Improved model derived from cryo-EM map of Staphylococcus aureus large ribosomal subunit

2025-10-22 REL PDBe INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY EXPERIMENTAL_SUMMARY em_admin _em_admin.last_update 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 DATA_COLLECTION chem_comp_atom chem_comp_bond em_admin _chem_comp_atom.atom_id _chem_comp_atom.pdbx_aromatic_flag _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.pdbx_aromatic_flag _chem_comp_bond.value_order _em_admin.last_update DATABASE_REFERENCES citation citation_author em_admin _citation.country _citation.journal_abbrev _citation.journal_id_CSD _citation.journal_id_ISSN _citation.journal_volume _citation.page_first _citation.page_last _citation.pdbx_database_id_DOI _citation.pdbx_database_id_PubMed _citation.title _citation.year _em_admin.last_update PDBe PDBe 2018-09-12 2018-11-14 2018-11-14 2025-10-22 Improved model derived from cryo-EM map of Staphylococcus aureus large ribosomal subunit Eyal Z Cimicata G ribosomal RNA, ribosome, pathogen, ribosomal protein, cryo-EM Cimicata G Fridkin G Bose T Eyal Z Halfon Y Breiner-Goldstein E Fox T Zimmerman E Bashan A de Val N Wlodawer A Yonath A Structural Studies Reveal the Role of Helix 68 in the Elongation Step of Protein Biosynthesis. Mbio US 13 e0030622 e0030622 2022 35348349 doi:10.1128/mbio.00306-22 2150-7511 Eyal Z Matzov D Krupkin M Wekselman I Paukner S Zimmerman E Rozenberg H Bashan A Yonath A Structural insights into species-specific features of the ribosome from the pathogen Staphylococcus aureus Proc.Natl.Acad.Sci.Usa US 112 E5805 E5814 2015 26464510 doi:10.1073/pnas.1517952112 0027-8424 0040 PNASA6 6hma FULLOVERLAP PDB 4WCE unspecified

crystal structure of Staphylococcus aures large ribosomal subunit

EMDB EMD-0243 associated EM volume

Staphylococcus aureus large ribosomal subunit Staphylococcus aureus large 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 28 29 Staphylococcus aureus 23S ribosomal RNA Staphylococcus aureus 0.9467386879999999 1 GAUUAAGUUAUUAAGGGCGCACGGUGGAUGCCUUGGCACUAGAAGCCGAUGAAGGACGUUACUAACGACGAUAUGCUUUG GGGAGCUGUAAGUAAGCUUUGAUCCAGAGAUUUCCGAAUGGGGAAACCCAGCAUGAGUUAUGUCAUGUUAUCGAUAUGUG AAUACAUAGCAUAUCAGAAGGCACACCCGGAGAACUGAAACAUCUUAGUACCCGGAGGAAGAGAAAGAAAAUUCGAUUCC CUUAGUAGCGGCGAGCGAAACGGGAAGAGCCCAAACCAACAAGCUUGCUUGUUGGGGUUGUAGGACACUCUAUACGGAGU UACAAAGGACGACAUUAGACGAAUCAUCUGGAAAGAUGAAUCAAAGAAGGUAAUAAUCCUGUAGUCGAAAAUGUUGUCUC UCUUGAGUGGAUCCUGAGUACGACGGAGCACGUGAAAUUCCGUCGGAAUCUGGGAGGACCAUCUCCUAAGGCUAAAUACU CUCUAGUGACCGAUAGUGAACCAGUACCGUGAGGGAAAGGUGAAAAGCACCCCGGAAGGGGAGUGAAAUAGAACCUGAAA CCGUGUGCUUACAAGUAGUCAGAGCCCGUUAAUGGGUGAUGGCGUGCCUUUUGUAGAAUGAACCGGCGAGUUACGAUUUG AUGCAAGGUUAAGCAGUAAAUGUGGAGCCGUAGCGAAAGCGAGUCUGAAUAGGGCGUUUAGUAUUUGGUCGUAGACCCGA AACCAGGUGAUCUACCCUUGGUCAGGUUGAAGUUCAGGUAACACUGAAUGGAGGACCGAACCGACUUACGU(5MU)GAAA AGUGAGCGGAUGAACUGAGGGUAGCGGAGAAAUUCCAAUCGAACCUGGAGAUAGCUGGUUCUCUCCGAAAUAGCUUUAGG GCUAGCCUCAAGUGAUGAUUAUUGGAGGUAGAGCACUGUUUGGACGAGGGGCCCCUCUCGGGUUACCGAAUUCAGACAAA CUCCGAAUGCCAAUUAAUUUAACUUGGGAGUCAGAACAUGGGUGAUAAGGUCCGUGUUCGAAAGGGAAACAGCCCAGACC ACCAGCUAAGGUCCCAAAAUAUAUGUUAAGUGGAAAAGGAUGUGGCGUUGCCCAGACAACUAGGAUGUUGGCUUAGAAGC AGCCAUCAUUUAAAGAGUGCGUAAUAGCUCACUAGUCGAGUGACACUGCGCCGAAAAUGUACCGGGGCUAAACAUAUUAC CGAAGCUGUGGAUUGUCCUUUGGACAAUGGUAGGAGAGCGUUCUAAGGGCGUUGAAGCAUGAUCGUAAGGACAUGUGGAG CGCUUAGAAGUGAGAAUGCCGGUGUGAGUAGCGAAAGACGGGUGAGAAUCCCGUCCACCGAUUGACUAAGGUUUCCAGAG GAAGGCUCGUCCGCUCUGGGUUAGUCGGGUCCUAAGCUGAGGCCGACAGGCGUAGGCGAUGGAUAACAGGUUGAUAUUCC UGUACCACCUAUAAUCGUUUUAAUCGAUGGGGGGACGCAGUAGGAUAGGCGAAGCGUGCGAUUGGAUUGCACGUCUAAGC AGUAAGGCUGAGUAUUAGGCAAAUCCGGUACUCGUUAAGGCUGAGCUGUGAUGGGGAGAAGACAUUGUGUCUUCGAGUCG UUGAUUUCACACUGCCGAGAAAAGCCUCUAGAUAGAAAAUAGGUGCCCGUACCGCAAACCGACACAGGUAGUCAAGAUGA GAAUUCUAAGGUGAGCGAGCGAACUCUCGUUAAGGAACUCGGCAAAAUGACCCCGUAACUUCGGGAGAAGGGGUGCUCUU UAGGGUUAACGCCCAGAAGAGCCGCAGUGAAUAGGCCCAAGCGACUGUUUAUCAAAAACACAGGUCUCUGCUAAACCGUA AGGUGAUGUAUAGGGGCUGACGCCUGCCCGGUGCUGGAAGGUUAAGAGGAGUGGUUAGCUUCUGCGAAGCUACGAAUCGA AGCCCCAGUAAACGGCGGCCGUAACUAUAACGGUCCUAAGGUAGCGAAA(5MU)UCCUUGUCGGGUAAGUUCCGACCCGC ACGAAAGGCGUAACGAUUUGGGCACUGUCUCAACGAGAGACUCGGUGAAAUCAUAGUACCUGUGAAGAUGCAGGUUACCC GCGACAGGACGGAAAGACCCCGUGGAGCUUUACUGUAGCCUGAUAUUGAAAUUCGGCACAGCUUGUACAGGAUAGGUAGG AGCCUUUGAAACGUGAGCGCUAGCUUACGUGGAGGCGCUGGUGGGAUACUACCCUAGCUGUGUUGGCUUUCUAACCCGCA CCACUUAUCGUGGUGGGAGACAGUGUCAGGCGGGCAGUUUGACUGGGGCGGUCGCCUCCUAAAAGGUAACGGAGGCGCUC AAAGGUUCCCUCAGAAUGGUUGGAAAUCAUUCAUAGAGUGUAAAGGCAUAAGGGAGCUUGACUGCGAGACCUACAAGUCG AGCAGGGUCGAAAGACGGACUUAGUGAUCCGGUGGUUCCGCAUGGAAGGGCCAUCGCUCAACGGAUAAAAGCUACCCCGG GGAUAACAGGCUUAUCUCCCCCAAGAGUUCACAUCGACGGGGAGGUUUGGCACCUCG(2MA)UGUCGGCUCAUCGCAUCC UGGGGCUGUAGUCGGUCCCAAGGGUUGGGCUGUUCGCCCAUUAAAGCGGUACGCGAGCUGGGUUCAGAACGUCGUGAGAC AGUUCGGUCCCUAUCCGUCGUGGGCGUAGGAAAUUUGAGAGGAGCUGUCCUUAGUACGAGAGGACCGGGAUGGACAUACC UCUGGUGUACCAGUUGUCGUGCCAACGGCAUAGCUGGGUAGCUAUGUGUGGACGGGAUAAGUGCUGAAAGCAUCUAAGCA UGAAGCCCCCCUCAAGAUGAGAUUUCCCAACUUCGGUUAUAAGAUCCCUCAAAGAUGAUGAGGUUAAUAGGUUCGAGGUG GAAGCAUGGUGACAUGUGGAGCUGACGAAUACUAAUCGAUCGAAGACUUAAUCAA CP030323.1 5S ribosomal RNA Staphylococcus aureus 0.036974944999999995 1 UCUGGUGACUAUAGCAAGGAGGUCACACCUGUUCCCAUGCCGAACACAGAAGUUAAGCUCCUUAGCGUCGAUGGUAGUCG AACUUACGUUCCGCUAGAGUAGAACGUUGCCAGGC LT992461.1 50S ribosomal protein L2 Staphylococcus aureus 0.029827607 1 LEVO AIKKYKPITNGRRNMTSLDFAEITKTTPEKSLLKPLPKKAGRNNQGKLTVRHHGGGHKRQYRVIDFKRNKDGINAKVDSI QYDPNRSANIALVVYADGEKRYIIAPKGLEVGQIVESGAEADIKVGNALPLQNIPVGTVVHNIELKPGKGGQIARSAGAS AQVLGKEGKYVLIRLRSGEVRMILSTCRATIGQVGNLQHELVNVGKAGRSRWKGIRPTVRGSVMNPNDHPHGGGEGRAPI GRPSPMSPWGKPTLGKKTRRGKKSSDKLIVRGRK Q2YYP9 50S ribosomal protein L3 Staphylococcus aureus 0.023199545 1 LEVO TKGILGRKIGMTQVFGENGELIPVTVVEAKENVVLQKKTVEVDGYNAIQVGFEDKKAYKKDAKSNKYANKPAEGHAKKAD AAPKRFIREFRNVDVDAYEVGQEVSVDTFVAGDVIDVTGVSKGKGFQGAIKRHGQSRGPMSHGSHFHRAPGSVGMASDAS RVFKGQKMPGRMGGNTVTVQNLEVVQVDTENKVILVKGNVPGPKKGLVEIRTSIK Q2YYP6 50S ribosomal protein L4 Staphylococcus aureus 0.022364504 1 LEVO ANYDVLKLDGTKSGSIELSDAVFGIEPNNSVLFEAINLQRASLRQGTHAVKNRSAVSGGGRKPWKQKGTGRARQGTIRAP QWRGGGIVFGPTPRSYAYKMPKKMRRLALRSALSFKAQENGLTVVDAFNFEAPKTKEFKNVLSTLEQPKKVLVVTENEDV NVELSARNIPGVQVTTAQGLNVLDITNADSLVITEAAAKKVEEVLG Q2YYP7 50S ribosomal protein L5 Staphylococcus aureus 0.017651478999999998 1 LEVO KFNYSSVMEVPKIDKIVVNMGVGDAVQNSKVLDNAVEELELITGQKPLVTKAKKSIATFRLREGMPIGAKVTLRGERMYE FLDKLISVSLPRVRDFQGVSKKAFDGRGNYTLGVKEQLIFPEIDYDKVSKVRGMDIVIVTTANTDEEARELLANFGMP A0A2S6D0C0 50S ribosomal protein L6 Staphylococcus aureus 0.019501153999999996 1 LEVO SRVGKKIIDIPSDVTVTFDGNHVTVKGPKGELSRTLNERMTFKQEENTIEVVRPSDSKEDRTNHGTTRALLNNMVQGVSQ GYVKVLELVGVGYRAQMQGKDLILNVGYSHPVEIKAEENITFSVEKNTVVKVEGISKEQVGALASNIRSVRPPEPYKGKG IRYQGEYVRRKEGKT Q2YYL2 50S ribosomal protein L13 Staphylococcus aureus 0.016359427 1 LEVO MRQTFMANESNIERKWYVIDAEGQTLGRLSSEVASILRGKNKVTYTPHVDTGDYVIVINASKIEFTGNKETDKVYYRHSN HPGGIKSITAGELRRTNPERLIENSIKGMLPSTRLGEKQGKKLFVYGGAEHPHAAQQPENYELRG Q2YYM8 50S ribosomal protein L14 Staphylococcus aureus 0.013157342 1 LEVO MIQQETRLKVADNSGAREVLTIKVLGGSGRKTANIGDVIVCTVKNATPGGVVKKGDVVKAVIVRTKSGVRRNDGSYIKFD ENACVIIRDDKGPRGTRIFGPVARELREGNFMKIVSLAPEVL Q2YYK7 50S ribosomal protein L15 Staphylococcus aureus 0.01562889 1 LEVO MKLHELKPAEGSRKERNRVGRGVATGNGKTSGRGHKGQKARSGGGVRPGFEGGQLPLFRRLPKRGFTNINRKEYAIVNLD QLNKFEDGTEVTPALLVESGVVKNEKSGIKILGNGSLDKKLTVKAHKFSASAAEAIDAKGGAHEVI Q2YYL6 50S ribosomal protein L16 Staphylococcus aureus 0.015599434999999998 1 LEVO MLLPKRVKYRRQHRPKTTGRSKGGNYVTFGEFGLQATTTSWITSRQIESARIAMTRYMKRGGKVWIKIFPHTPYTKKPLE VRMGAGKGAVEGWIAVVKPGRILFEVAGVSEEVAREALRLASHKLPVKTKFVKREEL Q2YYQ3 50S ribosomal protein L17 Staphylococcus aureus 0.013583522999999998 1 LEVO YRKLGRTSDQRKAMLRDLATSLIISERIETTEARAKEVRSVVEKLITLGKKGDLASRRNAAKTLRNVEILNEDETTQTAL QKLFGEIAERYTERQGGYTRILKQGPRRGDGAESVIIELV Q2YYM3 50S ribosomal protein L18 Staphylococcus aureus 0.013124093 1 LEVO MISKIDKNKVRLKRHARVRTNLSGTAEKPRLNVYRSNKHIYAQIIDDNKGVTLAQASSKDSDIATTATKVELATKVGEAI AKKAADKGIKEIVFDRGGYLYHGRVKALAEAARESGLEF W8TRE0 50S ribosomal protein L19 Staphylococcus aureus 0.013392771 1 LEVO MTNHKLIEAVTKSQLRTDLPSFRPGDTLRVHVRIIEGTRERIQVFEGVVIKRRGGGVSETFTVRKISSGVGVERTFPLHT PKIEKIEVKRRGKVRRAKLYYLRSLRGKAARIQEIR Q2YXM4 50S ribosomal protein L20 Staphylococcus aureus 0.013459918999999999 1 LEVO PRVKGGTVTRARRKKTIKLAKGYFGSKHTLYKVAKQQVMKSGQYAFRDRRQRKRDFRKLWITRINAAARQHEMSYSRLMN GLKKAGIDINRKMLSEIAISDEKAFAQLVTKAKDAL Q2YTB1 50S ribosomal protein L21 Staphylococcus aureus 0.011354081 1 LEVO MFAIIETGGKQIKVEEGQEIFVEKLDVNEGDTFTFDKVLFVGGDSVKVGAPTVEGATVTATVNKQGRGKKITVFTYKRRK NSKRKKGHRQPYTKLTIDKINA Q2YT83 50S ribosomal protein L22 Staphylococcus aureus 0.012328358 1 LEVO MEAKAVARTIRIAPRKVRLVLDLIRGKNAAEAIAILKLTNKASSPVIEKVLMSALANAEHNYDMNTDELVVKEAYANEGP TLKRFRPRAQGRASAINKRTSHITIVVSDGKE Q2YYQ1 50S ribosomal protein L23 Staphylococcus aureus 0.0103801 1 LEVO EARDILKRPVITEKSSEAMAEDKYTFDVDTRVNKTQVKMAVEEIFNVKVASVNIMNYKPKKKRMGRYQGYTNKRRKAIVT LKEGSIDLF Q2YYP8 50S ribosomal protein L24 Staphylococcus aureus 0.011316205 1 LEVO HIKKGDNVKVIAGKDKGKEGKVIATLPKKDRVVVEGVNIMKKHQKPTQLNPEGGILETEAAIHVSNVQLLDPKTNEPTRV GYKFVDGKKVRIAKKSGEEIKSN Q2YYK8 50S ribosomal protein L25 Staphylococcus aureus 0.0104622 1 LEVO ASLKSIIRQGKQTRSDLKQLRKSGKVPAVVYGYGTKNVSVKVDEVEFIKVIREVGRNGVIELGVGSKTIKVMVADYQFDP LKNQITHIDFLAIN A0A133Q8Z9 50S ribosomal protein L27 Staphylococcus aureus 0.008595687999999999 1 LEVO VSSTKNGRDSESKRLGAKRADGQFVTGGSILYRQRGTKIYPGENVGRGGDDTLFAKIDGVVKFERKGRDKKQVSVYAVA Q2YT85 50S ribosomal protein L28 Staphylococcus aureus 0.005499431999999999 1 LEVO ASTGNRRSHALNSTKRRWNANLQKVRILVDGKPKKVWVSARALKSGKVT Q2YXJ2 50S ribosomal protein L29 Staphylococcus aureus 0.007845942 1 LEVO KAKEIRDLTTSEIEEQIKSSKEELFNLRFQLATGQLEETARIRTVRKTIARLKTVAREREIEQSKAN Q2YYN0 50S ribosomal protein L30 Staphylococcus aureus 0.006434487 1 LEVO AKLQITLTRSVIGRPETQRKTVEALGLKKTNSSVVVEDNPAIRGQINKVKHLVTVEEK Q2YYL5 50S ribosomal protein L32 Staphylococcus aureus 0.005569564999999999 1 LEVO AVPKRRTSKTRKNKRRTHFKISVPGMTECPNCGEYKLSHRVCKNCGSY A0A1Q8DAT0 50S ribosomal protein L33 Staphylococcus aureus 0.0056845609999999994 1 LEVO RVNVTLACTECGDRNYITTKNKRNNPERIEMKKYCPRLNKYTLHRET A0A077V2P0 50S ribosomal protein L34 Staphylococcus aureus 0.005252369 1 LEVO VKRTYQPNKRKHSKVHGFRKRMSTKNGRKVLARRRRKGRKVLS Q2YZB6 50S ribosomal protein L35 Staphylococcus aureus 0.007461992 1 LEVO PKMKTHRGAAKRVKRTASGQLKRSRAFTSHLFANKSTKQKRQLRKARLVSKSDMKRVKQLLAYK Q2YTB0 50S ribosomal protein L36 Staphylococcus aureus 0.004318422 1 LEVO MKVRPSVKPICEKCKVIKRKGKVMVICENPKHKQRQG A0A077UGV8 MAGNESIUM ION 2.4305e-05 237 MG singleParticle particle 1 7.6 ETHANE FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 GATAN K2 SUMMIT (4k x 4k) 40.0 1 NONE 2.65 FSC 0.143 CUT-OFF 211046 OTHER OTHER emd_0243.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 328 328 328 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0.8579999 0.8579999 0.8579999 AUTHOR ::::EMDATABANK.org::::EMD-0243::::