2026-03-04 REL PDBe INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY DATA_COLLECTION em_admin _em_admin.last_update EXPERIMENTAL_SUMMARY em_admin _em_admin.last_update PDBe PDBe 2025-01-28 2025-08-20 2025-08-20 2026-03-04 Other private THE HELEN AND MILTON A. KIMMELMAN CENTER FOR BIOMOLECULAR STRUCTURE AND ASSEMBLY Hiregange DG Bashan A Yonath A Ribosome, antibiotics, macrolide-resistance Hiregange DG Samiya S Mizgalska D Ben-Zeev E Waghalter M Rivalta A Rajan KS Halfon Y Breiner-Goldstein E Kaczmarczyk I Sroka A Taoka M Nobe Y Isobe T Paukner S Zimmerman E Bashan A Potempa J Yonath A Nucleic Acids Res. UK 53 2025 40444637 doi:10.1093/nar/gkaf458 1362-4962 0389 NARHAD 9i5t FULLOVERLAP EMDB EMD-52635 associated EM volume

50S subunit of P. gingivalis ribosome with Lefamulin

50S subunit of P. gingivalis ribosome with Lefamulin 50S subunit of P. gingivalis ribosome with Lefamulin 0 1 2 3 4 5 6 7 8 9 10 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 Porphyromonas gingivalis Large ribosomal subunit protein bL28 Porphyromonas gingivalis 0.009027753 1 LEVO MSKICQITGKKAMVGNNVSHSKRRTKRVFDVNLFRKKFYWVEQDCWVVLRISAAGLRLINKIGLDAAIKRAAEKGFLNA B2RM15 Large ribosomal subunit protein uL29 Porphyromonas gingivalis 0.007499825 1 LEVO MKIAEIKELATKELQERLDAEVAAYDQMRINHAVSPLDSPAKLKHQRRMIAQMKTVLRQRELNK B2RLY4 Large ribosomal subunit protein uL5 Porphyromonas gingivalis 0.020912633 1 LEVO MSATANLKKDYQERIVPALMKQFGYTSVMQVPVLKKIVINQGLGMATGDKKIIDVAVSELTAITGQKAVPTVSKKDISNF KLRKKMPIGVMVTLRREQMYEFLERLVRIALPRIRDFKGIESKLDGRGNYTLGINEQIIFPEINIDAITKILGMNITFVT SAQSDEEGYALLKEFGLPFKNAKKQN B2RLY0 Large ribosomal subunit protein bL31B Porphyromonas gingivalis 0.009816323 1 LEVO MKKGIHPENYRPVVFKDMSNEDIFITRSTMEAKETIEIDGVTYPLIKVEISNTSHPFFTGKAKLVDTAGRVDKFMSRYGD RNKKK B2RIG0 Large ribosomal subunit protein uL30 Porphyromonas gingivalis 0.006700087 1 LEVO MAKIKIQQVRSRIRCPKDQKRTLDALGLRKLNQIVEHEATPSILGMVNKVRHLVLIVE B2RLX4 Large ribosomal subunit protein bL32 Porphyromonas gingivalis 0.006958198999999999 1 LEVO MAHPKRRQSKTRTAKRRTHDKAVMPTLAKCPNCGAWHIYHTVCGDCGYYRGKLAIEKEVAV B2RH62 Large ribosomal subunit protein bL34 Porphyromonas gingivalis 0.005761748 1 LEVO MKRTYQPSNRKRLNKHGFRSRMATANGRRVLAARRAKGRAKLTVSDEFVG B2RIL8 Large ribosomal subunit protein bL35 Porphyromonas gingivalis 0.007518082 1 LEVO MPKLKTNSGAKKRFALTGTGKIKRKHAFKSHILTKKTKKQKRNLTYFSTVHKVDENAVKQLLCLR B2RJD8 Large ribosomal subunit protein bL36 Porphyromonas gingivalis 0.004601648 1 LEVO MKVRASVKKRTPECKIVRRKGRLYVINKKNPKYKQRQG B2RLW9 23S rRNA Porphyromonas gingivalis 0.9342176879999999 1 UAAGGGCAGACGGUGGAUGCCUAGGCUCUCGGAGGCGAAGAAGGACGUGAUAAGCUGCGAAAAGCUGCGGGAAUCGGCAC AUACGAAUUGAUCCGCAGAUAUCCGAAUGGGGCAACCCGUCAGGCCAAGGCCUGACACAUGAAUUGAUUUCAUGAGCGAA CGCGGGGAACUGAAACAUCUCAUUACCCGUAGGAGAAGAAAACAAAAGUGAUUCCCUCAGUAGUGGCGAGCGAACGGGGA UUAGCCCAAACCGGCUUUGUUUCGGCAAAGUCGGGGUAAUAGGACUUCGACAAAAGUUUAAUGAUAGAUAUAGGAGAACC UACUGGAAAGUAUGGCCGAAGAGCAUGAAAGCUGCGUAUCCGACAUAUCGAACAAUAGACGACGGAGCACCUGAGUAGCG CGGGACACGAGACAUCCUGUGUGAAUUGGCGGGGCCCAUCCCGUAAGGCUAAAUACUCCCGAGAGACCGAUAGUGAACCA GUACCGUGAGGGAAAGGUGAAAAGAACCUCGAACAGAGGAGUGCAAUAGACCCUGAACCCGUCUGCCUACAAGCGGUAGG AGCGCCAUUAAGGUGUGACUGCGUGCCUUUUGCAUAAUGAACCUACGAGUUACUGUUUGUGGCAAGGUUAAUUGUUAUAA UCAAGACAAGGAGCCGAAGCGAAAGCGAGUCUUAAAAGGGCGCCCAUUUAGUCACGAGCAGUAGACGCGAAACCAAGUGA UCUACCCUUGGUCAGGUUGAAGGUUAGGUAACACUAACUGGAGGACCGAAUCGGUAAGCG(H2U)UGAAAAGCUUUCGAA UGAACUGAGGGUAGGGGUGAAAGGCUAAUCAAACUUGGAGAUAGCUCGUACUCCCCGAAAUGCAUUUAGGUGCAGCCUG (H2U)UGGAUGUUAUCAUGAGGUAGAGCGACUGAUUGGAUGCGAGGGUUUCACCGCCUAUCAAGUCCAGAUAAACUCCGA AUGCAUGAUAAUUGACCGAUGGAGUGAGGGCAUGGGUGCUAAGGUCCAUGUCCGAGAGGAGAAGAAUCCGGACCACCGGC UAAGGUCCCGAAAUAAUUGCUAAGUUGUAAAAACGAAGUCAAGAAGCAGAGACAGCUAGGAUGUUGGCUUGGAAGCAGCC AUUCAUUUAAAGAGUGCGUAACAGCUCACUAGUCGAGGAUUUUGGCAUGGAUAAUACACGGGCAUAAGCAAUUUACCGAA GCCGUGGGAUAUAGUUAAUAUAUCGGUAGGGGAGCAUUCCAGCGACGUAGAAGGGAAAAGGGCGACUUUUUCUGGAGUUU CUGGAAAAGCAAAUGUAGGUAUAAGUAACGAUAAAGGGGGCGAGAACCCCCCUCGCCGAAAGACCAAGGUUUCCUGAUCA ACGCUAAUCGGAUCAGGGUUAGUCGGGGCCUAAGGAUAAGCCGAAUGGCGAUUCCGAUGGAAGAACCGGUUAAUAUUCCG GUACUGAUACUAGAGGCGAUGUGGUGACGGAGAAGUGACAGUCCGGCCGUCUGACGGAUUAGGCGGUUAAAGGGUGUAGA UGUUAUUCGGGGUAGGCAAAUCCGCCCUCAGAGUGCAACCUGACAGUACCGGAGUACAAGUACGAAGGGAUAAAGGACGU AACCCGGCUCCCAAGAAAACCCGCUAAGAUAUUUCUUGUGUUACCCGUACCGUAAACCGACACAGGUGGUUGGGUUGAGU AUACUAAGGCGCUCGAGAGAUUCGCGGUUAAGGAACUAGGCAAAAUGGUCCUGUAACUUCGGGAGAAAGGACGCCUGUCC CGGGACAGGCCGCAGAAACCAGGCCCAGGCGACUGUUUAACAAAAACACAAGGCUAUGCAAAAAAGCAAUUUGAGGUAUA UAGUCUGACACCUGCCCGGUGCUGGAAGGUUAAGAGGAGGAGUCAUGUCAAGGAGAAGCUCUGAAUUGAAGCCCCAGUAA ACGGCGCCGUAACUAUAACGGUCC(5MC)UAAGGUAGCGAAA(5MU)UCCUUGUCGGGUAAGUUCCGAC(5MC)UGCACG AAUGGUGUAACGAUCUGGGCACUGUCUCAACCGCGAUCUCGGUGAAAUUGUAGUAUCGGUGAAGAUGCCGAUUACCCGCA ACGGGACG(6MA)(MA6)(6MA)AGACCCCGUGAACCUUUACUAUAGCUUUACAUUGUAUUGGGCAUCAGAUGUGUAGGA UAGGCCGGAGGCAGAGAAGCGGGUACGCCAGUAUUCGUGGAGUCGAUGUUGAAAUACGGCCCUUUUGAUGUUUGGGAUAC UAACUCGCGGGUGGCGAGGACAGUGUAUGGUGGGUAGUUUGACUG(OMG)GGUGGUCGCCUCCAAAAGCGUAACGGAGGC UUCUAAAGGUACCCUCAGGCCGAUUGUAAACCGGUCGCAGAGUGUAAUGGCACAAGGGUGCUUGACUGGGAGACAAACAA GUCGCACAGGUAGGAAACUAGAGCAUAGUGAUCCGGUGGUCCCGCAUGGAAGGGCCAUCGCUCAAAGGAUAAAAGGUACU CCG(2MG)GGA(OMU)AACAGGCUGAUCACUCCCAAGAGUCCAUAUCGACGGAGUGGUUUGGCACCU(5OC)G(2MA)UG UCGGCUCGUCACAUCCUGGGGCUGGAGAAGGUCCCAAGGGUUGGGCU(OMG)UUCGCCCAUUAAAGUGGCACGCGAGC (PSU)GGGUUCAGAACGUCGUGAGACAGU(PSU)CGGUCUCUAUCUG(H2U)UGUGGGCGCAGGAAAUUUGCGAGGGUCU GACACUAGUACGAGAGGACCGUG(H2U)UGGACAGACCCCUGGUUUACCGGUUGUACCGCCAGGUGCACCGCCGGGUAUC CACGUCUGGUAAGGAUAAGUGCUGAAAGCAUCUAAGCACGAAGCCGGCCUCAAGAUAAGAUUUCCAUAAAUAGGGUGGUU AAAGACUAUGACCUUGAUAGGCUGCAGGUGUAUGAUUGGUAACAAUUAAGCCGAGCAGUACUAAUAGCCCGAACUUU 5S rRNA Porphyromonas gingivalis 0.035186926 1 UCAGGUGGUUAUAACGUUGGGGAUCCACCUCUUCCCAUUCCGAACAGAGAAGUUAAGCCCAACGGUGCCGAUGGUACUGC GUCACAGUGGGAGAGUAGGACGCCGCCGA Large ribosomal subunit protein uL2 Porphyromonas gingivalis 0.029778553 1 LEVO MGIRKLKPTTPGQRHKVIGAFDKITASTPEKSLVVGKKKTGGRNNTGKMTMRYIGGGHKQKYRFIDFKRTKDGIPATVKT IEYDPNRSSRIALLYYADGAKAYIIAPDGLEVGHTVMSGSEAAPEVGNALPLANIPVGTIIHNIELRPGQGAKMVRSAGS FAQLTSREGTYVVIKMPSGEVRRILSTCKATIGSVGNSDHALEKSGKAGRSRWLGRRPHNRGVVMNPVDHPMGGGEGRQS GGHPRSRKGLYAKGLKTRAPKKHSSKYIIERRKK B2RLY9 Large ribosomal subunit protein uL3 Porphyromonas gingivalis 0.021925488 1 LEVO MPGLLGKKIGMTSVFSAEGKNLPCTVIEVGPCVVTQVKTLEKDGYSALQLGFVDAKEKHTTKPLAGHFKKANVAPKRHLA EFKNFEGEHKLGDVLNVEFFSDADFVDVVGTSKGKGFQGVVKRHGFGGVGQATHGQHNRLRAPGAVGACSYPAKVFKGTR MAGQMGNERVTVQNLEVIKVMPEHNLLLVKGSVPGAKGSILLIEK B2RLZ2 Large ribosomal subunit protein uL4 Porphyromonas gingivalis 0.023247879 1 LEVO MELSVYNIKGEDTGKKVVLDDSIFAIEPNDHAIYLDVKQYMANQRQGTHKAKERSELSGSTRKLIRQKGSGGARRGDINS PLLSGGARVFGPRPRNYSFKLNKKLKALARRSALSYKAKNNEIIVVEDFNFDAPKTKAFKAISAALKVGEKKVLYVLPEV NKNVYLSARNLPNTNLILANLINTYTVLASKNLVLTERSVAVVNELFKA Q7MTL4 Large ribosomal subunit protein uL13 Porphyromonas gingivalis 0.017075833999999998 1 LEVO MDTLSFKTISANKATVTKEWVIVDAEGQTLGRMCAKVAKLLRGKYKPNFTPHVDCGDNVIVINADKIVLSGNKWDGRIYL RHTGYPGGQRQFTPRDFMNKGPEYLFRKVVKGMLPKNRLGAKIIGNLYVYAGTEHKHEAQQPRQLDINSLK Q7MX43 Large ribosomal subunit protein uL15 Porphyromonas gingivalis 0.01561607 1 LEVO MNLSSLKPAEGAVKSRKRIGRGPGSGLGGTSTRGHKGAKSRSGYSKKIGFEGGQMPIQRRLPKFGFKNINRVEYKPINLS VLQTLSEANSLTKISVEDLIAAGLVSRNSLVKILANGTVTTALTVEAHAFSKTAEEAIVRAGGSVVKL Q7MTN2 Large ribosomal subunit protein uL16 Porphyromonas gingivalis 0.016344123 1 LEVO MLQPKKTKFRRQQKGRMKGFAQRGNQLSFGSFGIKSLQSKWITGRQIEAARIAVTRYMQRQGQVWVRIFPDKPITKKGEG VRMGKGKGAPEGFVAPITPGRIIFEVEGVPYEIAKEALRLAAQKLPVTTKFVVRHDYDIQNQNA B2RLY5 Large ribosomal subunit protein bL17 Porphyromonas gingivalis 0.018074081999999998 1 LEVO MRHNKKFNHLGRKAAHRKAMLSNMAASLILHKRIFTTVAKAKALRIYVEPLLTKTKEDTTHSRRIAFSYLQNKYALKELF GDVAAKIADRPGGYTRILKTGYRLGDNAAMCFIELVDYNENMLGEAAKKATKTRRSRKRKSADVVVEAAPAEETPKAAEE B2RLW4 Large ribosomal subunit protein uL18 Porphyromonas gingivalis 0.012560597 1 LEVO MVTKEQRRQKIKARVRGKISGTQEKPRLTVFRSNKQIYAQLIDDIAGRTLASASSLKLEMTGSKKEIAAKVGDEIAKAAT EAGISTVVFDRNGYLFHGRIKELADAARKGGLKF Q7MTM9 Large ribosomal subunit protein bL19 Porphyromonas gingivalis 0.014120454 1 LEVO MDFIKIVNEEFKSGKEHPKFNSGDTITVEYRIKEGNKERIQKYRGVVIRISGHGDKKRFTVRKISDGIGVERIFPIESPF IENITVEKYGKVRRAKLYYLRGLTGKKARIKERRVALSSKD B2RGQ9 Large ribosomal subunit protein bL20 Porphyromonas gingivalis 0.013324705 1 LEVO MPRSVNHVASRAKRKRILKLTRGYFGARKNVWTVAKNTWEKGLTYAYRDRKSKKRNFRALWIQRINAAARLEGMSYSRLM GALHANGIEINRKVLADLAMNHPEAFRAIVAKVKN Q7MVQ8 Large ribosomal subunit protein bL21 Porphyromonas gingivalis 0.011843913 1 LEVO MYVIVDIQGQQMKVEQGRRLFVHHIKDVESGASVEFDKVLLVDNNGAITVGSPLVEGAKVVCEVLTPLVKGDKVLIFHKK RRKGYRKLNGHRQQFTEILVKEVVA Q7MX95 Large ribosomal subunit protein uL22 Porphyromonas gingivalis 0.01535775 1 LEVO MGARKHNSAEARKEALKQMYFAKLRNVPTSPRKMRLVADMIRGMEVNRALGVLKFSNKEASARVEKLLRSAVANWEEKNE RKAEEGELFVSRICVDGASTLKRLRPAPQGRGYRIRKRSNHVTIYVDTLNNDNN B2RLY7 Large ribosomal subunit protein uL23 Porphyromonas gingivalis 0.011116101 1 LEVO MGIIIKPIISEKMTAVTEKMSERYGFRVSPNANKIEIKKAVEAMYNVKVEDVNTMRYDGKRKNRYTKSGLIRGKEASFKK AIVTLKKGETIDFFSNI A0A134DR82 Large ribosomal subunit protein uL24 Porphyromonas gingivalis 0.011627664 1 LEVO MSKLHIKKGDTVMVISGEDKGHSGRVLEVLVKEQRAIVEGLNMIKKHAKPSAKNPQGGIISKEAPIHISNLNVVDPKTGK ATRIGRRLNENGKLVRYAKKSGEEIK B2RLY1 Large ribosomal subunit protein bL25 Porphyromonas gingivalis 0.021028605 1 LEVO MKTFQLTGTPRAEFGKKAAKAIRKEDQIPAVLYGGKGEGVNFIVSQDAVRNLIYSPEIFLVELTVEGSGSYKAILKEIQF HPVTDRIIHIDFLQVTDEKPVVMEVPVVLTGHAEGVKAGGKLSLEMRKLKVKALYSEIPEKLDIDVSDLQLGKTIQVGEL HFEGLTLMNAKNAVVCAVKLTRAARGAAVKKQ B2RHF3 Large ribosomal subunit protein bL27 Porphyromonas gingivalis 0.009244612999999999 1 LEVO MAHKKGVGSSKNGRESESKRLGVKVYGGEMAKAGNILVRQRGTVHHPGENVGIGKDHTLYALKSGVVVFTRKKNDRSYVS IKTES B2RLC1 Large ribosomal subunit protein bL9 Porphyromonas gingivalis 0.019356210999999998 1 LEVO MQVILKEDVVNLGYKDDIVTVKDGYGRNFLIPQGKAVIASESAKKVLAENLRQRAHKIAQIKKEAEEKAASMQGISLTIK AKTSSTGTIFGSVTNIQIAEELAKKGVEVDRKIIVLKPAVKEVGNYTAVVRLHKEVTVEIPFEVVSENETIIEAKPEGAP VPVAEEPAAEAEQAEVAAE B2RIG5 DUF4295 domain-containing protein Porphyromonas gingivalis 0.005559542 1 LEVO MAKKSVATFKKGDGRTYSKVIKMVKSPKTGAYTFQEEMVPNEAVKDFFK A0AAE9XCN0 Large ribosomal subunit protein uL6 Porphyromonas gingivalis 0.020389811 1 LEVO MSRIGKLPISIPAGVTVSHKDEIVTVKGPKGELSQYVDPRITVVIEGGMIHLERKTDDRIERSLHGLYRSLINNMVQGVS AGFKRELELVGVGYRASNQGQLLELSLGFTHSIFMQLPKEVTVETKSERNKNPLIILESADKQLLGQVCMKIRSFRKPEP YKGKGVKFVGEQIRRKSGKSAGK B2RLX7 Large ribosomal subunit protein uL14 Porphyromonas gingivalis 0.013086285999999999 1 LEVO MIQQESRLVVADNSGAKEALCIRVLGGTRRRYASVGDIIVVSVKSVIPSSDIKKGAVSKAVIVRTKKEVRRPDGSYIRFD DNACVLLNAAGDIRGSRIFGPVARELRGTNMKIVSLAPEVL B2RLY2 Large ribosomal subunit protein bL33 Porphyromonas gingivalis 0.007356796 1 LEVO MAKKVKGNRVQVILECTEHKESGMPGISRYITTKNRKNTTQRLELKKYNPILRRMTLHKEIK B2RM14 MAGNESIUM ION 2.4305e-05 139 MG ZINC ION 6.5409e-05 1 ZN Lefamulin 0.000507726 1 62B POTASSIUM ION 3.9098e-05 18 K SODIUM ION 2.299e-05 15 NA water 1.8015e-05 1380 HOH singleParticle particle 7.5 Quantifoil R2/2 COPPER 300 CARBON CONTINUOUS ETHANE TFS KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 0.5 1.5 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN GATAN K3 BIOQUANTUM (6k x 4k) 1.0 1 PHASE FLIPPING AND AMPLITUDE CORRECTION 2.6 FSC 0.143 CUT-OFF 223396 MAXIMUM LIKELIHOOD MAXIMUM LIKELIHOOD emd_52635_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 440 440 440 0 0 0 440 440 440 374.0 374.0 374.0 90.0 90.0 90.0 X Y Z -0.042323075 0.112129815 -0.00030181452 0.005076466 0.85 0.85 0.85 AUTHOR ::::EMDATABANK.org::::EMD-52635:::: emd_52635_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 440 440 440 0 0 0 440 440 440 374.0 374.0 374.0 90.0 90.0 90.0 X Y Z -0.043944146 0.10336089 -0.0003028081 0.0050713643 0.85 0.85 0.85 AUTHOR ::::EMDATABANK.org::::EMD-52635::::