2025-07-02 REL PDBe INITIAL_RELEASE REPOSITORY DATABASE_REFERENCES citation citation_author em_admin _citation.country _citation.journal_abbrev _citation.journal_id_ISSN _citation.journal_volume _citation.pdbx_database_id_PubMed _citation.title _citation_author.identifier_ORCID _citation_author.name _em_admin.last_update DATA_COLLECTION em_admin _em_admin.last_update PDBe PDBe 2025-03-10 2025-06-04 2025-06-04 2025-07-02 Other private Rivalta A Yonath A RIBOSOME Rivalta A Fedorenko A Le Scornet A Thompson S Halfon Y Breiner Goldstein E Cavdaroglu S Melenitzky T Hiregange DG Zimmerman E Bashan A Yap MF Yonath A Life Sci Alliance US 8 2025 40490363 doi:10.26508/lsa.202503325 2575-1077 9qeh FULLOVERLAP A2085-methylated 50S ribosome of a MLSb resistant S. aureus strain "MNY196" in complex with solithromycin A2085-methylated 50S ribosome of a MLSb resistant S. aureus strain "MNY196" in complex with solithromycin 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 Staphylococcus aureus subsp. aureus USA300 Large ribosomal subunit protein bL33A Staphylococcus aureus subsp. aureus USA300 0.006305343 1 LEVO MFNVRVNVTLACTECGDRNYITTKNKRNNPERIEMKKYCPRLNKYTLHRETK Q2FH98 Large ribosomal subunit protein bL34 Staphylococcus aureus subsp. aureus USA300 0.005454642 1 LEVO MVKRTYQPNKRKHSKVHGFRKRMSTKNGRKVLARRRRKGRKVLSA Q2FDE6 Large ribosomal subunit protein bL35 Staphylococcus aureus subsp. aureus USA300 0.007722368 1 LEVO MPKMKTHRGAAKRVKRTASGQLKRSRAFTSHLFANKSTKQKRQLRKARLVSKSDMKRVKQLLAYKK Q2FG57 Large ribosomal subunit protein bL36 Staphylococcus aureus subsp. aureus USA300 0.004318422 1 LEVO MKVRPSVKPICEKCKVIKRKGKVMVICENPKHKQRQG Q2FER2 Large ribosomal subunit protein bL17 Staphylococcus aureus subsp. aureus USA300 0.013771773 1 LEVO MGYRKLGRTSDQRKAMLRDLATSLIISERIETTEARAKEVRSVVEKLITLGKKGDLASRRNAAKTLRNVEILNEDETTQT ALQKLFGEIAERYTERQGGYTRILKQGPRRGDGAESVIIELV Q2FER6 23S rRNA Staphylococcus aureus subsp. aureus USA300 0.94685075 1 GAUUAAGUUAUUAAGGGCGCACGGUGGAUGCCUUGGCACUAGAAGCCGAUGAAGGACGUUACUAACGACGAUAUGCUUUG GGGAGCUGUAAGUAAGCUUUGAUCCAGAGAUUUCCGAAUGGGGAAACCCAGCAUGAGUUAUGUCAUGUUAUCGAUAUGUG AAUACAUAGCAUAUCAGAAGGCACACCCGGAGAACUGAAACAUCUUAGUACCCGGAGGAAGAGAAAGAAAAUUCGAUUCC CUUAGUAGCGGCGAGCGAAACGGGAAGAGCCCAAACCAACAAGCUUGCUUGUUGGGGUUGUAGGACACUCUGUACGGAGU UACAAAGGACGACAUUAGACGAAUCAUCUGGAAAGAUGAAUCAAAGAAGGUAAUAAUCCUGUAGUCGAAAAUGUUGUCUC UCUUGAGUGGAUCCUGAGUACGACGGAGCACGUGAAAUUCCGUCGGAAUCUGGGAGGACCAUCUCCUAAGGCUAAAUACU CUCUAGUGACCGAUAGUGAACCAGUACCGUGAGGGAAAGGUGAAAAGCACCCCGGAAGGGGAGUGAAAUAGAACCUGAAA CCGUGUGCUUACAAGUAGUCAGAGCCCGUUAAUGGGUGAUGGCGUGCCUUUUGUAGAAUGAACCGGCGAGUUACGAUUUG AUGCAAGGUUAAGCAGUAAAUGUGGAGCCGUAGCGAAAGCGAGUCUGAAUAGGGCGUUUAGUAUUUGGUCGUAGACCCGA AACCAGGUGAUCUACCCUUGGUCAGGUUGAAGUUCAGGUAACACUGAAUGGAGGACCGAACCGACUUACGU(5MU)GAAA AGUGAGCGGAUGAACUGAGGGUAGCGGAGAAAUUCCAAUCGAACCUGGAGAUAGCUGGUUCUCUCCGAAAUAGCUUUAGG GCUAGCCUCAAGUGAUGAUUAUUGGAGGUAGAGCACUGUUUGGACGAGGGGCCCCUCUCGGGUUACCGAAUUCAGACAAA CUCCGAAUGCCAAUUAAUUUAACUUGGGAGUCAGAACAUGGGUGAUAAGGUCCGUGUUCGAAAGGGAAACAGCCCAGACC ACCAGCUAAGGUCCCAAAAUAUAUGUUAAGUGGAAAAGGAUGUGGCGUUGCCCAGACAACUAGGAUGUUGGCUUAGAAGC AGCCAUCAUUUAAAGAGUGCGUAAUAGCUCACUAGUCGAGUGACACUGCGCCGAAAAUGUACCGGGGCUAAACAUAUUAC CGAAGCUGUGGAUUGUCCUUUGGACAAUGGUAGGAGAGCGUUCUAAGGGCGUUGAAGCAUGAUCGUAAGGACAUGUGGAG CGCUUAGAAGUGAGAAUGCCGGUGUGAGUAGCGAAAGACGGGUGAGAAUCCCGUCCACCGAUUGACUAAGGUUUCCAGAG GAAGGCUCGUCCGCUCUGGGUUAGUCGGGUCCUAAGCUGAGGCCGACAGGCGUAGGCGAUGGAUAACAGGUUGAUAUUCC UGUACCACCUAUAAUCGUUUUAAUCGAUGGGGGGACGCAGUAGGAUAGGCGAAGCGUGCGAUUGGAUUGCACGUCUAAGC AGUAAGGCUGAGUAUUAGGCAAAUCCGGUACUCGUUAAGGCUGAGCUGUGAUGGGGAGAAGACAUUGAGUCUUCGAGUCG UUGAUUUCACACUGCCGAGAAAAGCCUCUAGAUAGAAAAUAGGUGCCCGUACCGCAAACCGACACAGGUAGUCAAGAUGA GAAUUCUAAGGUGAGCGAGCGAACUCUCGUUAAGGAACUCGGCAAAAUGACCCCGUAACUUCGGGAGAAGGGGUGCUCUU UAGGGUUAACGCCCAGAAGAGCCGCAGUGAAUAGGCCCAAGCGACUGUUUAUCAAAAACACAGGUCUCUGCUAAACCGUA AGGUGAUGUAUAGGGGCUGACGCCUGCCCGGUGCUGGAAGGUUAAGAGGAGUGGUUAGCUUCUGCGAAGCUACGAAUCGA AGCCCCAGUAAACGGCGGCCGUAACUAUAACGGUCCUAAGGUAGCGAAA(5MU)UCCUUGUCGGGUAAGUUCCGACCCGC ACGAAAGGCGUAACGAUUUGGGCACUGUCUCAACGAGAGACUCGGUGAAAUCAUAGUACCUGUGAAGAUGCAGGUUACCC GCGACAGGACGG(MA6)AAGACCCCGUGGAGCUUUACUGUAGCCUGAUAUUGAAAUUCGGCACAGCUUGUACAGGAUAGG UAGGAGCCUUUGAAACGUGAGCGCUAGCUUACGUGGAGGCGCUGGUGGGAUACUACCCUAGCUGUGUUGGCUUUCUAACC CGCACCACUUAUCGUGGUGGGAGACAGUGUCAGGCGGGCAGUUUGACUG(OMG)GGCGGUCGCCUCCUAAAAGGUAACGG AGGCGCUCAAAGGUUCCCUCAGAAUGGUUGGAAAUCAUUCAUAGAGUGUAAAGGCAUAAGGGAGCUUGACUGCGAGACCU ACAAGUCGAGCAGGGUCGAAAGACGGACUUAGUGAUCCGGUGGUUCCGCAUGGAAGGGCCAUCGCUCAACGGAUAAAAGC UACCCCG(2MG)GGA(H2U)AACAGGC(PSU)UAUCUCCCCCAAGAGUUCACAUCGACGGGGAGGUUUGGCACCUCG (2MA)UGUCGGCUCAUCGCAUCCUGGGGCUGUAGUCGGUCCCAAGGGUUGGGCUGUUCGCCCAUUAAAGCGGUAC(G7M) CGAGC(PSU)GGGUUCAGAACGUCGUGAGACAGU(PSU)CGGUCCCUAUCCGUCGUGGGCGUAGGAAAUUUGAGAGGAGC UGUCCUUAGUACGAGAGGACCGGGAUGGACAUACCUCUGGUGUACCAGUUGUCGUGCCAACGGCAUAGCUGGGUAGCUAU GUGUGGACGGGAUAAGUGCUGAAAGCAUCUAAGCAUGAAGCCCCCCUCAAGAUGAGAUUUCCCAACUUCGGUUAUAAGAU CCCUCAAAGAUGAUGAGGUUAAUAGGUUCGAGGUGGAAGCAUGGUGACAUGUGGAGCUGACGAAUACUAAUCGAUCGAAG ACUUAAUCAA 5S rRNA Staphylococcus aureus subsp. aureus USA300 0.036974944999999995 1 UCUGGUGACUAUAGCAAGGAGGUCACACCUGUUCCCAUGCCGAACACAGAAGUUAAGCUCCUUAGCGUCGAUGGUAGUCG AACUUACGUUCCGCUAGAGUAGAACGUUGCCAGGC CP030384.1 Large ribosomal subunit protein uL2 Staphylococcus aureus subsp. aureus USA300 0.030217163999999998 1 LEVO MAIKKYKPITNGRRNMTSLDFAEITKTTPEKSLLKPLPKKAGRNNQGKLTVRHHGGGHKRQYRVIDFKRNKDGINAKVDS IQYDPNRSANIALVVYADGEKRYIIAPKGLEVGQIVESGAEADIKVGNALPLQNIPVGTVVHNIELKPGKGGQIARSAGA SAQVLGKEGKYVLIRLRSGEVRMILSTCRATIGQVGNLQHELVNVGKAGRSRWKGIRPTVRGSVMNPNDHPHGGGEGRAP IGRPSPMSPWGKPTLGKKTRRGKKSSDKLIVRGRKKK Q2FEP2 Large ribosomal subunit protein uL3 Staphylococcus aureus subsp. aureus USA300 0.023760256 1 LEVO MTKGILGRKIGMTQVFGENGELIPVTVVEAKENVVLQKKTVEVDGYNAIQVGFEDKKAYKKDAKSNKYANKPAEGHAKKA DAAPKRFIREFRNVDVDAYEVGQEVSVDTFVAGDVIDVTGVSKGKGFQGAIKRHGQSRGPMSHGSHFHRAPGSVGMASDA SRVFKGQKMPGRMGGNTVTVQNLEVVQVDTENKVILVKGNVPGPKKGLVEIRTSIKKGNK Q2FEN9 Large ribosomal subunit protein uL4 Staphylococcus aureus subsp. aureus USA300 0.022495697 1 LEVO MANYDVLKLDGTKSGSIELSDAVFGIEPNNSVLFEAINLQRASLRQGTHAVKNRSAVSGGGRKPWKQKGTGRARQGTIRA PQWRGGGIVFGPTPRSYAYKMPKKMRRLALRSALSFKAQENGLTVVDAFNFEAPKTKEFKNVLSTLEQPKKVLVVTENED VNVELSARNIPGVQVTTAQGLNVLDITNADSLVITEAAAKKVEEVLG Q2FEP0 Large ribosomal subunit protein uL5 Staphylococcus aureus subsp. aureus USA300 0.020296637 1 LEVO MNRLKEKFNTEVTENLMKKFNYSSVMEVPKIDKIVVNMGVGDAVQNSKVLDNAVEELELITGQKPLVTKAKKSIATFRLR EGMPIGAKVTLRGERMYEFLDKLISVSLPRVRDFQGVSKKAFDGRGNYTLGVKEQLIFPEIDYDKVSKVRGMDIVIVTTA NTDEEARELLANFGMPFRK Q2FEQ1 Large ribosomal subunit protein uL6 Staphylococcus aureus subsp. aureus USA300 0.019818580000000002 1 LEVO MSRVGKKIIDIPSDVTVTFDGNHVTVKGPKGELSRTLNERMTFKQEENTIEVVRPSDSKEDRTNHGTTRALLNNMVQGVS QGYVKVLELVGVGYRAQMQGKDLILNVGYSHPVEIKAEENITFSVEKNTVVKVEGISKEQVGALASNIRSVRPPEPYKGK GIRYQGEYVRRKEGKTGK Q2FEQ4 Large ribosomal subunit protein uL13 Staphylococcus aureus subsp. aureus USA300 0.016359427 1 LEVO MRQTFMANESNIERKWYVIDAEGQTLGRLSSEVASILRGKNKVTYTPHVDTGDYVIVINASKIEFTGNKETDKVYYRHSN HPGGIKSITAGELRRTNPERLIENSIKGMLPSTRLGEKQGKKLFVYGGAEHPHAAQQPENYELRG Q2FES1 Large ribosomal subunit protein uL14 Staphylococcus aureus subsp. aureus USA300 0.013157342 1 LEVO MIQQETRLKVADNSGAREVLTIKVLGGSGRKTANIGDVIVCTVKNATPGGVVKKGDVVKAVIVRTKSGVRRNDGSYIKFD ENACVIIRDDKGPRGTRIFGPVARELREGNFMKIVSLAPEVL Q2FEP9 Large ribosomal subunit protein uL15 Staphylococcus aureus subsp. aureus USA300 0.01562889 1 LEVO MKLHELKPAEGSRKERNRVGRGVATGNGKTSGRGHKGQKARSGGGVRPGFEGGQLPLFRRLPKRGFTNINRKEYAIVNLD QLNKFEDGTEVTPALLVESGVVKNEKSGIKILGNGSLDKKLTVKAHKFSASAAEAIDAKGGAHEVI Q2FEQ8 Large ribosomal subunit protein uL16 Staphylococcus aureus subsp. aureus USA300 0.016274049 1 LEVO MLLPKRVKYRRQHRPKTTGRSKGGNYVTFGEFGLQATTTSWITSRQIESARIAMTRYMKRGGKVWIKIFPHTPYTKKPLE VRMGAGKGAVEGWIAVVKPGRILFEVAGVSEEVAREALRLASHKLPVKTKFVKREELGGETNES Q2FEP6 Large ribosomal subunit protein uL18 Staphylococcus aureus subsp. aureus USA300 0.013124093 1 LEVO MISKIDKNKVRLKRHARVRTNLSGTAEKPRLNVYRSNKHIYAQIIDDNKGVTLAQASSKDSDIATTATKVELATKVGEAI AKKAADKGIKEIVFDRGGYLYHGRVKALAEAARESGLEF Q2FEQ5 Large ribosomal subunit protein bL19 Staphylococcus aureus subsp. aureus USA300 0.013392771 1 LEVO MTNHKLIEAVTKSQLRTDLPSFRPGDTLRVHVRIIEGTRERIQVFEGVVIKRRGGGVSETFTVRKISSGVGVERTFPLHT PKIEKIEVKRRGKVRRAKLYYLRSLRGKAARIQEIR Q2FHJ7 Large ribosomal subunit protein bL20 Staphylococcus aureus subsp. aureus USA300 0.013720294999999999 1 LEVO MPRVKGGTVTRARRKKTIKLAKGYFGSKHTLYKVAKQQVMKSGQYAFRDRRQRKRDFRKLWITRINAAARQHEMSYSRLM NGLKKAGIDINRKMLSEIAISDEKAFAQLVTKAKDALK Q2FG58 Large ribosomal subunit protein bL21 Staphylococcus aureus subsp. aureus USA300 0.011354081 1 LEVO MFAIIETGGKQIKVEEGQEIFVEKLDVNEGDTFTFDKVLFVGGDSVKVGAPTVEGATVTATVNKQGRGKKITVFTYKRRK NSKRKKGHRQPYTKLTIDKINA Q2FG80 Large ribosomal subunit protein uL22 Staphylococcus aureus subsp. aureus USA300 0.012857921999999999 1 LEVO MEAKAVARTIRIAPRKVRLVLDLIRGKNAAEAIAILKLTNKASSPVIEKVLMSALANAEHNYDMNTDELVVKEAYANEGP TLKRFRPRAQGRASAINKRTSHITIVVSDGKEEAKEA Q2FEP4 Large ribosomal subunit protein uL23 Staphylococcus aureus subsp. aureus USA300 0.010625398 1 LEVO MEARDILKRPVITEKSSEAMAEDKYTFDVDTRVNKTQVKMAVEEIFNVKVASVNIMNYKPKKKRMGRYQGYTNKRRKAIV TLKEGSIDLFN Q2FEP1 Large ribosomal subunit protein uL24 Staphylococcus aureus subsp. aureus USA300 0.011561504 1 LEVO MHIKKGDNVKVIAGKDKGKEGKVIATLPKKDRVVVEGVNIMKKHQKPTQLNPEGGILETEAAIHVSNVQLLDPKTNEPTR VGYKFVDGKKVRIAKKSGEEIKSNN Q2FEQ0 50S ribosomal protein L25 Staphylococcus aureus subsp. aureus USA300 0.023810609 1 LEVO MASLKSIIRQGKQTRSDLKQLRKSGKVPAVVYGYGTKNVSVKVDEVEFIKVIREVGRNGVIELGVGSKTIKVMVADYQFD PLKNQITHIDFLAINMSEERTVEVPVQLVGEAVGAKEGGVVEQPLFNLEVTATPDNIPEAIEVDITELNINDSLTVADVK VTGDFKIENDSAESVVTVVAPTEEPTEEEIEAMEGEQQTEEPEVVGESKEDEEKTEE Q2FJE0 Large ribosomal subunit protein bL27 Staphylococcus aureus subsp. aureus USA300 0.010334798000000001 1 LEVO MLKLNLQFFASKKGVSSTKNGRDSESKRLGAKRADGQFVTGGSILYRQRGTKIYPGENVGRGGDDTLFAKIDGVVKFERK GRDKKQVSVYAVAE Q2FG82 Large ribosomal subunit protein bL28 Staphylococcus aureus subsp. aureus USA300 0.006995288999999999 1 LEVO MGKQCFVTGRKASTGNRRSHALNSTKRRWNANLQKVRILVDGKPKKVWVSARALKSGKVTRV Q2FHL4 Large ribosomal subunit protein uL29 Staphylococcus aureus subsp. aureus USA300 0.008592899999999999 1 LEVO MVKQMKAKEIRDLTTSEIEEQIKSSKEELFNLRFQLATGQLEETARIRTVRKTIARLKTVAREREIEQSKANQ A0A0H2XHC7 Large ribosomal subunit protein uL30 Staphylococcus aureus subsp. aureus USA300 0.006565683 1 LEVO MAKLQITLTRSVIGRPETQRKTVEALGLKKTNSSVVVEDNPAIRGQINKVKHLVTVEEK Q2FEQ7 Large ribosomal subunit protein bL32 Staphylococcus aureus subsp. aureus USA300 0.006500609 1 LEVO MAVPKRRTSKTRKNKRRTHFKISVPGMTECPNCGEYKLSHRVCKNCGSYNGEEVAAK Q2FHV3 P_site tRNA Staphylococcus aureus subsp. aureus USA300 0.022969724999999996 1 CGCGGGAUGGAGCAGGAGCUCGUCGGGCUCAUAGGCCGAAGGCGGUGGUUCAAAUCCGCCUCCCGCAACCA E_site tRNA Staphylococcus aureus subsp. aureus USA300 0.004170574 1 GGCCGGGCCACCA ZINC ION 6.5409e-05 3 ZN MAGNESIUM ION 2.4305e-05 231 MG (3aS,4R,7S,9R,10R,11R,13R,15R,15aR)-1-{4-[4-(3-aminophenyl)-1H-1,2,3-triazol-1-yl]butyl}-4-ethyl-7-fluoro-11-methoxy-3a ,7,9,11,13,15-hexamethyl-2,6,8,14-tetraoxotetradecahydro-2H-oxacyclotetradecino[4,3-d][1,3]oxazol-10-yl 3,4,6-trideoxy-3-(dimethylamino)-beta-D-xylo-hexopyranoside 0.000845009 1 EM1 POTASSIUM ION 3.9098e-05 12 K water 1.8015e-05 665 HOH singleParticle particle 7.5 Quantifoil R2/2 COPPER CARBON HOLEY GLOW DISCHARGE ETHANE TFS KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 0.5 1.8 GATAN K3 BIOQUANTUM (6k x 4k) 40.0 1 PHASE FLIPPING AND AMPLITUDE CORRECTION EMD-10079 2.08 FSC 0.143 CUT-OFF RELION

Resolution refers to gold-standard FSC 0.143 cutoff calculated on the postprocessed, solvent mask map

263087 MAXIMUM LIKELIHOOD MAXIMUM LIKELIHOOD emd_53067_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 440 440 440 0 0 0 440 440 440 362.56 362.56 362.56 90.0 90.0 90.0 X Y Z -0.024426859 0.11320433 -0.00026847035 0.004396073 0.824 0.824 0.824 AUTHOR ::::EMDATABANK.org::::EMD-53067:::: Half-map 1 of the focused refinement of the large subunit emd_53067_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 440 440 440 0 0 0 440 440 440 362.56 362.56 362.56 90.0 90.0 90.0 X Y Z -0.025502477 0.11301249 -0.00026753492 0.0044027404 0.824 0.824 0.824 AUTHOR ::::EMDATABANK.org::::EMD-53067:::: Half-map 2 of the focused refinement of the large subunit