2020-10-14RELPDBePDBePDBe2020-03-302020-09-162020-09-162020-10-14Wellcome Trust203743/Z/16/ZUnited KingdomWellcome Trust108466/Z/15/ZUnited KingdomAcinetobacter baumannii ribosome-amikacin complex - 50S subunitNicholson DEdwards TAO'Neill AJRanson NANicholson DEdwards TAO'Neill AJRanson NAStructure of the 70S Ribosome from the Human Pathogen Acinetobacter baumannii in Complex with Clinically Relevant Antibiotics.StructureUK2810871100.e3202032857965doi:10.1016/j.str.2020.08.0040969-21262005STRUE6EMD-10809associated EM volumeA. baumannii ribosome-amikacin complex - 50S subunitEMD-10869other EM volumeA. baumannii ribosome-amikacin complex - 30S subunit body6yhsFULLOVERLAPAcinetobacter baumannii ribosome-amikacin complex - 50S subunitAcinetobacter baumannii ribosome-amikacin complex - 50S subunit0123456789101112131415161718192021222324252627282930Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 684123S ribosomal RNAAcinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 68410.9403301251AGUCAAGUAAUUAAGUGCAUGUGGUGGAUGCCUUGGCAGUCAGAGGCGAUGAAAGACGUGAUAGCCUGCGAAAAGCUCCG
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
GAGGCUUGACUAUACAACACCCA5S ribosomal RNAAcinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 68410.0376083441UGCUGGCGACCAUAGCAAGAGUGAACCACCUGAUCCCUUCCCGAACUCAGAAGUGAAACCUCUUAGCGCUGAUGGUAGUG
UGGGAUUACCCAUGUGAGAGUAAGUCAUCGCCAGCUCE-site tRNAAcinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 68410.024346498E. coli fMet-tRNA from PDB 5AFI fitted into EM density - represents a mixture of tRNAs2CGCGGGG(N)GGAGCAGCCUGG(N)AGCUCGUCGGGCUCAUAACCCGAAGAUCGUCGG(N)(N)CAAAUCCGGCCCCCGC
AACCA50S ribosomal protein L2Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 68410.0303190921LEVOMPIQKCKPTSPGRRFVEKVVHDHLHKGAPYAPLVEAKKRTGGRNNNGHITTRHVGGGHKQHYRIVDFKRNKDGVPAVVER
IEYDPSRTAHIALLKYADGERRYIIAPKGLRAGDKVQSGNDAPIRPGNCLPLRNMPIGSTLHNVELKIGKGAQLARSAGA
SVQLLGRDGSYAIIRLRSGEMRKVHVECRAVIGEVSNQENNLRSLGKAGAARWRGVRPTVRGMAMNPIDHPHGGGEGRNK
GIQPVSPWGQKAKGYKTRTNKRTTKMIIRDRRVK50S ribosomal protein L3Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 68410.0225126391LEVOMAIGLVGRKCGMTRIFTDAGVSVPVTVIEVDPNRITQIKTLETDGYQAVQVTTGERRESRVTNAQKGHFAKAGVAAGRLV
KEFRVTEAELEGREVGGTIGVDLFTVGQIVDVTGQSKGKGFQGGVKRWNFRTQDATHGNSVSHRVLGSTGQNQTPGRVFK
GKKMAGHLGDERVTVQGLEIVSVDTERSVLVVKGAIPGATGGDVIVRPTIKA50S ribosomal protein L4Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 68410.021583904residues 2-12 modelled without side chains1LEVOMNLKTVSGSAVELSEVAFGREFNEALVHQVVTAYLAGGRQGTRAHKSRADVSGGGKKPFRQKGTGRARAGSIRSPIWVGG
GKTFAARPQDWSQKVNRKMYRGAMQCILAELVRQDRLVLVEEFAVAAPKTKELLAKLNDLNAARALIVTDAVDENLYLAA
RNLPHVDVVDATAIDPVSLIAFDKVVMSVAAAKKIEVELG50S ribosomal protein L5Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 68410.020051471modelled without side chains1LEVOMARLKARYNDELKAKLQEELSIKNVMEIPRITKITLNMGVGAAATDKKLLDGAVADMQLIAGQKPVVTLARKSIAGFKIR
DGWPIGCKVTLRGDQMYEFLDRLISIAIPRIRDFRGFSAKSFDGRGNYSMGLKEQIVFPEIDFDKIDRIRGMDITITTTA
RTDDEGRALMRAFGFPFK50S ribosomal protein L6Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 68410.0191260471LEVOMSRVAKAPVTVPNGVTVTQNGRQVEVKGSKGTLSFNLHALVELKQEEGKLQLAPAKESKDAWMQAGTARAVLNNLVKGVS
EGFERKLQLVGVGYKAAVKGTVVNLNLGYSHPIDYALPEGVTAETPTATEIILKSANKQLLGQVAAEIRAYRSPEPYKGK
GVRYSDEVILRKEAKKK50S ribosomal protein L13Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 68410.015951441LEVOMKTLSAKPAEVQHDWFVVDATGKTLGRLATEIARRLRGKHKTSYTPHVDAGDYIIVINAEQVQVTGNKALDKKYYRHTEF
PGGLKETNFEKLVAHKPEEIFERAVKGMLPKGPLGYAMIKKMKVYAGSEHPHAAQQPQVLDI50S ribosomal protein L14Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 68410.0135238631LEVOMIQTETMLDVADNSGARRVQCIKVLGGSHRRYASVGDIIKVTVKEAIPRARVKKGDVMNAVVVRTKFGIRRPDGSVIRFD
DNAAVILNNNKAPIATRIFGPVTRELRTEQFMKIISLAPEVL50S ribosomal protein L15Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 68410.0155099151LEVOMTLRLNELAPAEGAKREHRRLGRGIGSGVGKTGGRGIKGQKSRKSGGVRPGFEGGQTAIYRRLPKFGFTSQIALKTAEVR
LSELSKVEGDIVSLETLKAANVVRRDQIRARIVLSGEITRAFTVQGVALTKGAKAAIEAAGGKVEE50S ribosomal protein L16Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 68410.0154983121LEVOMLQPKRTKFRKVHKGRNTGLAHRGSTVSFGSIAIKATERGRMTARQIEAARRTISRRIKRGGKIFIRVFPDKPITEKPLE
VRMGNGKGNVEYWVCEIKPGKILYEIEGVNEDLAREAFALAAAKLPFKTTIVTRTVM50S ribosomal protein L17Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 68410.014021231LEVOMRHRNSGVKLGRTSSHRKAMFQNLANSLFEHELIKTTLPKAKELRRVAEPLITLAKNDTVANRRLAFARTRNAATVGKLF
TVLGPRYKERNGGYLRVLKAGFRAGDAAPMAYVELVDREVNTSAE50S ribosomal protein L18Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 68410.0124433411LEVOMNEKKQSRLRRAKSTRLHIRALGATRLCVNRTPRHIYAQVISADGGKVLAQASTLDASLRSGTTGNIEAATKVGALIAER
AKAAGVTKVAFDRSGFKYHGRIKALADAAREGGLEF50S ribosomal protein L19Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 68410.0136198651LEVOMSGKHPLVQAIENSQLKTDLPEFAPGDTVVVQVKVKEGDRERLQAFEGVVIAKKNRGLNSAFTVRKISSGVGVERVFQTH
SPVVAKIEVKRRGDVRRAKLYYLRDLSGKAARIREKLPARKA50S ribosomal protein L20Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 68410.0134689461LEVOMARVKRGVVAHRRHKKILARAKGYYGARSRVYRVAFQAVIKAGQYAYRDRRQKKRQFRALWIARINAGARQNGLSYSRMI
DGLKKAQVIIDRRVLADIAMHDAVAFAALAEKAKGALAA50S ribosomal protein L21Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 68410.0114963641LEVOMYAVIQSGGKQHRVVEGETLKVELLKAESGATITFDDVLMVVNGDNIQIGAPVVAGAKVTAEVIGHGRHDKIRIIKMRRR
KHYRKQQGHRQWFTELKITGISG50S ribosomal protein L22Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 68410.0119601261LEVOMMEVTAKLRGAAISAQKARLVADLIRGKSVAHALNILNFSNKKAAVLVKKALESAIANAEHNNSLDVDDLKVSTIYVDEG
MSLKRIMPRAKGRADRITKRTCHITVKVGV50S ribosomal protein L23Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 68410.0116073921LEVOMNNERIYQVLKGPVFSEKAQVLGDTAGVQVFKVDINATKLEIKKAVEKLFGVEVVKVNTTITKGKTKRFGRTLGRRSDVK
KAYVTLKAGQDVEMADLGDTAESAAE50S ribosomal protein L24Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 68410.0111879291LEVOMAKIKKGDQVIVIAGKEKGKQGTVLSVSEDRVKVEGLNLVKKHQKPNRVTGAEGGIVTQEASLHISNVAILNATTQKADR
VGYQVIDGVKTRVYKSTGESVAVAK50S ribosomal protein L25Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 68410.0109145391LEVOMANFVLNAQARAEDKQGKGASRRLRRESLVPAIIYGGNAEPVAVTLELRELVKALESNAFFEEVVEIKVGDKVENVKIQA
LQRHPAKNTPMHADFKRA50S ribosomal protein L27Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 68410.0090723871LEVOMATKKAGGSTKNGRDSNPKMLGVKVYGGQTVTAGNIIVRQRGTEFHAGANVGMGRDHTLFATADGVVKFEVKGQFGRRYV
KVETV50S ribosomal protein L28Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 68410.0091257561LEVOMSKVCQVTGKRPVVGNNVSHANNKTKRRFEPNLHHHRFWLESEKRFVRLRLTTKGMRIIDKLGIEKVVADLRAQGQKI50S ribosomal protein L29Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 68410.0074496781LEVOMKTKDLREKSVEELKALLDEQQLNQFRLRMAKATGQLGKSHEVQVARKTIARIKTLLTEKQGNGQ50S ribosomal protein L30Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 68410.0066547881LEVOMKTIKVTQTKSSSHRLKNHKLCLQGLGLRRIGHTVEVQDTPSNRGMINKVYYMVSVEE50S ribosomal protein L32Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 68410.0070968881LEVOMAVQQNRKSRSRRDMRRSHDALTENALTVDQATGETHRRHHVTKDGFYRGRQLFAKAADAE50S ribosomal protein L33Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 68410.006105311LEVOMRDKIRLVSSAGTGYFYTTTKNKRTMPEKMEIKKFDPKIRQHVIFKEAKIK50S ribosomal protein L34Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 68410.0051922471LEVOMKRTFQPSELKRKRVHGFRARMATKAGRQVLARRRAKGRHSLTV50S ribosomal protein L35Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 68410.0074240981LEVOMAKLKTRRGAAKRFKATANGFKRKQAFKRHILTKKSAKRIRQLRGCVMVHVSDVASVRRMCPYI50S ribosomal protein L36Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 68410.0042762011LEVOMKVQASVKKICGSCKVIRRNGVIRVICSAEPRHKQRQGMAGNESIUM ION2.4305e-05160MGZINC ION6.5409e-051ZNsingleParticleparticle7.5ETHANEFEI TITAN KRIOSFLOOD BEAMBRIGHT FIELDFIELD EMISSION GUN3000.82.7130000.0GATAN K2 SUMMIT (4k x 4k)COUNTING10.058.01Gctf1.18Made by stochastic gradient descent in RELION 3.0C12.7FSC 0.143 CUT-OFFRELION3.0Multi-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.51958MAXIMUM LIKELIHOODRELION3.0MAXIMUM LIKELIHOODRELION3.05MDZ5AFIwRIGID BODY FITcorrelation coefficientREALemd_10809_msk_1.mapemd_10809_additional_1.map.gz1IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
400
400400
0
00400400400428.00003428.00003428.0000390.090.090.0XYZ-0.377282320.83724740.00013238710.0133362211.071.071.07Acinetobacter baumannii ribosome-amikacin complex, consensus map filtered by local resolutionemd_10809_half_map_1.map.gz1IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
400
400400
0
00400400400428.00003428.00003428.0000390.090.090.0XYZ-0.0647337960.16116051-0.000281993740.0073339471.071.071.07Acinetobacter baumannii ribosome-amikacin complex - 50S subunit, half map 1emd_10809_half_map_2.map.gz1IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)