Acinetobacter baumannii ribosome-tigecycline complex

2024-05-22 REL PDBe PDBe PDBe 2020-04-22 2020-09-16 2020-09-16 2024-05-22 Wellcome Trust 203743/Z/16/Z United Kingdom Wellcome Trust 108466/Z/15/Z United Kingdom Acinetobacter baumannii ribosome-tigecycline complex - 50S subunit Nicholson D Edwards TA antibiotic, tigecycline, translation, ribosome Nicholson D Edwards TA O'Neill AJ Ranson NA Structure of the 70S Ribosome from the Human Pathogen Acinetobacter baumannii in Complex with Clinically Relevant Antibiotics. Structure UK 28 1087 1100.e3 2020 32857965 doi:10.1016/j.str.2020.08.004 0969-2126 2005 STRUE6 6ysi FULLOVERLAP Acinetobacter baumannii ribosome-tigecycline complex - 50S subunit Acinetobacter baumannii ribosome-tigecycline complex - 50S subunit 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 Acinetobacter baumannii 50S ribosomal protein L2 Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841 0.030319092 1 LEVO MPIQKCKPTSPGRRFVEKVVHDHLHKGAPYAPLVEAKKRTGGRNNNGHITTRHVGGGHKQHYRIVDFKRNKDGVPAVVER IEYDPSRTAHIALLKYADGERRYIIAPKGLRAGDKVQSGNDAPIRPGNCLPLRNMPIGSTLHNVELKIGKGAQLARSAGA SVQLLGRDGSYAIIRLRSGEMRKVHVECRAVIGEVSNQENNLRSLGKAGAARWRGVRPTVRGMAMNPIDHPHGGGEGRNK GIQPVSPWGQKAKGYKTRTNKRTTKMIIRDRRVK D0CD00 50S ribosomal protein L3 Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841 0.022512638999999997 1 LEVO MAIGLVGRKCGMTRIFTDAGVSVPVTVIEVDPNRITQIKTLETDGYQAVQVTTGERRESRVTNAQKGHFAKAGVAAGRLV KEFRVTEAELEGREVGGTIGVDLFTVGQIVDVTGQSKGKGFQGGVKRWNFRTQDATHGNSVSHRVLGSTGQNQTPGRVFK GKKMAGHLGDERVTVQGLEIVSVDTERSVLVVKGAIPGATGGDVIVRPTIKA D0CCZ7 50S ribosomal protein L4 Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841 0.021583903999999998

residues 2-12 modelled without side chains

1 LEVO MNLKTVSGSAVELSEVAFGREFNEALVHQVVTAYLAGGRQGTRAHKSRADVSGGGKKPFRQKGTGRARAGSIRSPIWVGG GKTFAARPQDWSQKVNRKMYRGAMQCILAELVRQDRLVLVEEFAVAAPKTKELLAKLNDLNAARALIVTDAVDENLYLAA RNLPHVDVVDATAIDPVSLIAFDKVVMSVAAAKKIEVELG D0CCZ8 50S ribosomal protein L5 Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841 0.020051471

modelled without side chains

1 LEVO MARLKARYNDELKAKLQEELSIKNVMEIPRITKITLNMGVGAAATDKKLLDGAVADMQLIAGQKPVVTLARKSIAGFKIR DGWPIGCKVTLRGDQMYEFLDRLISIAIPRIRDFRGFSAKSFDGRGNYSMGLKEQIVFPEIDFDKIDRIRGMDITITTTA RTDDEGRALMRAFGFPFK D0CD09 50S ribosomal protein L6 Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841 0.019126046999999997 1 LEVO MSRVAKAPVTVPNGVTVTQNGRQVEVKGSKGTLSFNLHALVELKQEEGKLQLAPAKESKDAWMQAGTARAVLNNLVKGVS EGFERKLQLVGVGYKAAVKGTVVNLNLGYSHPIDYALPEGVTAETPTATEIILKSANKQLLGQVAAEIRAYRSPEPYKGK GVRYSDEVILRKEAKKK D0CD12 50S ribosomal protein L13 Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841 0.01595144 1 LEVO MKTLSAKPAEVQHDWFVVDATGKTLGRLATEIARRLRGKHKTSYTPHVDAGDYIIVINAEQVQVTGNKALDKKYYRHTEF PGGLKETNFEKLVAHKPEEIFERAVKGMLPKGPLGYAMIKKMKVYAGSEHPHAAQQPQVLDI D0CG35 50S ribosomal protein L14 Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841 0.013523862999999999 1 LEVO MIQTETMLDVADNSGARRVQCIKVLGGSHRRYASVGDIIKVTVKEAIPRARVKKGDVMNAVVVRTKFGIRRPDGSVIRFD DNAAVILNNNKAPIATRIFGPVTRELRTEQFMKIISLAPEVL D0CD07 50S ribosomal protein L15 Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841 0.015509915 1 LEVO MTLRLNELAPAEGAKREHRRLGRGIGSGVGKTGGRGIKGQKSRKSGGVRPGFEGGQTAIYRRLPKFGFTSQIALKTAEVR LSELSKVEGDIVSLETLKAANVVRRDQIRARIVLSGEITRAFTVQGVALTKGAKAAIEAAGGKVEE D0CD16 50S ribosomal protein L16 Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841 0.015498311999999998 1 LEVO MLQPKRTKFRKVHKGRNTGLAHRGSTVSFGSIAIKATERGRMTARQIEAARRTISRRIKRGGKIFIRVFPDKPITEKPLE VRMGNGKGNVEYWVCEIKPGKILYEIEGVNEDLAREAFALAAAKLPFKTTIVTRTVM D0CD04 50S ribosomal protein L17 Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841 0.014021229999999999 1 LEVO MRHRNSGVKLGRTSSHRKAMFQNLANSLFEHELIKTTLPKAKELRRVAEPLITLAKNDTVANRRLAFARTRNAATVGKLF TVLGPRYKERNGGYLRVLKAGFRAGDAAPMAYVELVDREVNTSAE D0CD23 50S ribosomal protein L18 Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841 0.012443341 1 LEVO MNEKKQSRLRRAKSTRLHIRALGATRLCVNRTPRHIYAQVISADGGKVLAQASTLDASLRSGTTGNIEAATKVGALIAER AKAAGVTKVAFDRSGFKYHGRIKALADAAREGGLEF D0CD13 50S ribosomal protein L19 Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841 0.013619864999999998 1 LEVO MSGKHPLVQAIENSQLKTDLPEFAPGDTVVVQVKVKEGDRERLQAFEGVVIAKKNRGLNSAFTVRKISSGVGVERVFQTH SPVVAKIEVKRRGDVRRAKLYYLRDLSGKAARIREKLPARKA D0CCR8 50S ribosomal protein L20 Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841 0.013468945999999999 1 LEVO MARVKRGVVAHRRHKKILARAKGYYGARSRVYRVAFQAVIKAGQYAYRDRRQKKRQFRALWIARINAGARQNGLSYSRMI DGLKKAQVIIDRRVLADIAMHDAVAFAALAEKAKGALAA D0CA76 50S ribosomal protein L21 Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841 0.011496363999999999 1 LEVO MYAVIQSGGKQHRVVEGETLKVELLKAESGATITFDDVLMVVNGDNIQIGAPVVAGAKVTAEVIGHGRHDKIRIIKMRRR KHYRKQQGHRQWFTELKITGISG D0CDQ6 50S ribosomal protein L22 Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841 0.011960126 1 LEVO MMEVTAKLRGAAISAQKARLVADLIRGKSVAHALNILNFSNKKAAVLVKKALESAIANAEHNNSLDVDDLKVSTIYVDEG MSLKRIMPRAKGRADRITKRTCHITVKVGV D0CD02 50S ribosomal protein L23 Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841 0.011607392 1 LEVO MNNERIYQVLKGPVFSEKAQVLGDTAGVQVFKVDINATKLEIKKAVEKLFGVEVVKVNTTITKGKTKRFGRTLGRRSDVK KAYVTLKAGQDVEMADLGDTAESAAE D0CCZ9 50S ribosomal protein L24 Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841 0.011187929 1 LEVO MAKIKKGDQVIVIAGKEKGKQGTVLSVSEDRVKVEGLNLVKKHQKPNRVTGAEGGIVTQEASLHISNVAILNATTQKADR VGYQVIDGVKTRVYKSTGESVAVAK D0CD08 50S ribosomal protein L25 Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841 0.010914539000000001 1 LEVO MANFVLNAQARAEDKQGKGASRRLRRESLVPAIIYGGNAEPVAVTLELRELVKALESNAFFEEVVEIKVGDKVENVKIQA LQRHPAKNTPMHADFKRA D0C9L7 50S ribosomal protein L27 Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841 0.009072387 1 LEVO MATKKAGGSTKNGRDSNPKMLGVKVYGGQTVTAGNIIVRQRGTEFHAGANVGMGRDHTLFATADGVVKFEVKGQFGRRYV KVETV D0CDQ7 50S ribosomal protein L28 Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841 0.009125755999999999 1 LEVO MSKVCQVTGKRPVVGNNVSHANNKTKRRFEPNLHHHRFWLESEKRFVRLRLTTKGMRIIDKLGIEKVVADLRAQGQKI D0CAL0 50S ribosomal protein L29 Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841 0.0074496779999999995 1 LEVO MKTKDLREKSVEELKALLDEQQLNQFRLRMAKATGQLGKSHEVQVARKTIARIKTLLTEKQGNGQ D0CD05 50S ribosomal protein L30 Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841 0.006654787999999999 1 LEVO MKTIKVTQTKSSSHRLKNHKLCLQGLGLRRIGHTVEVQDTPSNRGMINKVYYMVSVEE D0CD15 50S ribosomal protein L31 Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841 0.008343693

modelled without side chains

1 LEVO MRADIHPKYEKLVATCSCGNVIETRSALGKETIYLDVCSACHPFYTGKQKNVDTGGRIDKFKQRFAGMSRSIKR D0CBZ8 50S ribosomal protein L32 Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841 0.007096888 1 LEVO MAVQQNRKSRSRRDMRRSHDALTENALTVDQATGETHRRHHVTKDGFYRGRQLFAKAADAE D0C9K5 50S ribosomal protein L33 Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841 0.00610531 1 LEVO MRDKIRLVSSAGTGYFYTTTKNKRTMPEKMEIKKFDPKIRQHVIFKEAKIK D0CAL1 50S ribosomal protein L34 Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841 0.005192247 1 LEVO MKRTFQPSELKRKRVHGFRARMATKAGRQVLARRRAKGRHSLTV D0CG06 23S ribosomal RNA Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841 0.9403301249999999 1 AGUCAAGUAAUUAAGUGCAUGUGGUGGAUGCCUUGGCAGUCAGAGGCGAUGAAAGACGUGAUAGCCUGCGAAAAGCUCCG GGGAGGCGGCAAAUAUCCUUUGAUCCGGAGAUGUCUGAAUGGGGGAACCCACCUACUUUAAGGUAGGUAUUGCAACAUGA AUACAUAGUGUUGCAAGGCGAACGAGGGGAAGUGAAACAUCUCAGUACCCUUAGGAAAAGAAAUCAAUUGAGAUUCCCUC AGUAGCGGCGAGCGAACGGGGAUCAGCCCAUUAAGUUAUGUGUGUUUUAGUGGAACGCUCUGGGAAGUGCGAACGUAGAG GGUGAUAUUCCCGUACACGAAAGGGCACACAUAAUGAUGACGAGUAGGGCGAGGCACGUGAAACCUUGUCUGAAUAUGGG GGGACCAUCCUCCAAGGCUAAAUACUCCUGACUGACCGAUAGUGAACCAGUACCGUGAGGGAAAGGCGAAAAGAACCCCU GUGAGGGGAGUGAAAUAGAUCCUGAAACCGCAUGCAUACAAGCAGUGGGAGCACCUUUGUGGUGUGACUGCGUACCUUUU GUAUAAUGGGUCAGCGACUUAUAUUCAGUAGCGAGGUUAACCGUAUAGGGGAGCCGUAGAGAAAUCGAGUCUUAAUAGGG CGUUUAGUUGCUGGGUAUAGACCCGAAACCAGGCGAUCUAUCCAUGAGCAGGUUGAAGGUUGGGUAACACUAACUGGAGG ACCGAACCCACUGUCGUUGAAAAGCCAGGGGAUGACUUGUGGAUAGGGGUGAAAGGCUAAUCAAGCCUGGUGAUAGCUGG UUCUCCCCGAAAGCUAUUUAGGUAGCGCCUCGGACGAAUACCAUAGGGGGUAGAGCACUGUUUCGGCUAGGGGGUCAUCC CGACUUACCAAACCGAUGCAAACUCCGAAUACCUAUGAGUACUAUCCGGGAGACAGACUGCGGGUGCUAACGUCCGUAGU CAAGAGGAAAACAAUCCAGACCGCCAGCUAAGGCCCCAAAAUCAUAGUUAAGUGGGAAACGAUGUGGGAAGGCAUAGACA GCUAGGAGGUUGGCUUAGAAGCAGCCACCCUUUAAAGAAAGCGUAAUAGCUCACUAGUCGAGUCGGCCUGCGCGGAAGAU GUAACGGGGCUAAAACUAUGUGCCGAAGCUGCGGAUGUAUACUUUGUAUACGUGGUAGGGGAGCGUUCUGUAAGCCGAUG AAGGUGUGUUGAGAAGCAUGCUGGAGGUAUCAGAAGUGCGAAUGCUGACGUGAGUAACGACAAAACGGGUGAAAAACCCG UUCGCCGAAAGACCAAGGGUUCCAGUCCAACGUUAAUCGGGGCUGGGUGAGUCGACCCCUAAGGCGAGGCCGAAAGGCGU AGUCGAUGGGAAAAUGGUUAAUAUUCCAUUACUUCUGUGUAAUGCGAUGAGAGGACGGAGAAGGCUAAAUCAGCCUGGCG UUGGUUGUCCAGGUGAAAGGAUGUAGGCAUGUAUCUUAGGCAAAUCCGGGGUACUCUAUGCUGAGAUCUGAUAGCAAGCU GUACUUGUACAGCGAAGUGGUUGAUGCCAUGCUUCCAGGAAAAGUCUCUAAGCUUCAGUUACACAGGAAUCGUACCCGAA ACCGACACAGGUGGUCAGGUCGAGUAGACCAAGGCGCUUGAGAGAACUCUGCUGAAGGAACUAGGCAAAAUGGUACCGUA ACUUCGGGAGAAGGUACGCUGUUGUUGGUGAUGGAACUCGCUUCCUGAGCUGACGACAGCCGCAGAAACCAGGCCGCUGC AACUGUUUAUUAAAAACAUAGCACUCUGCAAACACGAAAGUGGACGUAUAGGGUGUGAUGCCUGCCCGGUGCUGGAAGGU UAAUUGAUGGGGUUAGCGUAAGCGAAGCUCUUGAUCGAAGCCCCAGUAAACGGCGGCCGUAACUAUAACGGUCCUAAGGU AGCGAAAUUCCUUGUCGGGUAAGUUCCGACCUGCACGAAUGGCAUAAUGAUGGCGGCGCUGUCUCCAGCAGAGGCUCAGU GAAAUCGAAAUCGCUGUGAAGAUGCAGUGUACCCGCGGCUAGACGGAAAGACCCCGUGAACCUUUACUGCAGCUUGACAC UGAACUUUGACCUUACUUGUGUAGGAUAGGUGGGAGGCUUUGAAGCUGGAACGCUAGUUCCAGUGGAGCCGUCCUUGAAA UACCACCCUGGUAAUGUUGAGGUUCUAACUCUGUCCCGUGAUCCGGGACGAGGACCGUGUCUGGUGGGUAGUUUGACUGG GGCGGUCUCCUCCUAAAGAGUAACGGAGGAGUACGAAGGUGCGCUCAGCGUGGUCGGAAAUCACGCGUAGAGUAUAAAGG CAAAAGCGCGCUUAACUGCGAGACCCACAAGUCGAGCAGGUACGAAAGUAGGUCUUAGUGAUCCGGUGGUUCUGUAUGGA AGGGCCAUCGCUCAACGGAUAAAAGGUACUCUGGGGAUAACAGGCUGAUACCGCCCAAGAGUUCAUAUCGACGGCGGUGU UUGGCACCUCGAUGUCGGCUCAUCUCAUCCUGGGGCUGAAGCAGGUCCCAAGGGUAUGGCUGUUCGCCAUUUAAAGAGGU ACGCGAGCUGGGUUUAGAACGUCGUGAGACAGUUCGGUCCCUAUCUACCGUGGGCGCUGGAAAUUUGAGAGGAUCUGCUC CUAGUACGAGAGGACCAGAGUGGACGAACCUCUGGUGUACCGGUUGUGACGCCAGUCGCAUCGCCGGGUAGCUAUGUUCG GAAGGGAUAACCGCUGAAAGCAUCUAAGCGGGAAGCCUACCUCAAGAUAAGAUUUCCCUAGGACUUUAUGUCCUCUAAAG AGCCGUUCGAGACUAGGACGUUGAUAGGUUGGAUGUGGAAGCAUAGUGAUAUGUGAAGCUGACCAAUACUAAUUGCUCGU GAGGCUUGACUAUACAACACCCA CP015121.1 5S ribosomal RNA Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841 0.037608343999999995 1 UGCUGGCGACCAUAGCAAGAGUGAACCACCUGAUCCCUUCCCGAACUCAGAAGUGAAACCUCUUAGCGCUGAUGGUAGUG UGGGAUUACCCAUGUGAGAGUAAGUCAUCGCCAGCUC CP035183.1 E-site tRNA Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841 0.024346497999999998

E. coli fMet-tRNA from PDB 5AFI fitted into EM density - represents a mixture of tRNAs

2 CGCGGGG(N)GGAGCAGCCUGG(N)AGCUCGUCGGGCUCAUAACCCGAAGAUCGUCGG(N)(N)CAAAUCCGGCCCCCGC AACCA 50S ribosomal protein L35 Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841 0.007424098 1 LEVO MAKLKTRRGAAKRFKATANGFKRKQAFKRHILTKKSAKRIRQLRGCVMVHVSDVASVRRMCPYI D0CA77 50S ribosomal protein L36 Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841 0.0042762009999999994 1 LEVO MKVQASVKKICGSCKVIRRNGVIRVICSAEPRHKQRQG D0CD18 MAGNESIUM ION 2.4305e-05 162 MG TIGECYCLINE 0.0005876649999999999 3 T1C ZINC ION 6.5409e-05 1 ZN singleParticle particle 7.5 ETHANE FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 0.8 2.6 75000.0 FEI FALCON III (4k x 4k) INTEGRATING 1.1 62.0 1 Made by stochastic gradient descent in RELION 3.0 C1 2.5 FSC 0.143 CUT-OFF RELION 3.0

Multi-body refinement was carried out in RELION 3.0 to obtain the final '50S subunit' reconstruction. The mask used for this procedure is deposited with this entry.

231159 MAXIMUM LIKELIHOOD RELION 3.0 MAXIMUM LIKELIHOOD RELION 3.0 emd_10898.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 400 400 400 0 0 0 400 400 400 426.00003 426.00003 426.00003 90.0 90.0 90.0 X Y Z -0.27180347 0.576126 0.00060091226 0.012268005 1.065 1.065 1.065 0.05 AUTHOR ::::EMDATABANK.org::::EMD-10898:::: Acinetobacter baumannii ribosome-tigecycline complex - 50S subunit, post-processed map 5MDZ PDB experimental model 5AFI w PDB experimental model RIGID BODY FIT correlation coefficient REAL emd_10898_msk_1.map emd_10898_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 400 400 400 0 0 0 400 400 400 426.00003 426.00003 426.00003 90.0 90.0 90.0 X Y Z -0.8172547 1.5702523 -0.0003268833 0.02836894 1.065 1.065 1.065 AUTHOR ::::EMDATABANK.org::::EMD-10898:::: Acinetobacter baumannii ribosome-tigecycline complex, consensus map filtered by local resolution emd_10898_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 400 400 400 0 0 0 400 400 400 426.00003 426.00003 426.00003 90.0 90.0 90.0 X Y Z -0.039602697 0.16511251 -0.000587501 0.0073080724 1.065 1.065 1.065 AUTHOR ::::EMDATABANK.org::::EMD-10898:::: Acinetobacter baumannii ribosome-tigecycline complex - 50S subunit, half map 2 emd_10898_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 400 400 400 0 0 0 400 400 400 426.00003 426.00003 426.00003 90.0 90.0 90.0 X Y Z -0.041484904 0.16392194 -0.0005727786 0.007293079 1.065 1.065 1.065 AUTHOR ::::EMDATABANK.org::::EMD-10898:::: Acinetobacter baumannii ribosome-tigecycline complex - 50S subunit, half map 1