Cryo-EM structure of Escherichia coli hibernating ribosome with RNase I mutant

2025-07-30 REL PDBj INITIAL_RELEASE REPOSITORY PDBj PDBj 2024-07-09 2025-07-30 2025-07-30 2025-07-30 Japan Agency for Medical Research and Development (AMED) JP22ama121001 Japan Japan Society for the Promotion of Science (JSPS) 20K21266 Japan Cryo-EM structure of Escherichia coli hibernating ribosome with RNase I mutant Tanzawa T Minami A Yoshida H Kato T Ogawa T Complex, Hibernating, Protein synthesis, RNase, RIBOSOME Minami A Tanzawa T Miyata T Makino F Yang Z Funatsu T Kuzuyama T Yoshida H Kato T Ogawa T Molecular basis of RNase I-mediated rRNA degradation regulated by ribosomes Biorxiv US 2025 doi:10.1101/2024.07.29.605612 2692-8205 9iot FULLOVERLAP Escherichia coli 70S ribosome in complex with HPF, RMF, and RNase I Escherichia coli 70S ribosome in complex with HPF, RMF, and RNase I 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 55 56 Escherichia coli 0.9 50S Large ribosomal subunit 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 Escherichia coli 30S Small ribosomal subunit 1 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 56 Escherichia coli Large ribosomal subunit protein uL29 Escherichia coli 0.0072864639999999994 1 LEVO MKAKELREKSVEELNTELLNLLREQFNLRMQAASGQLQQSHLLKQVRRDVARVKTLLNEKAGA P0A7M6 Large ribosomal subunit protein uL30 Escherichia coli 0.006554819999999999 1 LEVO MAKTIKITQTRSAIGRLPKHKATLLGLGLRRIGHTVEREDTPAIRGMINAVSFMVKVEE P0AG51 Large ribosomal subunit protein bL32 Escherichia coli 0.006463444999999999 1 LEVO MAVQQNKPTRSKRGMRRSHDALTAVTSLSVDKTSGEKHLRHHITADGYYRGRKVIAK P0A7N4 Large ribosomal subunit protein bL33 Escherichia coli 0.006388631 1 LEVO MAKGIREKIKLVSSAGTGHFYTTTKNKRTKPEKLELKKFDPVVRQHVIYKEAKIK P0A7N9 50S ribosomal protein L34 Escherichia coli 0.005397463 1 LEVO MKRTFQPSVLKRNRSHGFRARMATKNGRQVLARRRAKGRARLTVSK P0A7P5 Large ribosomal subunit protein bL35 Escherichia coli 0.007313032 1 LEVO MPKIKTVRGAAKRFKKTGKGGFKHKHANLRHILTKKATKRKRHLRPKAMVSKGDLGLVIACLPYA P0A7Q1 50S ribosomal protein L36 Escherichia coli 0.00437739 1 LEVO MKVRASVKKLCRNCKIVKRDGVIRVICSAEPKHKQRQG P0A7Q6 5S rRNA Escherichia coli 0.038814113 1 UGCCUGGCGGCAGUAGCGCGGUGGUCCCACCUGACCCCAUGCCGAACUCAGAAGUGAAACGCCGUAGCGCCGAUGGUAGU GUGGGGUCUCCCCAUGCGAGAGUAGGGAACUGCCAGGCAU CP041110.1 Large ribosomal subunit protein uL2 Escherichia coli 0.029923619 1 LEVO MAVVKCKPTSPGRRHVVKVVNPELHKGKPFAPLLEKNSKSGGRNNNGRITTRHIGGGHKQAYRIVDFKRNKDGIPAVVER LEYDPNRSANIALVLYKDGERRYILAPKGLKAGDQIQSGVDAAIKPGNTLPMRNIPVGSTVHNVEMKPGKGGQLARSAGT YVQIVARDGAYVTLRLRSGEMRKVEADCRATLGEVGNAEHMLRVLGKAGAARWRGVRPTVRGTAMNPVDHPHGGGEGRNF GKHPVTPWGVQTKGKKTRSNKRTDKFIVRRRSK P60422 50S ribosomal protein L3 Escherichia coli 0.022291562 1 LEVO MIGLVGKKVGMTRIFTEDGVSIPVTVIEVEANRVTQVKDLANDGYRAIQVTTGAKKANRVTKPEAGHFAKAGVEAGRGLW EFRLAEGEEFTVGQSISVELFADVKKVDVTGTSKGKGFAGTVKRWNFRTQDATHGNSLSHRVPGSIGQN(MEQ)TPGKVF KGKKMAGQMGNERVTVQSLDVVRVDAERNLLLVKGAVPGATGSDLIVKPAVKA P60438 50S ribosomal protein L4 Escherichia coli 0.022121566 1 LEVO MELVLKDAQSALTVSETTFGRDFNEALVHQVVVAYAAGARQGTRAQKTRAEVTGSGKKPWRQKGTGRARSGSIKSPIWRS GGVTFAARPQDHSQKVNKKMYRGALKSILSELVRQDRLIVVEKFSVEAPKTKLLAQKLKDMALEDVLIITGELDENLFLA ARNLHKVDVRDATGIDPVSLIAFDKVVMTADAVKQVEEMLA P60723 Large ribosomal subunit protein uL5 Escherichia coli 0.020333611 1 LEVO MAKLHDYYKDEVVKKLMTEFNYNSVMQVPRVEKITLNMGVGEAIADKKLLDNAAADLAAISGQKPLITKARKSVAGFKIR QGYPIGCKVTLRGERMWEFFERLITIAVPRIRDFRGLSAKSFDGRGNYSMGVREQIIFPEIDYDKVDRVRGLDITITTTA KSDEEGRALLAAFDFPFRK P62399 Large ribosomal subunit protein uL6 Escherichia coli 0.018932791 1 LEVO MSRVAKAPVVVPAGVDVKINGQVITIKGKNGELTRTLNDAVEVKHADNTLTFGPRDGYADGWAQAGTARALLNSMVIGVT EGFTKKLQLVGVGYRAAVKGNVINLSLGFSHPVDHQLPAGITAECPTQTEIVLKGADKQVIGQVAADLRAYRRPEPYKGK GVRYADEVVRTKEAKKK P0AG55 Large ribosomal subunit protein bL9 Escherichia coli 0.00433008 1 LEVO MQVILLDKVANLGSLGDQVNVKAGYARNFLVPQGKAVPATK P0A7R1 50S ribosomal protein L13 Escherichia coli 0.016050606 1 LEVO MKTFTAKPETVKRDWYVVDATGKTLGRLATELARRLRGKHKAEYTPHVDTGDYIIVLNADKVAVTGNKRTDKVYYHHTGH IGGIKQATFEEMIARRPERVIEIAVKGMLPKGPLGRAMFRKLKVYAGNEHNHAAQQPQVLDI P0AA10 50S ribosomal protein L14 Escherichia coli 0.013565066999999998 1 LEVO MIQEQTMLNVADNSGARRVMCIKVLGGSHRRYAGVGDIIKITIKEAIPRGKVKKGDVLKAVVVRTKKGVRRPDGSVIRFD GNACVLLNNNSEQPIGTRIFGPVTRELRSEKFMKIISLAPEVL P0ADY3 Large ribosomal subunit protein uL15 Escherichia coli 0.014994442999999998 1 LEVO MRLNTLSPAEGSKKAGKRLGRGIGSGLGKTGGRGHKGQKSRSGGGVRRGFEGGQMPLYRRLPKFGFTSRKAAITAEVRLS DLAKVEGGVVDLNTLKAANIIGIQIEFAKVILAGEVTTPVTVRGLRVTKGARAAIEAAGGKIEE A7ZSJ0 Large ribosomal subunit protein uL16 Escherichia coli 0.015327261 1 LEVO MLQPKRTKFRKMHKGRNRGLAQGTDVSFGSFGLKAVGRGRLTARQIEAARRAMTRAVKRQGKIWIRVFPDKPITEKPLAV (4D4)MGKGKGNVEYWVALIQPGKVLYEMDGVPEELAREAFKLAAAKLPIKTTFVTKTVM P0ADY7 Large ribosomal subunit protein bL17 Escherichia coli 0.014393656999999999 1 LEVO MRHRKSGRQLNRNSSHRQAMFRNMAGSLVRHEIIKTTLPKAKELRRVVEPLITLAKTDSVANRRLAFARTRDNEIVAKLF NELGPRFASRAGGYTRILKCGFRAGDNAPMAYIELVDRSEKAEAAAE P0AG44 Large ribosomal subunit protein uL18 Escherichia coli 0.012794667999999999 1 LEVO MDKKSARIRRATRARRKLQELGATRLVVHRTPRHIYAQVIAPNGSEVLVAASTVEKAIAEQLKYTGNKDAAAAVGKAVAE RALEKGIKDVSFDRSGFQYHGRVQALADAAREAGLQF P0C018 Large ribosomal subunit protein bL19 Escherichia coli 0.013159278 1 LEVO MSNIIKQLEQEQMKQDVPSFRPGDTVEVKVWVVEGSKKRLQAFEGVVIAIRNRGLHSAFTVRKISNGEGVERVFQTHSPV VDSISVKRRGAVRKAKLYYLRERTGKAARIKERLN P0A7K6 Large ribosomal subunit protein bL20 Escherichia coli 0.013528024 1 LEVO MARVKRGVIARARHKKILKQAKGYYGARSRVYRVAFQAVIKAGQYAYRDRRQRKRQFRQLWIARINAAARQNGISYSKFI NGLKKASVEIDRKILADIAVFDKVAFTALVEKAKAALA P0A7L3 50S ribosomal protein L21 Escherichia coli 0.011586374 1 LEVO MYAVFQSGGKQHRVSEGQTVRLEKLDIATGETVEFAEVLMIANGEEVKIGVPFVDGGVIKAEVVAHGRGEKVKIVKFRRR KHYRKQQGHRQWFTDVKITGISA P0AG48 50S ribosomal protein L22 Escherichia coli 0.012253359 1 LEVO METIAKHRHARSSAQKVRLVADLIRGKKVSQALDILTYTNKKAAVLVKKVLESAIANAEHNDGADIDDLKVTKIFVDEGP SMKRIMPRAKGRADRILKRTSHITVVVSDR P61175 Large ribosomal subunit protein uL23 Escherichia coli 0.01122216 1 LEVO MIREERLLKVLRAPHVSEKASTAMEKSNTIVLKVAKDATKAEIKAAVQKLFEVEVEVVNTLVVKGKVKRHGQRIGRRSDW KKAYVTLKEGQNLDFVGGAE P0ADZ0 Large ribosomal subunit protein uL24 Escherichia coli 0.011210069 1 LEVO MAAKIRRDDEVIVLTGKDKGKRGKVKNVLSSGKVIVEGINLVKKHQKPVPALNQPGGIVEKEAAIQVSNVAIFNAATGKA DRVGFRFEDGKKVRFFKSNSETI P60624 50S ribosomal protein L25 Escherichia coli 0.010713465 1 LEVO MFTINAEVRKEQGKGASRRLRAANKFPAIIYGGKEAPLAIELDHDKVMNMQAKAEFYSEVLTIVVDGKEIKVKAQDVQRH PYKPKLQHIDFVRA P68919 Large ribosomal subunit protein bL27 Escherichia coli 0.00914654 1 LEVO MAHKKAGGSTRNGRDSEAKRLGVKRFGGESVLAGSIIVRQRGTKFHAGANVGCGRDHTLFAKADGKVKFEVKGPKNRKFI SIEAE P0A7L8 Large ribosomal subunit protein bL28 Escherichia coli 0.009027550999999998 1 LEVO MSRVCQVTGKRPVTGNNRSHALNATKRRFLPNLHSHRFWVESEKRFVTLRVSAKGMRVIDKKGIDTVLAELRARGEKY P0A7M2 Large ribosomal subunit protein bL31 Escherichia coli 0.007613806999999999 1 LEVO MKKDIHPKYEEITASCSCGNVMKIRSTVGHDLNLDVCSKCHPFFTGKQRDVATGGRVDRFNKRFNIP P0A7M9 23S rRNA Escherichia coli 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 16S rRNA Escherichia coli 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 CP032808.1 Small ribosomal subunit protein uS2 Escherichia coli 0.026795694999999998 1 LEVO MATVSMRDMLKAGVHFGHQTRYWNPKMKPFIFGARNKVHIINLEKTVPMFNEALAELNKIASRKGKILFVGTKRAASEAV KDAALSCDQFFVNHRWLGGMLTNWKTVRQSIKRLKDLETQSQDGTFEKLTKKEALMRTRELEKLENSLGGIKDMGGLPDA LFVIDADHEHIAIKEANNLGIPVFAIVDTNSDPDGVDFVIPGNDDAIRAVTLYLGAVAATVREGRSQDLASQAEESFVEA E A7ZHQ9 Small ribosomal subunit protein uS3 Escherichia coli 0.026031316 1 LEVO MGQKVHPNGIRLGIVKPWNSTWFANTKEFADNLDSDFKVRQYLTKELAKASVSRIVIERPAKSIRVTIHTARPGIVIGKK GEDVEKLRKVVADIAGVPAQINIAEVRKPELDAKLVADSITSQLERRVMFRRAMKRAVQNAMRLGAKGIKVEVSGRLGGA EIARTEWYREGRVPLHTLRADIDYNTSEAHTTYGVIGVKVWIFKGEILGGMAAVEQPEKPAAQPKKQQRKGRK P0A7V3 Small ribosomal subunit protein uS4 Escherichia coli 0.023514199 1 LEVO MARYLGPKLKLSRREGTDLFLKSGVRAIDTKCKIEQAPGQHGARKPRLSDYGVQLREKQKVRRIYGVLERQFRNYYKEAA RLKGNTGENLLALLEGRLDNVVYRMGFGATRAEARQLVSHKAIMVNGRVVNIASYQVSPNDVVSIREKAKKQSRVKAALE LAEQREKPTWLEVDAGKMEGTFKRKPERSDLSADINEHLIVELYSK P0A7V8 Small ribosomal subunit protein uS5 Escherichia coli 0.017629398 1 LEVO MAHIEKQAGELQEKLIAVNRVSKTVKGGRIFSFTALTVVGDGNGRVGFGYGKAREVPAAIQKAMEKARRNMINVALNNGT LQHPVKGVHTGSRVFMQPASEGTGIIAGGAMRAVLEVAGVHNVLAKAYGSTNPINVVRATIDGLENMNSPEMVAAKRGKS VEEILGK P0A7W1 Small ribosomal subunit protein bS6, fully modified isoform Escherichia coli 0.011897682 1 LEVO MRHYEIVFMVHPDQSEQVPGMIERYTAAITGAEGKIHRLEDWGRRQLAYPINKLHKAHYVLMNVEAPQEVIDELETTFRF NDAVIRSMVMRTKHAVTEASPM P02358 Small ribosomal subunit protein uS7 Escherichia coli 0.020055155999999998 1 LEVO MPRRRVIGQRKILPDPKFGSELLAKFVNILMVDGKKSTAESIVYSALETLAQRSGKSELEAFEVALENVRPTVEVKSRRV GGSTYQVPVEVRPVRRNALAMRWIVEAARKRGDKSMALRLANELSDAAENKGTAVKKREDVHRMAEANKAFAHYRWLSLR SFSHQAGASSKQPALGYLN P02359 Small ribosomal subunit protein uS8 Escherichia coli 0.014146557 1 LEVO MSMQDPIADMLTRIRNGQAANKAAVTMPSSKLKVAIANVLKEEGFIEDFKVEGDTKPELELTLKYFQGKAVVESIQRVSR PGLRIYKRKDELPKVMAGLGIAVVSTSKGVMTDRAARQAGLGGEIICYVA P0A7W7 Small ribosomal subunit protein uS9 Escherichia coli 0.01488627 1 LEVO MAENQYYGTGRRKSSAARVFIKPGNGKIVINQRSLEQYFGRETARMVVRQPLELVDMVEKLDLYITVKGGGISGQAGAIR HGITRALMEYDESLRSELRKAGFVTRDARQVERKKVGLRKARRRPQFSKR P0A7X3 Small ribosomal subunit protein uS10 Escherichia coli 0.011755597 1 LEVO MQNQRIRIRLKAFDHRLIDQATAEIVETAKRTGAQVRGPIPLPTRKERFTVLISPHVNKDARDQYEIRTHLRLVDIVEPT EKTVDALMRLDLAAGVDVQISLG P0A7R5 Small ribosomal subunit protein uS11 Escherichia coli 0.013871959 1 LEVO MAKAPIRARKRVRKQVSDGVAHIHASFNNTIVTITDRQGNALGWATAGGSGFRGSRKSTPFAAQVAAERCADAVKEYGIK NLEVMVKGPGPGRESTIRALNAAGFRITNITDVTPIPH(IAS)GCRPPKKRRV P0A7R9 Small ribosomal subunit protein uS12 Escherichia coli 0.013814248999999999 1 LEVO MATVNQLVRKPRARKVAKSNVPALEACPQKRGVCTRVYTTTPKKPNSALRKVCRVRLTNGFEVTSYIGGEGHNLQEHSVI LIRGGRVK(D2T)LPGVRYHTVRGALDCSGVKDRKQARSKYGVKRPKA P0A7S3 Small ribosomal subunit protein uS13 Escherichia coli 0.013128467 1 LEVO MARIAGINIPDHKHAVIALTSIYGVGKTRSKAILAAAGIAEDVKISELSEGQIDTLRDEVAKFVVEGDLRREISMSIKRL MDLGCYRGLRHRRGLPVRGQRTKTNARTRKGPRKPIKK P0A7S9 Small ribosomal subunit protein uS14 Escherichia coli 0.011606559999999998 1 LEVO MAKQSMKAREVKRVALADKYFAKRAELKAIISDVNASDEDRWNAVLKLQTLPRDSSPSRQRNRCRQTGRPHGFLRKFGLS RIKVREAAMRGEIPGLKKASW P0AG59 Small ribosomal subunit protein uS15 Escherichia coli 0.010290816 1 LEVO MSLSTEATAKIVSEFGRDANDTGSTEVQVALLTAQINHLQGHFAEHKKDHHSRRGLLRMVSQRRKLLDYLKRKDVARYTQ LIERLGLRR P0ADZ4 Small ribosomal subunit protein bS16 Escherichia coli 0.009207571999999999 1 LEVO MVTIRLARHGAKKRPFYQVVVADSRNARNGRFIERVGFFNPIASEKEEGTRLDLDRIAHWVGQGATISDRVAALIKEVNK AA P0A7T3 Small ribosomal subunit protein uS17 Escherichia coli 0.009724491 1 LEVO MTDKIRTLQGRVVSDKMEKSIVVAIERFVKHPIYGKFIKRTTKLHVHDENNECGIGDVVEIRECRPLSKTKSWTLVRVVE KAVL P0AG63 Small ribosomal subunit protein bS18 Escherichia coli 0.009005471999999999 1 LEVO MARYFRRRKFCRFTAEGVQEIDYKDIATLKNYITESGKIVPSRITGTRAKYQRQLARAIKRARYLSLLPYTDRHQ P0A7T7 Small ribosomal subunit protein uS19 Escherichia coli 0.010455355 1 LEVO MPRSLKKGPFIDLHLLKKVEKAVESGDKKPLRTWSRRSTIFPNMIGLTIAVHNGRQHVPVFVTDEMVGHKLGEFAPTRTY RGHAADKKAKKK P0A7U3 Small ribosomal subunit protein bS20 Escherichia coli 0.009708464 1 LEVO MANIKSAKKRAIQSEKARKHNASRRSMMRTFIKKVYAAIEAGDKAAAQKAFNEMQPIVDRQAAKGLIHKNKAARHKANLT AQINKLA P0A7U7 30S ribosomal protein S21 Escherichia coli 0.008524039 1 LEVO MPVIKVRENEPFDVALRRFKRSCEKAGVLAEVRRREFYEKPTTERKRAKASAVKRHAKKLARENARRTRLY P68679 Ribosome hibernation promoting factor Escherichia coli 0.010767245 1 LEVO MQLNITGNNVEITEALREFVTAKFAKLEQYFDRINQVYVVLKVEKVTHTSDATLHVNGGEIHASAEGQDMYAAIDGLIDK LARQLTKHKDKLKQH P0AFX0 Ribosome modulation factor Escherichia coli 0.006520522999999999 1 LEVO MKRQKRDRLERAHQRGYQAGIAGRSKEMCPYQTLNQRSQWLGGWREAMADRVVMA P0AFW2 Ribonuclease I Escherichia coli 0.029673652 1 Escherichia coli BL21(DE3) LEVO MKAFWRNAALLAVSLLPFSSANALALQAKQYGDFDRYVLALSWQTGFCQSQHDRNRNERDECRLQTETTNKADFLTVFGL WPGLPKSVAARGVDERRWMRFGCATRPIPNLPEARASRMCSSPETGLSLETAAKLSEVMPGAGGRSCLERYEYAKFGACF GFDPDAYFGTMVRLNQEIKESEAGKFLADNYGKTVSRRDFDAAFAKSWGKENVKAVKLTCQGNPAYLTEIQISIKADAIN APLSANSFLPQPHPGNCGKTFVIDKAGY P21338 4.6.1.21 Small ribosomal subunit protein bS1 Escherichia coli 0.061238887 1 LEVO MTESFAQLFEESLKEIETRPGSIVRGVVVAIDKDVVLVDAGLKSESAIPAEQFKNAQGELEIQVGDEVDVALDAVEDGFG ETLLSREKAKRHEAWITLEKAYEDAETVTGVINGKVKGGFTVELNGIRAFLPGSLVDVRPVRDTLHLEGKELEFKVIKLD QKRNNVVVSRRAVIESENSAERDQLLENLQEGMEVKGIVKNLTDYGAFVDLGGVDGLLHITDMAWKRVKHPSEIVNVGDE ITVKVLKFDRERTRVSLGLKQLGEDPWVAIAKRYPEGTKLTGRVTNLTDYGCFVEIEEGVEGLVHVSEMDWTNKNIHPSK VVNVGDVVEVMVLDIDEERRRISLGLKQCKANPWQQFAETHNKGDRVEGKIKSITDFGIFIGLDGGIDGLVHLSDISWNV AGEEAVREYKKGDEIAAVVLQVDAERERISLGVKQLAEDPFNNWVALNKKGAIVTGKVTAVDAKGATVELADGVEGYLRA SEASRDRVEDATLVLSVGDEVEAKFTGVDRKNRAISLSVRAKDEADEKDAIATVNKQEDANFSNNAMAEAFKAAKGE P0AG67 MAGNESIUM ION 2.4305e-05 475 MG CALCIUM ION 4.0078e-05 1 CA water 1.8015e-05 32 HOH singleParticle particle 7.6 20.0 HEPES hepes 10.0 Mg(OAc)2 magnesium acetate 30.0 NH4Cl ammonium chloride 6.0 2-mercaptoethanol 2-mercaptoethanol

20 mM HEPES-KOH (pH 7.6), 10 mM Mg(OAc)2, 30 mM NH4Cl, and 6 mM 2-mercaptoethanol

Quantifoil R2/2 GOLD 200 GLOW DISCHARGE 30 ETHANE 100 277 FEI VITROBOT MARK IV JEOL CRYO ARM 300 FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 1.0 2.0 GATAN K3 BIOQUANTUM (6k x 4k) 50.0 1 cryoSPARC 3.3.1 PHASE FLIPPING AND AMPLITUDE CORRECTION C1 2.7 FSC 0.143 CUT-OFF cryoSPARC 4.0.0 50955 MAXIMUM LIKELIHOOD cryoSPARC 3.3.1 MAXIMUM LIKELIHOOD cryoSPARC 3.3.1 cryoSPARC 3.3.1 emd_60747.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 400 400 400 0 0 0 400 400 400 487.2 487.2 487.2 90.0 90.0 90.0 X Y Z -1.5439248 3.296525 0.0005135601 0.119565405 1.218 1.218 1.218 0.5 AUTHOR ::::EMDATABANK.org::::EMD-60747:::: emd_60747_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 400 400 400 0 0 0 400 400 400 487.2 487.2 487.2 90.0 90.0 90.0 X Y Z -1.2043831 2.6511211 0.0006329855 0.08141347 1.218 1.218 1.218 AUTHOR ::::EMDATABANK.org::::EMD-60747:::: emd_60747_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 400 400 400 0 0 0 400 400 400 487.2 487.2 487.2 90.0 90.0 90.0 X Y Z -1.6110363 2.7227461 0.0021068333 0.21005803 1.218 1.218 1.218 AUTHOR ::::EMDATABANK.org::::EMD-60747:::: emd_60747_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 400 400 400 0 0 0 400 400 400 487.2 487.2 487.2 90.0 90.0 90.0 X Y Z -1.5963342 2.7624872 0.0021034346 0.20876715 1.218 1.218 1.218 AUTHOR ::::EMDATABANK.org::::EMD-60747::::