2024-05-22 REL PDBe PDBe PDBe 2020-04-24 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 - 30S subunit head Nicholson D Edwards TA O'Neill AJ Ranson NA 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 EMD-10898 other EM volume
Acinetobacter baumannii ribosome-tigecycline complex - 50S subunit
 EMD-10914 other EM volume
Acinetobacter baumannii ribosome-tigecycline complex - 30S subunit body
 6ytf FULLOVERLAP Acinetobacter baumannii ribosome-tigecycline complex - 30S subunit head Acinetobacter baumannii ribosome-tigecycline complex - 30S subunit head 0 1 2 3 4 5 6 7 8 9 10 Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841 16S ribosomal RNA Acinetobacter baumannii (strain ATCC 19606 / DSM 30007 / CIP 70.34 / JCM 6841 / NBRC 109757 / NCIMB 12457 / NCTC 12156 / 81) 0.500126156 1 UUUAACUGAAGAGUUUGAUCAUGGCUCAGAUUGAACGCUGGCGGCAGGCUUAACACAUGCAAGUCGAGCGGGGGAAGGUA GCUUGCUACCGGACCUAGCGGCGGACGGGUGAGUAAUGCUUAGGAAUCUGCCUAUUAGUGGGGGACAACAUCUCGAAAGG GAUGCUAAUACCGCAUACGUCCUACGGGAGAAAGCAGGGGAUCUUCGGACCUUGCGCUAAUAGAUGAGCCUAAGUCGGAU UAGCUAGUUGGUGGGGUAAAGGCCUACCAAGGCGACGAUCUGUAGCGGGUCUGAGAGGAUGAUCCGCCACACUGGGACUG AGACACGGCCCAGACUCCUACGGGAGGCAGCAGUGGGGAAUAUUGGACAAUGGGGGGAACCCUGAUCCAGCCAUGCCGCG UGUGUGAAGAAGGCCUUAUGGUUGUAAAGCACUUUAAGCGAGGAGGAGGCUACUUUAGUUAAUACCUAGAGAUAGUGGAC GUUACUCGCAGAAUAAGCACCGGCUAACUCUGUGCCAGCAGCCGCGGUAAUACAGAGGGUGCGAGCGUUAAUCGGAUUUA CUGGGCGUAAAGCGUGCGUAGGCGGCUUAUUAAGUCGGAUGUGAAAUCCCCGAGCUUAACUUGGGAAUUGCAUUCGAUAC UGGUGAGCUAGAGUAUGGGAGAGGAUGGUAGAAUUCCAGGUGUAGCGGUGAAAUGCGUAGAGAUCUGGAGGAAUACCGAU GGCGAAGGCAGCCAUCUGGCCUAAUACUGACGCUGAGGUACGAAAGCAUGGGGAGCAAACAGGAUUAGAUACCCUGGUAG UCCAUGCCGUAAACGAUGUCUACUAGCCGUUGGGGCCUUUGAGGCUUUAGUGGCGCAGCUAACGCGAUAAGUAGACCGCC UGGGGAGUACGGUCGCAAGACUAAAACUCAAAUGAAUUGACGGGGGCCCGCACAAGCGGUGGAGCAUGUGGUUUAAUUCG AUGCAACGCGAAGAACCUUACCUGGCCUUGACAUACUAGAAACUUUCCAGAGAUGGAUUGGUGCCUUCGGGAAUCUAGAU ACAGGUGCUGCAUGGCUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUUUUCCUUA CUUGCCAGCAUUUCGGAUGGGAACUUUAAGGAUACUGCCAGUGACAAACUGGAGGAAGGCGGGGACGACGUCAAGUCAUC AUGGCCCUUACGGCCAGGGCUACACACGUGCUACAAUGGUCGGUACAAAGGGUUGCUACACAGCGAUGUGAUGCUAAUCU CAAAAAGCCGAUCGUAGUCCGGAUUGGAGUCUGCAACUCGACUCCAUGAAGUCGGAAUCGCUAGUAAUCGCGGAUCAGAA UGCCGCGGUGAAUACGUUCCCGGGCCUUGUACACACCGCCCGUCACACCAUGGGAGUUUGUUGCACCAGAAGUAGCUAGC CUAACUGCAAAGAGGGCGGUUACCACGGUGUGGCCGAUGACUGGGGUGAAGUCGUAACAAGGUAGCCGUAGGGGAACCUG CGGCUGGAUCACCUCCUUAACGAA CP009534.1 E-site tRNA Acinetobacter baumannii (strain ATCC 19606 / DSM 30007 / CIP 70.34 / JCM 6841 / NBRC 109757 / NCIMB 12457 / NCTC 12156 / 81) 0.024818892999999998
E. coli fMet-tRNA from PDB 5AFI fitted into EM density - represents a mixture of tRNAs
1 CGCGGGG(4SU)GGAGCAGCCUGG(H2U)AGCUCGUCGGGCUCAUAACCCGAAGAUCGUCGG(5MU)(PSU)CAAAUCCG GCCCCCGCAACCA mRNA Acinetobacter baumannii (strain ATCC 19606 / DSM 30007 / CIP 70.34 / JCM 6841 / NBRC 109757 / NCIMB 12457 / NCTC 12156 / 81) 0.0011797059999999998
Mixture of mRNAs at the E-site, modelled as polyuridine
1 UUUU 30S ribosomal protein S3 Acinetobacter baumannii (strain ATCC 19606 / DSM 30007 / CIP 70.34 / JCM 6841 / NBRC 109757 / NCIMB 12457 / NCTC 12156 / 81) 0.027972460999999997 1 LEVO MGQKVHPIGIRLGVVKRHNANWYANPKQYAEYLLKDLQVREFLTKKLKNAMVSNILIERPSGAAKVTISTARPGIVIGKK GEDIEKLQRELTNIMGVPAQVSINEIDRPDLDARLVAEAIASQLEKRVMFRRAMKRAVQNTMRAGAKGIKVEVSGRLGGA EIARTEWYREGRVPLHTLRADIDYATMRAETTYGTIGVKVWIFRGEILGGMKQVMNPAPAEERPAKRGRGRGEGQERRGR RGDRAADKGE D0CD03 30S ribosomal protein S7 Acinetobacter baumannii (strain ATCC 19606 / DSM 30007 / CIP 70.34 / JCM 6841 / NBRC 109757 / NCIMB 12457 / NCTC 12156 / 81) 0.017733699
residues 126-145 modelled without side chains
1 LEVO MPRRRVVAAREILPDPKFSSQTIAKFMNHVMQDGKKSIAESIVYGALERVQEKNKVDPVEFFETTLEKVRPMVEVKARRV GGATYQVPMEVRPSRRTALAMRWLVDAAAKRSEKTMALRLAGELLDAAEGKGAAIKKREDVHRMAEANKAFSHYRF D0C9P7 30S ribosomal protein S9 Acinetobacter baumannii (strain ATCC 19606 / DSM 30007 / CIP 70.34 / JCM 6841 / NBRC 109757 / NCIMB 12457 / NCTC 12156 / 81) 0.01428761 1 LEVO MATNYGTGRRKTATARVFLSAGTGKLVINNRTLEQYFGRETARMVVRQPLELLEATEKYDLYITVKGGGIGGQAGAIRHG ITRALIAADETLKPVLRQAGFVTRDAREVERKKLGLRKARKRPQFSKR D0CG36 30S ribosomal protein S10 Acinetobacter baumannii (strain ATCC 19606 / DSM 30007 / CIP 70.34 / JCM 6841 / NBRC 109757 / NCIMB 12457 / NCTC 12156 / 81) 0.011718531 1 LEVO MSNQRIRIRLKSFDHRLIDQSAQEIVETAKRTGAQVCGPIPMPTRIERFNVLTSPHVNKDARDQYEIRTYKRLIDIVQPT DKTVDALMKLDLAAGVDVQIALG D0CCZ6 30S ribosomal protein S13 Acinetobacter baumannii (strain ATCC 19606 / DSM 30007 / CIP 70.34 / JCM 6841 / NBRC 109757 / NCIMB 12457 / NCTC 12156 / 81) 0.013295635 1 LEVO MARIAGVNIPDNKHAVISLTYIFGIGRHTAKNILAAVGITETTKIRELDDAQLDAIRAEVAKVPTEGDLRREISMNIKRL MDLGCYRGLRHRRSLPVRGQRTKTNARTRKGPRKPIKK D0CD19 30S ribosomal protein S14 Acinetobacter baumannii (strain ATCC 19606 / DSM 30007 / CIP 70.34 / JCM 6841 / NBRC 109757 / NCIMB 12457 / NCTC 12156 / 81) 0.011438427 1 LEVO MAKKGMINRELKREKTVAKYAAKRAELKATIANVNASDEERFEAMLKLQALPRNASPVRLRNRCGLTGRPHGYFRKFGLS RNKLRDTVMQGDVPGVVKASW D0CD10 30S ribosomal protein S19 Acinetobacter baumannii (strain ATCC 19606 / DSM 30007 / CIP 70.34 / JCM 6841 / NBRC 109757 / NCIMB 12457 / NCTC 12156 / 81) 0.010206957 1 LEVO MPRSLKKGPFVDAHLFAKVEAAVASNSRKPIKTWSRRSMILPDFVGLTISVHNGRNHVPVIVTEHMVGHKLGEFAPTRTY RGHGVDKKSKR D0CD01 MAGNESIUM ION 2.4305e-05 24 MG TIGECYCLINE 0.0005876649999999999 1 T1C 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 3.0 FSC 0.143 CUT-OFF RELION 3.0
Multi-body refinement was carried out in RELION 3.0 to obtain the final '30S subunit head' reconstruction. The mask used for this procedure is deposited with this entry.
231159 MAXIMUM LIKELIHOOD RELION 3.0 MAXIMUM LIKELIHOOD RELION 3.0 emd_10915.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 -0.242192 0.4075166 0.0001224 0.004186482 1.065 1.065 1.065 0.05 AUTHOR Acinetobacter baumannii ribosome-tigecycline complex - 30S subunit head, post-processed map 6YS5 PDB experimental model 5AFI w PDB experimental model RIGID BODY FIT
The quality of the map is relatively poor so the related PDB entry 6YS5 (A. baumannii ribosome-amikacin complex - 30S subunit head) was rigid body fitted into the map using Chimera X-0.9, tigecycline was placed into the density at the primary site, and one round of global real space refinement and local refinement were carried out using PHENIX and Coot respectively, using ligand restraints in both cases.
correlation coefficient REAL emd_10915_msk_1.map emd_10915_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 Acinetobacter baumannii ribosome-tigecycline complex, consensus map filtered by local resolution emd_10915_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 -0.0294337 0.1280648 -0.0012570345 0.0035502752 1.065 1.065 1.065 AUTHOR Acinetobacter baumannii ribosome-tigecycline complex - 30S subunit head, half map 1 emd_10915_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 -0.031622764 0.13576211 -0.0012399367 0.003583555 1.065 1.065 1.065 AUTHOR Acinetobacter baumannii ribosome-tigecycline complex - 30S subunit head, half map 2