Cryo-EM structure of the Acinetobacter baumannii Ribosome: 30S subunit

2024-10-16 REL RCSB RCSB RCSB 2019-11-25 2020-01-01 2020-02-05 2024-10-16 National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI) United States Cryo-EM structure of the Acinetobacter baumannii Ribosome: 30S subunit Morgan CE Yu EW Ribosome, Acinetobacter baumannii Morgan CE Huang W Rudin SD Taylor DJ Kirby JE Bonomo RA Yu EW Cryo-electron Microscopy Structure of the Acinetobacter baumannii 70S Ribosome and Implications for New Antibiotic Development. Mbio US 11 2020 31964740 doi:10.1128/mBio.03117-19 2150-7511 6v3e FULLOVERLAP Acinetobacter baumannii Small ribosomal subunit Acinetobacter baumannii Small ribosomal subunit 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 Acinetobacter baumannii AB0057 2.3 16s Ribosomal RNA Acinetobacter baumannii 0.500297531 1 UUUAACUGAAGAGUUUGAUCAUGGCUCAGAUUGAACGCUGGCGGCAGGCUUAACACAUGCAAGUCGAGCGGGGGAAGGUA GCUUGCUACCGGACCUAGCGGCGGACGGGUGAGUAAUGCUUAGGAAUCUGCCUAUUAGUGGGGGACAACAUCUCGAAAGG GAUGCUAAUACCGCAUACGUCCUACGGGAGAAAGCAGGGGAUCUUCGGACCUUGCGCUAAUAGAUGAGCCUAAGUCGGAU UAGCUAGUUGGUGGGGUAAAGGCCUACCAAGGCGACGAUCUGUAGCGGGUCUGAGAGGAUGAUCCGCCACACUGGGACUG AGACACGGCCCAGACUCCUACGGGAGGCAGCAGUGGGGAAUAUUGGACAAUGGGGGGAACCCUGAUCCAGCCAUGCCGCG UGUGUGAAGAAGGCCUUAUGGUUGUAAAGCACUUUAAGCGAGGAGGAGGCUACUCUAGUUAAUACCUAGGGAUAGUGGAC GUUACUCGCAGAAUAAGCACCGGCUAACUCUG(PSU)GCCAGCAGCC(7MG)CGGUAAUACAGAGGGUGCGAGCGUUAAU CGGAUUUACUGGGCGUAAAGCGUGCGUAGGCGGCUUAUUAAGUCGGAUGUGAAAUCCCCGAGCUUAACUUGGGAAUUGCA UUCGAUACUGGUGAGCUAGAGUAUGGGAGAGGAUGGUAGAAUUCCAGGUGUAGCGGUGAAAUGCGUAGAGAUCUGGAGGA AUACCGAUGGCGAAGGCAGCCAUCUGGCCUAAUACUGACGCUGAGGUACGAAAGCAUGGGGAGCAAACAGGAUUAGAUAC CCUGGUAGUCCAUGCCGUAAACGAUGUCUACUAGCCGUUGGGGCCUUUGAGGCUUUAGUGGCGCAGCUAACGCGAUAAGU AGACCGCCUGGGGAGUACGGUCGCAAGACUAAAACUCAAAUGAAUUGACGGGGGCCCGCACAAGCGGUGGAGCAUGUGGU UUAAUUCGAU(2MG)(5MC)AACGCGAAGAACCUUACCUGGCCUUGACAUACUAGAAACUUUCCAGAGAUGGAUUGGUGC CUUCGGGAAUCUAGAUACAGGUGCUGCAUGGCUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCGCAACGAGC GCAACCCUUUUCCUUACUUGCCAGCAUUUCGGAUGGGAACUUUAAGGAUACUGCCAGUGACAAACUGGAGGAAGGCGGGG ACGACGUCAAGUCAUCAUG(2MG)CCCUUACGGCCAGGGCUACACACGUGCUACAAUGGUCGGUACAAAGGGUUGCUACA CAGCGAUGUGAUGCUAAUCUCAAAAAGCCGAUCGUAGUCCGGAUUGGAGUCUGCAACUCGACUCCAUGAAGUCGGAAUCG CUAGUAAUCGCGGAUCAGAAUGCCGCGGUGAAUACGUUCCCGGGCCUUGUACACACCG(4OC)CCGUCACACCAUGGGAG UUUGUUGCACCAGAAGUAGCUAGCCUAACUGCAAAGAGGGCGGUUACCACGGUGUGGCCGAUGACUGGGGUGAAGUCG (UR3)AACAAGGUAGCCGUAGGGG(MA6)(MA6)CCUGCGGCUGGAUCACCUCCUUAACGAA CP044356.1 30S ribosomal protein S2 Acinetobacter baumannii 0.027680357 1 LEVO MADYNVSMRDLLQAGAHFGHQTRFWNPKMRQYIFGARNKIHIINLEHTVPALNDALNFANQLASKKNKVLFVGTKRAASN IIREQAQRAGQPYVDHRWLGGMLTNWKTLRQSINRLKDLQTQSQDGTFAKLTKREALERTREMEKLERSLGGVKNMGGLP DALFVIDVDHEAIAIKEAKNLGIPVIGIVDTNSNPDNVDYVIPGNDDAIRAVTLYASAMADAILAGKEYAQSQANAQAKG DDAAKDASEA V5VBC2 30S ribosomal protein S3 Acinetobacter baumannii 0.027972460999999997 1 LEVO MGQKVHPIGIRLGVVKRHNANWYANPKQYAEYLLKDLQVREFLTKKLKNAMVSNILIERPSGAAKVTISTARPGIVIGKK GEDIEKLQRELTNIMGVPAQVSINEIDRPDLDARLVAEAIASQLEKRVMFRRAMKRAVQNTMRAGAKGIKVEVSGRLGGA EIARTEWYREGRVPLHTLRADIDYATMRAETTYGTIGVKVWIFRGEILGGMKQVMNPAPAEERPAKRGRGRGEGQERRGR RGDRAADKGE V5V9N0 30S ribosomal protein S4 Acinetobacter baumannii (strain AB0057) AB0057 0.023311817999999998 1 LEVO MARYIGPKCKLSRREGTDLQLKSGVKPFDVKTKKANKAPGQHGQARGGKQSEYSLQLREKQKVRRIYGVLERQFSNYYKE AARVKGATGENLLKLLESRLDNVVYRMGFGSTRAEARQLVSHRSITLNGRRVNIASIQVKAGDVIAVHEGAKQQLRIKNA IELAAQRGIPAWIEVDHSKLEGTFKAAPDRSDLPAEINESLIVELYSK B7IA15 30S ribosomal protein S5 Acinetobacter baumannii (strain AB0057) AB0057 0.017181765999999998 1 LEVO MAKVEQNEGLVEKLVAVDRVAKVVKGGRIFSFTALTVVGDGNGRVGFGRGKAREVPAAISKALEAARRNMITVDLAGTTL QHPVNARHGASRVYMQPASEGTGVIAGGAMRAVLEAAGVHNVLAKCYGSTNAANVVNATFKGLRDMTSPEKVAAKRGKSV EEIQG B7IA22 30S ribosomal protein S6 Acinetobacter baumannii (strain AB0057) AB0057 0.014986951999999998 1 LEVO MRHYEIVLLVHPDQSDQVVGMVERYISQIKEADGQIHRLEDWGRRQLAYPINKIHKAHYILMNVECGQSTLDELEELFRY NDAIIRNLIIRREHAITEESLLAKSAEEKRARKAQREEAQQVAQEAE B7IBC1 30S ribosomal protein S7 Acinetobacter baumannii (strain AB0057) AB0057 0.017733699 1 LEVO MPRRRVVAAREILPDPKFSSQTIAKFMNHVMQDGKKSIAESIVYGALERVQEKNKVDPVEFFETTLEKVRPMVEVKARRV GGATYQVPMEVRPSRRTALAMRWLVDAAAKRSEKTMALRLAGELLDAAEGKGAAIKKREDVHRMAEANKAFSHYRF B7I7S0 30S ribosomal protein S8 Acinetobacter baumannii (strain AB0057) AB0057 0.014250666999999998 1 LEVO MSMQDTVADMLTRVRNAQMAKKQTVSMPSSKLKVAIANVLQQEGYISNVEVAQEETKSTLTITLKYFEGKPVIEMVKRVS RPGLRQYRGKDKLPSVKQGLGIAIVSTSKGIMTDRAARAAGIGGEVIAFVS B7IA25 30S ribosomal protein S9 Acinetobacter baumannii 0.01428761 1 LEVO MATNYGTGRRKTATARVFLSAGTGKLVINNRTLEQYFGRETARMVVRQPLELLEATEKYDLYITVKGGGIGGQAGAIRHG ITRALIAADETLKPVLRQAGFVTRDAREVERKKLGLRKARKRPQFSKR V5VBA5 30S ribosomal protein S10 Acinetobacter sp. ANC 5600 0.011718531 1 LEVO MSNQRIRIRLKSFDHRLIDQSAQEIVETAKRTGAQVCGPIPMPTRIERFNVLTSPHVNKDARDQYEIRTYKRLIDIVQPT DKTVDALMKLDLAAGVDVQIALG A0A1T1GZ10 30S ribosomal protein S11 Acinetobacter sp. 263903-1 0.013558512 1 LEVO MAKDTRTRKKVTRTVSEGVAHIHASFNNTIVTITDRQGNALAWATSGGQGFRGSRKSTPFAAQVAAEVAGKAALDYGLKN LDVLVKGPGPGRESAVRALGAVGYKINSITDVTPIPHNGCRPPKKRRV A0A062C259 30S ribosomal protein S12 Acinetobacter baumannii (strain AB0057) AB0057 0.013797133999999999 1 LEVO MATTNQLIRKGRTTLVEKSKVPALKACPQRRGVCTRVYTTTPKKPNSAMRKVCRVRLTSGFEVSSYIGGEGHNLQEHSVV LIRGGRVKDLPGVRYHTVRGSLDCAGVKDRNQSRSKYGAKRPKK B7I7R9 30S ribosomal protein S13 Acinetobacter baumannii (strain AB0057) AB0057 0.013295635 1 LEVO MARIAGVNIPDNKHAVISLTYIFGIGRHTAKNILAAVGITETTKIRELDDAQLDAIRAEVAKVPTEGDLRREISMNIKRL MDLGCYRGLRHRRSLPVRGQRTKTNARTRKGPRKPIKK B7IA17 30S ribosomal protein S14 Acinetobacter baumannii (strain AB0057) AB0057 0.011438427 1 LEVO MAKKGMINRELKREKTVAKYAAKRAELKATIANVNASDEERFEAMLKLQALPRNASPVRLRNRCGLTGRPHGYFRKFGLS RNKLRDTVMQGDVPGVVKASW B7IA26 30S ribosomal protein S15 Acinetobacter baumannii (strain AB0057) AB0057 0.0101456 1 LEVO MALTNADRAEIIAKFARAENDTGSPEVQVALLTAQINDLQGHFKAHKHDHHSRRGLIRMVNQRRKLLDYLNGKDHERYTA LIGALGLRR B7I3U0 30S ribosomal protein S16 Acinetobacter baumannii 0.011223059999999998 1 LEVO MLPMVGAGIIRKNYKAFIMVVIRLARGGAKKRPFYQIVVTDSRNARDGRFIERIGFFNPTAQGQAEKLRLDADRFAHWVS QGAQPSERVASLAAQAKKATA A0A1V3DIZ9 30S ribosomal protein S17 Acinetobacter baumannii (strain AB0057) AB0057 0.009543101 1 LEVO MSEKTVRTLTGKVVSDKMDKSIVVLIERRVQHPLYGKSIRRSTKLHAHDENNVAKIGDVVTIKESRPISKTKAWTLVEVV EAAAE B7IA30 30S ribosomal protein S18 Acinetobacter venetianus 0.009009452 1 LEVO MARFYRRRKFCRFTAENVAYIDYKDIDTLKQYITENGKIVPSRITGTKARYQRQLALAIKQARYLSLIPYTDNHK A0A150HZL5 30S ribosomal protein S19 Acinetobacter baumannii (strain AB0057) AB0057 0.010206957 1 LEVO MPRSLKKGPFVDAHLFAKVEAAVASNSRKPIKTWSRRSMILPDFVGLTISVHNGRNHVPVIVTEHMVGHKLGEFAPTRTY RGHGVDKKSKR B7IA35 30S ribosomal protein S20 Acinetobacter baumannii (strain AB0057) AB0057 0.00972342 1 LEVO MANSAQAKKRARQNVKARKHNASLRSMVRTYIKRTLSAIAGGDYAVATEAYKKAVPVIDRMADKGIIHKNKAARHKSRLN AQVKALAN B7I5N9 singleParticle particle 7.6 ETHANE FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 GATAN K2 SUMMIT (4k x 4k) SUPER-RESOLUTION 40.0 1 4.4 FSC 0.143 CUT-OFF cryoSPARC 10555 MAXIMUM LIKELIHOOD cryoSPARC MAXIMUM LIKELIHOOD cryoSPARC RELION Focused classification emd_21034.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 512 512 512 0 0 0 512 512 512 544.768 544.768 544.768 90.0 90.0 90.0 X Y Z -0.32376146 1.7774217 0.0023092674 0.032587904 1.064 1.064 1.064 0.25 AUTHOR ::::EMDATABANK.org::::EMD-21034:::: 30S composite map created with two separate masked refinements (30S head and 30S core). 5AFI PDB experimental model