Structure of the 50S subunit of the ribosome from Methicillin Resistant Staphylococcus aureus in complex with the antibiotic, radezolid

2025-05-28 REL RCSB INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY EXPERIMENTAL_SUMMARY em_admin em_software _em_admin.last_update _em_software.name STRUCTURE_SUMMARY chem_comp_atom chem_comp_bond database_2 em_admin pdbx_entry_details pdbx_modification_feature _database_2.pdbx_DOI _database_2.pdbx_database_accession _em_admin.last_update _pdbx_entry_details.has_protein_modification DATA_COLLECTION em_admin em_software _em_admin.last_update _em_software.name RCSB RCSB 2020-04-29 2020-06-03 2020-06-03 2025-05-28 Department of Defense (DOD, United States) W81XWH1910126 United States Structure of the 50S subunit of the ribosome from Methicillin Resistant Staphylococcus aureus in complex with the antibiotic, radezolid Belousoff MJ antibiotic, radezolid, oxazolidinone, RIBOSOME Wright A Deane-Alder K Marschall E Bamert R Venugopal H Lithgow T Lupton DW Belousoff MJ Characterization of the Core Ribosomal Binding Region for the Oxazolidone Family of Antibiotics Using Cryo-EM. Acs Pharmacol Transl Sci US 3 425 432 2020 32566908 doi:10.1021/acsptsci.0c00041 2575-910 6wqq FULLOVERLAP 50S ribosomal subunit 50S ribosomal 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 Staphylococcus aureus 50S ribosomal protein L19 Staphylococcus aureus 0.013392771 1 LEVO MTNHKLIEAVTKSQLRTDLPSFRPGDTLRVHVRIIEGTRERIQVFEGVVIKRRGGGVSETFTVRKISSGVGVERTFPLHT PKIEKIEVKRRGKVRRAKLYYLRSLRGKAARIQEIR A0A077UVB6 50S ribosomal protein L2 Staphylococcus aureus 0.030217163999999998 1 LEVO MAIKKYKPITNGRRNMTSLDFAEITKTTPEKSLLKPLPKKAGRNNQGKLTVRHHGGGHKRQYRVIDFKRNKDGINAKVDS IQYDPNRSANIALVVYADGEKRYIIAPKGLEVGQIVESGAEADIKVGNALPLQNIPVGTVVHNIELKPGKGGQIARSAGA SAQVLGKEGKYVLIRLRSGEVRMILSTCRATIGQVGNLQHELVNVGKAGRSRWKGIRPTVRGSVMNPNDHPHGGGEGRAP IGRPSPMSPWGKPTLGKKTRRGKKSSDKLIVRGRKKK A0A077W1J0 50S ribosomal protein L20 Staphylococcus aureus 0.013720294999999999 1 LEVO MPRVKGGTVTRARRKKTIKLAKGYFGSKHTLYKVAKQQVMKSGQYAFRDRRQRKRDFRKLWITRINAAARQHEMSYSRLM NGLKKAGIDINRKMLSEIAISDEKAFAQLVTKAKDALK A0A077VMP6 50S ribosomal protein L21 Staphylococcus aureus 0.011700483 1 LEVO MQSMFAIIETGGKQIKVEEGQEIFVEKLDVNEGDTFTFDKVLFVGGDSVKVGAPTVEGATVTATVNKQGRGKKITVFTYK RRKNSKRKKGHRQPYTKLTIDKINA A0A0E0VQU6 50S ribosomal protein L22 Staphylococcus aureus 0.012871947 1 LEVO MEAKAVARTIRIAPRKVRLVLDLIRGKNAAEAIAILKLTNKASSPVIEKVLMSALANAEHNYDMNTDELVVKEAYANEGP TLKRFRPRAQGRASAINKRTSHITIVVSDAKEEAKEA A0A077UKF9 50S ribosomal protein L23 Staphylococcus aureus 0.010627327999999998 1 LEVO MEARDILKRPVITEKSSEAMAEDKYTFDVDTRVNKTQVKMAVEEIFNVKVASVNIMNYKPKKKRMGRYQGYTNKRRKAIV TLKEGSDDLFN W8TUB4 50S ribosomal protein L24 Staphylococcus aureus 0.011591530000000001 1 LEVO MHIKKGDNVKVIAGKDKGKEGKVIATLPKKDRVVVEGVNIMKKHQKPTQLNPESGILETEAAIHVSNVQLLDPKTNEPTR VGYKFVDGKKVRIAKKSGEEIKSNN W8TRD5 50S ribosomal protein L25 Staphylococcus aureus 0.012063076999999998 1 LEVO MASLKSIIRQGKQTRSDLKQLRKSGKVPAVVYGYGTKNVSVKVDEVEFIKVIREVGRNGVIELGVGSKTIKVMVADYQFD PLKNQITHIDFLAINMSEDVLLKYQFN A0A2X2JWH5 50S ribosomal protein L28 Staphylococcus aureus 0.006967235 1 LEVO MGKQCFVTGRKASTGNRRSHALNSTKRRWNANLQKVRILVDGKPKKVWVSARALKSGKVTRA A0A077URJ8 50S ribosomal protein L29 Staphylococcus aureus 0.008491819999999999 1 LEVO MKKKKAKEIRNLTTSEIEEQIKSSKEELFNLRFQLATGQLEETARIRTVRKTIARLKTVAREREIEQSKANQ A0A2S6DIY7 50S ribosomal protein L3 Staphylococcus aureus 0.023459921999999998 1 LEVO MTKGILGRKIGMTQVFGENGELIPVTVVEAKENVVLQKKTVEVDGYNAIQVGFEDKKAYKKDAKSNKYANKPAEGHAKKA DAAPKRFIREFRNVDVDAYEVGQEVSVDTFVAGDVIDVTGVSKGKGFQGAIKRHGQSRGPMSHGSHFHRAPGSVGMASDA SRVFKGQKMPGRMGGNTVTVQNLEVVQVDTENKVILVKGNVPGPKKGLVEIRTSIKK W8U3W0 50S ribosomal protein L30 Staphylococcus aureus 0.006434487 1 LEVO AKLQITLTRSVIGRPETQRKTVEALGLKKTNSSVVVEDNPAIRGQINKVKHLVTVEEK W8UVN7 50S ribosomal protein L32 Staphylococcus aureus 0.006472555999999999 1 LEVO MAVPKRRTSKTRKNKRRTHFKISVPGMTECPNCGEYKLSHRVCKNCGSYNGEEAAAK A0A077UWR7 50S ribosomal protein L33 Staphylococcus aureus 0.005885783 1 LEVO MRVNVTLACTECGDRNYITTKNKRNNPERVEMKKFCSRENKQTLHRETK A0A077UXT4 50S ribosomal protein L34 Staphylococcus aureus 0.006064399999999999 1 LEVO MEVFCMVKRTYQPNKRKHSKVHGFRKRMSTKNGRKVLARRRRKGRKVLSA T1YD75 50S ribosomal protein L35 Staphylococcus aureus 0.007593188 1 LEVO MPKMKTHRGAAKRVKRTASGQLKRSRAFTSHLFANKSTKQKRQLRKARLVSKSDMKRVKQLLAYK A0A077UL47 50S ribosomal protein L36 Staphylococcus aureus 0.004318422 1 LEVO MKVRPSVKPICEKCKVIKRKGKVMVICENPKHKQRQG A0A077UGV8 50S ribosomal protein L4 Staphylococcus aureus 0.022523752 1 LEVO MANYDVLKLDGTKSGSIELSDAVFGIEPNNSVLFEAINLQRASLRQGTHAVKNRSAVSGGGRKPWKQKGTGRARQGTIRA PQWRGGGIVFGPTPRSYAYKMPKKMRRLALRSALSFKVQENGLTVVDAFNFEAPKTKEFKNVLSTLEQPKKVLVVTENED VNVELSARNIPGVQVTTAQGLNVLDITNADSLVITEAAAKKVEEVLG A0A166DK89 50S ribosomal protein L13 Staphylococcus aureus 0.016359427 1 LEVO MRQTFMANESNIERKWYVIDAEGQTLGRLSSEVASILRGKNKVTYTPHVDTGDYVIVINASKIEFTGNKETDKVYYRHSN HPGGIKSITAGELRRTNPERLIENSIKGMLPSTRLGEKQGKKLFVYGGAEHPHAAQQPENYELRG W8TUE6 50S ribosomal protein L14 Staphylococcus aureus 0.013157342 1 LEVO MIQQETRLKVADNSGAREVLTIKVLGGSGRKTANIGDVIVCTVKNATPGGVVKKGDVVKAVIVRTKSGVRRNDGSYIKFD ENACVIIRDDKGPRGTRIFGPVARELREGNFMKIVSLAPEVL A0A077UUA0 50S ribosomal protein L15 Staphylococcus aureus 0.01562889 1 LEVO MKLHELKPAEGSRKERNRVGRGVATGNGKTSGRGHKGQKARSGGGVRPGFEGGQLPLFRRLPKRGFTNINRKEYAIVNLD QLNKFEDGTEVTPALLVESGVVKNEKSGIKILGNGSLDKKLTVKAHKFSASAAEAIDAKGGAHEVI A0A077UGA7 50S ribosomal protein L16 Staphylococcus aureus 0.016274049 1 LEVO MLLPKRVKYRRQHRPKTTGRSKGGNYVTFGEFGLQATTTSWITSRQIESARIAMTRYMKRGGKVWIKIFPHTPYTKKPLE VRMGAGKGAVEGWIAVVKPGRILFEVAGVSEEVAREALRLASHKLPVKTKFVKREELGGETNES A0A077V4G0 50S ribosomal protein L17 Staphylococcus aureus 0.013771773 1 LEVO MGYRKLGRTSDQRKAMLRDLATSLIISERIETTEARAKEVRSVVEKLITLGKKGDLASRRNAAKTLRNVEILNEDETTQT ALQKLFGEIAERYTERQGGYTRILKQGPRRGDGAESVIIELV A0A077UG91 50S ribosomal protein L18 Staphylococcus aureus 0.013124093 1 LEVO MISKIDKNKVRLKRHARVRTNLSGTAEKPRLNVYRSNKHIYAQIIDDNKGVTLAQASSKDSDIATTATKVELATKVGEAI AKKAADKGIKEIVFDRGGYLYHGRVKALAEAARESGLEF W8TRE0 23S rRNA Staphylococcus aureus 0.9466806249999999 1 GAUUAAGUUAUUAAGGGCGCACGGUGGAUGCCUUGGCACUAGAAGCCGAUGAAGGACGUUACUAACGACGAUAUGCUUUG GGGAGCUGUAAGUAAGCUUUGAUCCAGAGAUUUCCGAAUGGGGAAACCCAGCAUGAGUUAUGUCAUGUUAUCGAUAUGUG AAUACAUAGCAUAUCAGAAGGCACACCCGGAGAACUGAAACAUCUUAGUACCCGGAGGAAGAGAAAGAAAAUUCGAUUCC CUUAGUAGCGGCGAGCGAAACGGGAAGAGCCCAAACCAACAAGCUUGCUUGUUGGGGUUGUAGGACACUCUAUACGGAGU UACAAAGGACGACAUUAGACGAAUCAUCUGGAAAGAUGAAUCAAAGAAGGUAAUAAUCCUGUAGUCGAAAAUGUUGUCUC UCUUGAGUGGAUCCUGAGUACGACGGAGCACGUGAAAUUCCGUCGGAAUCUGGGAGGACCAUCUCCUAAGGCUAAAUACU CUCUAGUGACCGAUAGUGAACCAGUACCGUGAGGGAAAGGUGAAAAGCACCCCGGAAGGGGAGUGAAAUAGAACCUGAAA CCGUGUGCUUACAAGUAGUCAGAGCCCGUUAAUGGGUGAUGGCGUGCCUUUUGUAGAAUGAACCGGCGAGUUACGAUUUG AUGCAAGGUUAAGCAGUAAAUGUGGAGCCGUAGCGAAAGCGAGUCUGAAUAGGGCGUUUAGUAUUUGGUCGUAGACCCGA AACCAGGUGAUCUACCCUUGGUCAGGUUGAAGUUCAGGUAACACUGAAUGGAGGACCGAACCGACUUACGUUGAAAAGUG AGCGGAUGAACUGAGGGUAGCGGAGAAAUUCCAAUCGAACCUGGAGAUAGCUGGUUCUCUCCGAAAUAGCUUUAGGGCUA GCCUCAAGUGAUGAUUAUUGGAGGUAGAGCACUGUUUGGACGAGGGGCCCCUCUCGGGUUACCGAAUUCAGACAAACUCC GAAUGCCAAUUAAUUUAACUUGGGAGUCAGAACAUGGGUGAUAAGGUCCGUGUUCGAAAGGGAAACAGCCCAGACCACCA GCUAAGGUCCCAAAAUAUAUGUUAAGUGGAAAAGGAUGUGGCGUUGCCCAGACAACUAGGAUGUUGGCUUAGAAGCAGCC AUCAUUUAAAGAGUGCGUAAUAGCUCACUAGUCGAGUGACACUGCGCCGAAAAUGUACCGGGGCUAAACAUAUUACCGAA GCUGUGGAUUGUCCUUUGGACAAUGGUAGGAGAGCGUUCUAAGGGCGUUGAAGCAUGAUCGUAAGGACAUGUGGAGCGCU UAGAAGUGAGAAUGCCGGUGUGAGUAGCGAAAGACGGGUGAGAAUCCCGUCCACCGAUUGACUAAGGUUUCCAGAGGAAG GCUCGUCCGCUCUGGGUUAGUCGGGUCCUAAGCUGAGGCCGACAGGCGUAGGCGAUGGAUAACAGGUUGAUAUUCCUGUA CCACCUAUAAUCGUUUUAAUCGAUGGGGGGACGCAGUAGGAUAGGCGAAGCGUGCGAUUGGAUUGCACGUCUAAGCAGUA AGGCUGAGUAUUAGGCAAAUCCGGUACUCGUUAAGGCUGAGCUGUGAUGGGGAGAAGACAUUGUGUCUUCGAGUCGUUGA UUUCACACUGCCGAGAAAAGCCUCUAGAUAGAAAAUAGGUGCCCGUACCGCAAACCGACACAGGUAGUCAAGAUGAGAAU UCUAAGGUGAGCGAGCGAACUCUCGUUAAGGAACUCGGCAAAAUGACCCCGUAACUUCGGGAGAAGGGGUGCUCUUUAGG GUUAACGCCCAGAAGAGCCGCAGUGAAUAGGCCCAAGCGACUGUUUAUCAAAAACACAGGUCUCUGCUAAACCGUAAGGU GAUGUAUAGGGGCUGACGCCUGCCCAGUGCUGGAAGGUUAAGAGGAGUGGUUAGCUUCUGCGAAGCUACGAAUCGAAGCC CCAGUAAACGGCGGCCGUAACUAUAACGGUCCUAAGGUAGCGAAAUUCCUUGUCGGGUAAGUUCCGACCCGCACGAAAGG CGUAACGAUUUGGGCACUGUCUCAACGAGAGACUCGGUGAAAUCAUAGUACCUGUGAAGAUGCAGGUUACCCGCGACAGG ACGGAAAGACCCCGUGGAGCUUUACUGUAGCCUGAUAUUGAAAUUCGGCACAGCUUGUACAGGAUAGGUAGGAGCCUUUG AAACGUGAGCGCUAGCUUACGUGGAGGCGCUGGUGGGAUACUACCCUAGCUGUGUUGGCUUUCUAACCCGCACCACUUAU CGUGGUGGGAGACAGUGUCAGGCGGGCAGUUUGACUGGGGCGGUCGCCUCCUAAAAGGUAACGGAGGCGCUCAAAGGUUC CCUCAGAAUGGUUGGAAAUCAUUCAUAGAGUGUAAAGGCAUAAGGGAGCUUGACUGCGAGACCUACAAGUCGAGCAGGGU CGAAAGACGGACUUAGUGAUCCGGUGGUUCCGCAUGGAAGGGCCAUCGCUCAACGGAUAAAAGCUACCCCGGGGAUAACA GGCUUAUCUCCCCCAAGAGUUCACAUCGACGGGGAGGUUUGGCACCUCGAUGUCGGCUCAUCGCAUCCUGGGGCUGUAGU CGGUCCCAAGGGUUGGGCUGUUCGCCCAUUAAAGCGGUACGCGAGCUGGGUUCAGAACGUCGUGAGACAGUUCGGUCCCU AUCCGUCGUGGGCGUAGGAAAUUUGAGAGGAGCUGUCCUUAGUACGAGAGGACCGGGAUGGACAUACCUCUGGUGUACCA GUUGUCGUGCCAACGGCAUAGCUGGGUAGCUAUGUGUGGACGGGAUAAGUGCUGAAAGCAUCUAAGCAUGAAGCCCCCCU CAAGAUGAGAUUUCCCAACUUCGGUUAUAAGAUCCCUCAAAGAUGAUGAGGUUAAUAGGUUCGAGGUGGAAGCAUGGUGA CAUGUGGAGCUGACGAAUACUAAUCGAUCGAAGACUUAAUCAA CP030689.1 5S rRNA Staphylococcus aureus 0.036957961000000004 1 UCUGGUGACUAUAGCAAGGAGGUCACACCUGUUCCCAUGCCGAACACAGAAGUUAAGCUCCUUAGCGACGAUGGUAGUCC AACUUACGUUCCGCUAGAGUAGAACGUUCCAGGGC CP044106.1 50S ribosomal protein L27 Staphylococcus aureus 0.009198369 1 LEVO ASKKGVSSTKNGRDSESKRLGAKRADGQFVTGGSILYRQRGTKIYPGENVGRGGDDTLFAKIDGVVKFERKGRDKKQVSV YAVAE A0A077ULC5 Radezolid 0.000438455 1 RD8 singleParticle particle 0.3 7.4 ETHANE TFS GLACIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 200 FEI FALCON III (4k x 4k) COUNTING 47.0 1 PHASE FLIPPING AND AMPLITUDE CORRECTION C1 3.1 FSC 0.143 CUT-OFF 250000 MAXIMUM LIKELIHOOD MAXIMUM LIKELIHOOD emd_21873.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 400 400 400 0 0 0 400 400 400 456.0 456.0 456.0 90.0 90.0 90.0 X Y Z -0.22243644 0.3756575 0.00027262006 0.008166281 1.14 1.14 1.14 0.02 AUTHOR ::::EMDATABANK.org::::EMD-21873:::: emd_21873_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 400 400 400 0 0 0 400 400 400 456.0 456.0 456.0 90.0 90.0 90.0 X Y Z -0.04679267 0.10495305 0.000107380314 0.00422731 1.14 1.14 1.14 AUTHOR ::::EMDATABANK.org::::EMD-21873:::: emd_21873_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 400 400 400 0 0 0 400 400 400 456.0 456.0 456.0 90.0 90.0 90.0 X Y Z -0.054184336 0.11761424 -0.000058124042 0.0057347864 1.14 1.14 1.14 AUTHOR ::::EMDATABANK.org::::EMD-21873:::: emd_21873_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 400 400 400 0 0 0 400 400 400 456.0 456.0 456.0 90.0 90.0 90.0 X Y Z -0.05548306 0.11914316 -0.000056898665 0.0057099145 1.14 1.14 1.14 AUTHOR ::::EMDATABANK.org::::EMD-21873::::