEHEVSFQVHSEVFAKVIVNVVAE P0A7R1 Large ribosomal subunit protein uL13 Escherichia coli BW25113 0.016050606 1 LEVO MKTFTAKPETVKRDWYVVDATGKTLGRLATELARRLRGKHKAEYTPHVDTGDYIIVLNADKVAVTGNKRTDKVYYHHTGH IGGIKQATFEEMIARRPERVIEIAVKGMLPKGPLGRAMFRKLKVYAGNEHNHAAQQPQVLDI P0AA10 Large ribosomal subunit protein uL14 Escherichia coli BW25113 0.013565066999999998 1 LEVO MIQEQTMLNVADNSGARRVMCIKVLGGSHRRYAGVGDIIKITIKEAIPRGKVKKGDVLKAVVVRTKKGVRRPDGSVIRFD GNACVLLNNNSEQPIGTRIFGPVTRELRSEKFMKIISLAPEVL P0ADY3 Large ribosomal subunit protein uL15 Escherichia coli BW25113 0.015008470999999999 1 LEVO MRLNTLSPAEGSKKAGKRLGRGIGSGLGKTGGRGHKGQKSRSGGGVRRGFEGGQMPLYRRLPKFGFTSRKAAITAEIRLS DLAKVEGGVVDLNTLKAANIIGIQIEFAKVILAGEVTTPVTVRGLRVTKGARAAIEAAGGKIEE P02413 Large ribosomal subunit protein uL16 Escherichia coli BW25113 0.015343326999999999 1 LEVO MLQPKRTKFRKMHKGRNRGLAQGTDVSFGSFGLKAVGRGRLTARQIEAARRAMTRAVKRQGKIWIRVFPDKPITEKPLAV (4D4)(MS6)GKGKGNVEYWVALIQPGKVLYEMDGVPEELAREAFKLAAAKLPIKTTFVTKTVM P0ADY7 Large ribosomal subunit protein bL17 Escherichia coli BW25113 0.014393656999999999 1 LEVO MRHRKSGRQLNRNSSHRQAMFRNMAGSLVRHEIIKTTLPKAKELRRVVEPLITLAKTDSVANRRLAFARTRDNEIVAKLF NELGPRFASRAGGYTRILKCGFRAGDNAPMAYIELVDRSEKAEAAAE P0AG44 Large ribosomal subunit protein uL18 Escherichia coli BW25113 0.012794667999999999 1 LEVO MDKKSARIRRATRARRKLQELGATRLVVHRTPRHIYAQVIAPNGSEVLVAASTVEKAIAEQLKYTGNKDAAAAVGKAVAE RALEKGIKDVSFDRSGFQYHGRVQALADAAREAGLQF P0C018 Large ribosomal subunit protein bL19 Escherichia coli BW25113 0.013159278 1 LEVO MSNIIKQLEQEQMKQDVPSFRPGDTVEVKVWVVEGSKKRLQAFEGVVIAIRNRGLHSAFTVRKISNGEGVERVFQTHSPV VDSISVKRRGAVRKAKLYYLRERTGKAARIKERLN P0A7K6 Large ribosomal subunit protein bL20 Escherichia coli BW25113 0.013528024 1 LEVO MARVKRGVIARARHKKILKQAKGYYGARSRVYRVAFQAVIKAGQYAYRDRRQRKRQFRQLWIARINAAARQNGISYSKFI NGLKKASVEIDRKILADIAVFDKVAFTALVEKAKAALA P0A7L3 Large ribosomal subunit protein bL21 Escherichia coli BW25113 0.011586374 1 LEVO MYAVFQSGGKQHRVSEGQTVRLEKLDIATGETVEFAEVLMIANGEEVKIGVPFVDGGVIKAEVVAHGRGEKVKIVKFRRR KHYRKQQGHRQWFTDVKITGISA P0AG48 Large ribosomal subunit protein uL22 Escherichia coli BW25113 0.012253359 1 LEVO METIAKHRHARSSAQKVRLVADLIRGKKVSQALDILTYTNKKAAVLVKKVLESAIANAEHNDGADIDDLKVTKIFVDEGP SMKRIMPRAKGRADRILKRTSHITVVVSDR P61175 Large ribosomal subunit protein uL23 Escherichia coli BW25113 0.01122216 1 LEVO MIREERLLKVLRAPHVSEKASTAMEKSNTIVLKVAKDATKAEIKAAVQKLFEVEVEVVNTLVVKGKVKRHGQRIGRRSDW KKAYVTLKEGQNLDFVGGAE P0ADZ0 Large ribosomal subunit protein uL24 Escherichia coli BW25113 0.011339249999999999 1 LEVO MAAKIRRDDEVIVLTGKDKGKRGKVKNVLSSGKVIVEGINLVKKHQKPVPALNQPGGIVEKEAAIQVSNVAIFNAATGKA DRVGFRFEDGKKVRFFKSNSETIK P60624 Large ribosomal subunit protein bL25 Escherichia coli BW25113 0.010713465 1 LEVO MFTINAEVRKEQGKGASRRLRAANKFPAIIYGGKEAPLAIELDHDKVMNMQAKAEFYSEVLTIVVDGKEIKVKAQDVQRH PYKPKLQHIDFVRA P68919 Large ribosomal subunit protein bL27 Escherichia coli BW25113 0.00914654 1 LEVO MAHKKAGGSTRNGRDSEAKRLGVKRFGGESVLAGSIIVRQRGTKFHAGANVGCGRDHTLFAKADGKVKFEVKGPKNRKFI SIEAE P0A7L8 Large ribosomal subunit protein bL28 Escherichia coli BW25113 0.009027550999999998 1 LEVO MSRVCQVTGKRPVTGNNRSHALNATKRRFLPNLHSHRFWVESEKRFVTLRVSAKGMRVIDKKGIDTVLAELRARGEKY P0A7M2 Large ribosomal subunit protein uL29 Escherichia coli BW25113 0.0072864639999999994 1 LEVO MKAKELREKSVEELNTELLNLLREQFNLRMQAASGQLQQSHLLKQVRRDVARVKTLLNEKAGA P0A7M6 Large ribosomal subunit protein uL30 Escherichia coli BW25113 0.006554819999999999 1 LEVO MAKTIKITQTRSAIGRLPKHKATLLGLGLRRIGHTVEREDTPAIRGMINAVSFMVKVEE P0AG51 Large ribosomal subunit protein bL32 Escherichia coli BW25113 0.006463444999999999 1 LEVO MAVQQNKPTRSKRGMRRSHDALTAVTSLSVDKTSGEKHLRHHITADGYYRGRKVIAK P0A7N4 Large ribosomal subunit protein bL33 Escherichia coli BW25113 0.006388631 1 LEVO MAKGIREKIKLVSSAGTGHFYTTTKNKRTKPEKLELKKFDPVVRQHVIYKEAKIK P0A7N9 Large ribosomal subunit protein bL34 Escherichia coli BW25113 0.005397463 1 LEVO MKRTFQPSVLKRNRSHGFRARMATKNGRQVLARRRAKGRARLTVSK P0A7P5 Large ribosomal subunit protein bL35 Escherichia coli BW25113 0.007313032 1 LEVO MPKIKTVRGAAKRFKKTGKGGFKHKHANLRHILTKKATKRKRHLRPKAMVSKGDLGLVIACLPYA P0A7Q1 Large ribosomal subunit protein bL36A Escherichia coli BW25113 0.00437739 1 LEVO MKVRASVKKLCRNCKIVKRDGVIRVICSAEPKHKQRQG P0A7Q6 Large ribosomal subunit protein bL31 Escherichia coli BW25113 0.007887116999999999 1 LEVO MKKDIHPKYEEITASCSCGNVMKIRSTVGHDLNLDVCSKCHPFFTGKQRDVATGGRVDRFNKRFNIPGSK P0A7M9 mRNA Escherichia phage T4 0.021199773 1 GGCAACCUAAAACUUACACAAAUUAAAAAGGAAAUAGACAUGUUCAAAGUCGAAAAAUCUACUACU P-site tRNA-fMet Escherichia coli BW25113 0.024832918 1 CGCGGGG(4SU)GGAGCAGCCUGG(H2U)AGCUCGUCGGG(OMC)UCAUAACCCGAAGAUCGUCGG(5MU)(PSU)CAAA UCCGGCCCCCGCAACCA LN832404.1 MAGNESIUM ION 2.4305e-05 457 MG singleParticle particle 7.6 20.0 C8H18N2O4S HEPES, 4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid 10.0 Mg(C2H3O2)2 Magnesium acetate 100.0 NH4Cl Ammonium chloride 6.0 C2H6OS 2-mercaptoethanol

The Buffer pH was adjusted to 7.6 using KOH.

ETHANE 100 277 FEI VITROBOT MARK IV

50nM ribosomes were incubated with 250nM tRNA and mRNA

FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 0.5 2.5 105000.0 GATAN K3 (6k x 4k) COUNTING 1 6057 40.0 1 764584 RELION 3.1.3 PHASE FLIPPING AND AMPLITUDE CORRECTION 5 2.59 FSC 0.143 CUT-OFF RELION 3.1.3 244856 MAXIMUM LIKELIHOOD RELION 3.1.3 MAXIMUM LIKELIHOOD crYOLO 1.8.2 10 39006.0 RELION 3.1.3 emd_60059.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 530 530 530 0 0 0 530 530 530 439.9 439.9 439.9 90.0 90.0 90.0 X Y Z -0.122126 0.2391415 -0.00053414976 0.008432967 0.83 0.83 0.83 0.024 AUTHOR ::::EMDATABANK.org::::EMD-60059:::: 7K00 PDB experimental model FLEXIBLE FIT emd_60059_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 530 530 530 0 0 0 530 530 530 439.9 439.9 439.9 90.0 90.0 90.0 X Y Z -0.016256036 0.07604819 -0.0005341691 0.0034491788 0.83 0.83 0.83 AUTHOR ::::EMDATABANK.org::::EMD-60059:::: Before postprocess emd_60059_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 530 530 530 0 0 0 530 530 530 439.9 439.9 439.9 90.0 90.0 90.0 X Y Z -0.038565185 0.09496674 -0.00053499825 0.00546315 0.83 0.83 0.83 AUTHOR ::::EMDATABANK.org::::EMD-60059:::: emd_60059_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 530 530 530 0 0 0 530 530 530 439.9 439.9 439.9 90.0 90.0 90.0 X Y Z -0.034953415 0.098604426 -0.0005333013 0.0053910213 0.83 0.83 0.83 AUTHOR ::::EMDATABANK.org::::EMD-60059::::