9QEH
Cryo-em structure of the a2085-methylated 50s ribosome of a mlsb resistant s. aureus strain ""mny196"" in complex with solithromycin
PDB DOI: 10.2210/pdb9qeh/pdb
Classification: RIBOSOME Organism(s): Staphylococcus Aureus Subsp. Aureus Usa300
Deposited: 2025-03-10 Deposition Author(s): Rivalta, A. , Yonath, A.
Experimental Data Snapshot
Method: ELECTRON MICROSCOPY Resolution: 2.08 Å
Cryo-em structure of the a2085-methylated 50s ribosome of a mlsb resistant s. aureus strain ""mny196"" in complex with solithromycin
Primary Citation of Related Structures: 9QEH
| Proteins | ||||
|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Sequence |
| Large ribosomal subunit protein bL33A | 1 | 52 | Staphylococcus Aureus Subsp. Aureus Usa300 | MFNVRVNVTLACTECGDRNYITTKNKRNNPERIEMKKYCPRLNKYTLHRETK |
| Large ribosomal subunit protein uL4 | E | 207 | Staphylococcus Aureus Subsp. Aureus Usa300 | MANYDVLKLDGTKSGSIELSDAVFGIEPNNSVLFEAINLQRASLRQGTHAVKNRSAVSGGGRKPWKQKGTGRARQGTIRAPQWRGGGIVFGPTPRSYAYKMPKKMRRLALRSALSFKAQENGLTVVDAFNFEAPKTKEFKNVLSTLEQPKKVLVVTENEDVNVELSARNIPGVQVTTAQGLNVLDITNADSLVITEAAAKKVEEVLG |
| Large ribosomal subunit protein uL5 | F | 179 | Staphylococcus Aureus Subsp. Aureus Usa300 | MNRLKEKFNTEVTENLMKKFNYSSVMEVPKIDKIVVNMGVGDAVQNSKVLDNAVEELELITGQKPLVTKAKKSIATFRLREGMPIGAKVTLRGERMYEFLDKLISVSLPRVRDFQGVSKKAFDGRGNYTLGVKEQLIFPEIDYDKVSKVRGMDIVIVTTANTDEEARELLANFGMPFRK |
| Large ribosomal subunit protein uL6 | G | 178 | Staphylococcus Aureus Subsp. Aureus Usa300 | MSRVGKKIIDIPSDVTVTFDGNHVTVKGPKGELSRTLNERMTFKQEENTIEVVRPSDSKEDRTNHGTTRALLNNMVQGVSQGYVKVLELVGVGYRAQMQGKDLILNVGYSHPVEIKAEENITFSVEKNTVVKVEGISKEQVGALASNIRSVRPPEPYKGKGIRYQGEYVRRKEGKTGK |
| Large ribosomal subunit protein uL13 | H | 145 | Staphylococcus Aureus Subsp. Aureus Usa300 | MRQTFMANESNIERKWYVIDAEGQTLGRLSSEVASILRGKNKVTYTPHVDTGDYVIVINASKIEFTGNKETDKVYYRHSNHPGGIKSITAGELRRTNPERLIENSIKGMLPSTRLGEKQGKKLFVYGGAEHPHAAQQPENYELRG |
| Large ribosomal subunit protein uL14 | I | 122 | Staphylococcus Aureus Subsp. Aureus Usa300 | MIQQETRLKVADNSGAREVLTIKVLGGSGRKTANIGDVIVCTVKNATPGGVVKKGDVVKAVIVRTKSGVRRNDGSYIKFDENACVIIRDDKGPRGTRIFGPVARELREGNFMKIVSLAPEVL |
| Large ribosomal subunit protein uL15 | J | 146 | Staphylococcus Aureus Subsp. Aureus Usa300 | MKLHELKPAEGSRKERNRVGRGVATGNGKTSGRGHKGQKARSGGGVRPGFEGGQLPLFRRLPKRGFTNINRKEYAIVNLDQLNKFEDGTEVTPALLVESGVVKNEKSGIKILGNGSLDKKLTVKAHKFSASAAEAIDAKGGAHEVI |
| Large ribosomal subunit protein uL16 | K | 144 | Staphylococcus Aureus Subsp. Aureus Usa300 | MLLPKRVKYRRQHRPKTTGRSKGGNYVTFGEFGLQATTTSWITSRQIESARIAMTRYMKRGGKVWIKIFPHTPYTKKPLEVRMGAGKGAVEGWIAVVKPGRILFEVAGVSEEVAREALRLASHKLPVKTKFVKREELGGETNES |
| Large ribosomal subunit protein uL18 | M | 119 | Staphylococcus Aureus Subsp. Aureus Usa300 | MISKIDKNKVRLKRHARVRTNLSGTAEKPRLNVYRSNKHIYAQIIDDNKGVTLAQASSKDSDIATTATKVELATKVGEAIAKKAADKGIKEIVFDRGGYLYHGRVKALAEAARESGLEF |
| Large ribosomal subunit protein bL19 | N | 116 | Staphylococcus Aureus Subsp. Aureus Usa300 | MTNHKLIEAVTKSQLRTDLPSFRPGDTLRVHVRIIEGTRERIQVFEGVVIKRRGGGVSETFTVRKISSGVGVERTFPLHTPKIEKIEVKRRGKVRRAKLYYLRSLRGKAARIQEIR |
| Large ribosomal subunit protein bL20 | O | 118 | Staphylococcus Aureus Subsp. Aureus Usa300 | MPRVKGGTVTRARRKKTIKLAKGYFGSKHTLYKVAKQQVMKSGQYAFRDRRQRKRDFRKLWITRINAAARQHEMSYSRLMNGLKKAGIDINRKMLSEIAISDEKAFAQLVTKAKDALK |
| Large ribosomal subunit protein bL34 | 2 | 45 | Staphylococcus Aureus Subsp. Aureus Usa300 | MVKRTYQPNKRKHSKVHGFRKRMSTKNGRKVLARRRRKGRKVLSA |
| Large ribosomal subunit protein bL21 | P | 102 | Staphylococcus Aureus Subsp. Aureus Usa300 | MFAIIETGGKQIKVEEGQEIFVEKLDVNEGDTFTFDKVLFVGGDSVKVGAPTVEGATVTATVNKQGRGKKITVFTYKRRKNSKRKKGHRQPYTKLTIDKINA |
| Large ribosomal subunit protein uL22 | Q | 117 | Staphylococcus Aureus Subsp. Aureus Usa300 | MEAKAVARTIRIAPRKVRLVLDLIRGKNAAEAIAILKLTNKASSPVIEKVLMSALANAEHNYDMNTDELVVKEAYANEGPTLKRFRPRAQGRASAINKRTSHITIVVSDGKEEAKEA |
| Large ribosomal subunit protein uL23 | R | 91 | Staphylococcus Aureus Subsp. Aureus Usa300 | MEARDILKRPVITEKSSEAMAEDKYTFDVDTRVNKTQVKMAVEEIFNVKVASVNIMNYKPKKKRMGRYQGYTNKRRKAIVTLKEGSIDLFN |
| Large ribosomal subunit protein uL24 | S | 105 | Staphylococcus Aureus Subsp. Aureus Usa300 | MHIKKGDNVKVIAGKDKGKEGKVIATLPKKDRVVVEGVNIMKKHQKPTQLNPEGGILETEAAIHVSNVQLLDPKTNEPTRVGYKFVDGKKVRIAKKSGEEIKSNN |
| 50S ribosomal protein L25 | T | 217 | Staphylococcus Aureus Subsp. Aureus Usa300 | MASLKSIIRQGKQTRSDLKQLRKSGKVPAVVYGYGTKNVSVKVDEVEFIKVIREVGRNGVIELGVGSKTIKVMVADYQFDPLKNQITHIDFLAINMSEERTVEVPVQLVGEAVGAKEGGVVEQPLFNLEVTATPDNIPEAIEVDITELNINDSLTVADVKVTGDFKIENDSAESVVTVVAPTEEPTEEEIEAMEGEQQTEEPEVVGESKEDEEKTEE |
| Large ribosomal subunit protein bL27 | U | 94 | Staphylococcus Aureus Subsp. Aureus Usa300 | MLKLNLQFFASKKGVSSTKNGRDSESKRLGAKRADGQFVTGGSILYRQRGTKIYPGENVGRGGDDTLFAKIDGVVKFERKGRDKKQVSVYAVAE |
| Large ribosomal subunit protein bL28 | V | 62 | Staphylococcus Aureus Subsp. Aureus Usa300 | MGKQCFVTGRKASTGNRRSHALNSTKRRWNANLQKVRILVDGKPKKVWVSARALKSGKVTRV |
| Large ribosomal subunit protein uL29 | W | 73 | Staphylococcus Aureus Subsp. Aureus Usa300 | MVKQMKAKEIRDLTTSEIEEQIKSSKEELFNLRFQLATGQLEETARIRTVRKTIARLKTVAREREIEQSKANQ |
| Large ribosomal subunit protein uL30 | X | 59 | Staphylococcus Aureus Subsp. Aureus Usa300 | MAKLQITLTRSVIGRPETQRKTVEALGLKKTNSSVVVEDNPAIRGQINKVKHLVTVEEK |
| Large ribosomal subunit protein bL32 | Z | 57 | Staphylococcus Aureus Subsp. Aureus Usa300 | MAVPKRRTSKTRKNKRRTHFKISVPGMTECPNCGEYKLSHRVCKNCGSYNGEEVAAK |
| Large ribosomal subunit protein bL35 | 3 | 66 | Staphylococcus Aureus Subsp. Aureus Usa300 | MPKMKTHRGAAKRVKRTASGQLKRSRAFTSHLFANKSTKQKRQLRKARLVSKSDMKRVKQLLAYKK |
| Large ribosomal subunit protein bL36 | 4 | 37 | Staphylococcus Aureus Subsp. Aureus Usa300 | MKVRPSVKPICEKCKVIKRKGKVMVICENPKHKQRQG |
| Large ribosomal subunit protein bL17 | L | 122 | Staphylococcus Aureus Subsp. Aureus Usa300 | MGYRKLGRTSDQRKAMLRDLATSLIISERIETTEARAKEVRSVVEKLITLGKKGDLASRRNAAKTLRNVEILNEDETTQTALQKLFGEIAERYTERQGGYTRILKQGPRRGDGAESVIIELV |
| Large ribosomal subunit protein uL2 | C | 277 | Staphylococcus Aureus Subsp. Aureus Usa300 | MAIKKYKPITNGRRNMTSLDFAEITKTTPEKSLLKPLPKKAGRNNQGKLTVRHHGGGHKRQYRVIDFKRNKDGINAKVDSIQYDPNRSANIALVVYADGEKRYIIAPKGLEVGQIVESGAEADIKVGNALPLQNIPVGTVVHNIELKPGKGGQIARSAGASAQVLGKEGKYVLIRLRSGEVRMILSTCRATIGQVGNLQHELVNVGKAGRSRWKGIRPTVRGSVMNPNDHPHGGGEGRAPIGRPSPMSPWGKPTLGKKTRRGKKSSDKLIVRGRKKK |
| Large ribosomal subunit protein uL3 | D | 220 | Staphylococcus Aureus Subsp. Aureus Usa300 | MTKGILGRKIGMTQVFGENGELIPVTVVEAKENVVLQKKTVEVDGYNAIQVGFEDKKAYKKDAKSNKYANKPAEGHAKKADAAPKRFIREFRNVDVDAYEVGQEVSVDTFVAGDVIDVTGVSKGKGFQGAIKRHGQSRGPMSHGSHFHRAPGSVGMASDASRVFKGQKMPGRMGGNTVTVQNLEVVQVDTENKVILVKGNVPGPKKGLVEIRTSIKKGNK |
| Nucleic Acids / Hybrid | ||||
|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Sequence |
| P_site tRNA | 8 | 71 | NA | CGCGGGAUGGAGCAGGAGCUCGUCGGGCUCAUAGGCCGAAGGCGGUGGUUCAAAUCCGCCUCCCGCAACCA |
| E_site tRNA | 11 | 13 | NA | GGCCGGGCCACCA |
| 23S rRNA | a | 2923 | NA | GAUUAAGUUAUUAAGGGCGCACGGUGGAUGCCUUGGCACUAGAAGCCGAUGAAGGACGUUACUAACGACGAUAUGCUUUGGGGAGCUGUAAGUAAGCUUUGAUCCAGAGAUUUCCGAAUGGGGAAACCCAGCAUGAGUUAUGUCAUGUUAUCGAUAUGUGAAUACAUAGCAUAUCAGAAGGCACACCCGGAGAACUGAAACAUCUUAGUACCCGGAGGAAGAGAAAGAAAAUUCGAUUCCCUUAGUAGCGGCGAGCGAAACGGGAAGAGCCCAAACCAACAAGCUUGCUUGUUGGGGUUGUAGGACACUCUGUACGGAGUUACAAAGGACGACAUUAGACGAAUCAUCUGGAAAGAUGAAUCAAAGAAGGUAAUAAUCCUGUAGUCGAAAAUGUUGUCUCUCUUGAGUGGAUCCUGAGUACGACGGAGCACGUGAAAUUCCGUCGGAAUCUGGGAGGACCAUCUCCUAAGGCUAAAUACUCUCUAGUGACCGAUAGUGAACCAGUACCGUGAGGGAAAGGUGAAAAGCACCCCGGAAGGGGAGUGAAAUAGAACCUGAAACCGUGUGCUUACAAGUAGUCAGAGCCCGUUAAUGGGUGAUGGCGUGCCUUUUGUAGAAUGAACCGGCGAGUUACGAUUUGAUGCAAGGUUAAGCAGUAAAUGUGGAGCCGUAGCGAAAGCGAGUCUGAAUAGGGCGUUUAGUAUUUGGUCGUAGACCCGAAACCAGGUGAUCUACCCUUGGUCAGGUUGAAGUUCAGGUAACACUGAAUGGAGGACCGAACCGACUUACGUUGAAAAGUGAGCGGAUGAACUGAGGGUAGCGGAGAAAUUCCAAUCGAACCUGGAGAUAGCUGGUUCUCUCCGAAAUAGCUUUAGGGCUAGCCUCAAGUGAUGAUUAUUGGAGGUAGAGCACUGUUUGGACGAGGGGCCCCUCUCGGGUUACCGAAUUCAGACAAACUCCGAAUGCCAAUUAAUUUAACUUGGGAGUCAGAACAUGGGUGAUAAGGUCCGUGUUCGAAAGGGAAACAGCCCAGACCACCAGCUAAGGUCCCAAAAUAUAUGUUAAGUGGAAAAGGAUGUGGCGUUGCCCAGACAACUAGGAUGUUGGCUUAGAAGCAGCCAUCAUUUAAAGAGUGCGUAAUAGCUCACUAGUCGAGUGACACUGCGCCGAAAAUGUACCGGGGCUAAACAUAUUACCGAAGCUGUGGAUUGUCCUUUGGACAAUGGUAGGAGAGCGUUCUAAGGGCGUUGAAGCAUGAUCGUAAGGACAUGUGGAGCGCUUAGAAGUGAGAAUGCCGGUGUGAGUAGCGAAAGACGGGUGAGAAUCCCGUCCACCGAUUGACUAAGGUUUCCAGAGGAAGGCUCGUCCGCUCUGGGUUAGUCGGGUCCUAAGCUGAGGCCGACAGGCGUAGGCGAUGGAUAACAGGUUGAUAUUCCUGUACCACCUAUAAUCGUUUUAAUCGAUGGGGGGACGCAGUAGGAUAGGCGAAGCGUGCGAUUGGAUUGCACGUCUAAGCAGUAAGGCUGAGUAUUAGGCAAAUCCGGUACUCGUUAAGGCUGAGCUGUGAUGGGGAGAAGACAUUGAGUCUUCGAGUCGUUGAUUUCACACUGCCGAGAAAAGCCUCUAGAUAGAAAAUAGGUGCCCGUACCGCAAACCGACACAGGUAGUCAAGAUGAGAAUUCUAAGGUGAGCGAGCGAACUCUCGUUAAGGAACUCGGCAAAAUGACCCCGUAACUUCGGGAGAAGGGGUGCUCUUUAGGGUUAACGCCCAGAAGAGCCGCAGUGAAUAGGCCCAAGCGACUGUUUAUCAAAAACACAGGUCUCUGCUAAACCGUAAGGUGAUGUAUAGGGGCUGACGCCUGCCCGGUGCUGGAAGGUUAAGAGGAGUGGUUAGCUUCUGCGAAGCUACGAAUCGAAGCCCCAGUAAACGGCGGCCGUAACUAUAACGGUCCUAAGGUAGCGAAAUUCCUUGUCGGGUAAGUUCCGACCCGCACGAAAGGCGUAACGAUUUGGGCACUGUCUCAACGAGAGACUCGGUGAAAUCAUAGUACCUGUGAAGAUGCAGGUUACCCGCGACAGGACGGAAAGACCCCGUGGAGCUUUACUGUAGCCUGAUAUUGAAAUUCGGCACAGCUUGUACAGGAUAGGUAGGAGCCUUUGAAACGUGAGCGCUAGCUUACGUGGAGGCGCUGGUGGGAUACUACCCUAGCUGUGUUGGCUUUCUAACCCGCACCACUUAUCGUGGUGGGAGACAGUGUCAGGCGGGCAGUUUGACUGGGGCGGUCGCCUCCUAAAAGGUAACGGAGGCGCUCAAAGGUUCCCUCAGAAUGGUUGGAAAUCAUUCAUAGAGUGUAAAGGCAUAAGGGAGCUUGACUGCGAGACCUACAAGUCGAGCAGGGUCGAAAGACGGACUUAGUGAUCCGGUGGUUCCGCAUGGAAGGGCCAUCGCUCAACGGAUAAAAGCUACCCCGGGGAUAACAGGCUUAUCUCCCCCAAGAGUUCACAUCGACGGGGAGGUUUGGCACCUCGAUGUCGGCUCAUCGCAUCCUGGGGCUGUAGUCGGUCCCAAGGGUUGGGCUGUUCGCCCAUUAAAGCGGUACGCGAGCUGGGUUCAGAACGUCGUGAGACAGUUCGGUCCCUAUCCGUCGUGGGCGUAGGAAAUUUGAGAGGAGCUGUCCUUAGUACGAGAGGACCGGGAUGGACAUACCUCUGGUGUACCAGUUGUCGUGCCAACGGCAUAGCUGGGUAGCUAUGUGUGGACGGGAUAAGUGCUGAAAGCAUCUAAGCAUGAAGCCCCCCUCAAGAUGAGAUUUCCCAACUUCGGUUAUAAGAUCCCUCAAAGAUGAUGAGGUUAAUAGGUUCGAGGUGGAAGCAUGGUGACAUGUGGAGCUGACGAAUACUAAUCGAUCGAAGACUUAAUCAA |
| 5S rRNA | b | 115 | NA | UCUGGUGACUAUAGCAAGGAGGUCACACCUGUUCCCAUGCCGAACACAGAAGUUAAGCUCCUUAGCGUCGAUGGUAGUCGAACUUACGUUCCGCUAGAGUAGAACGUUGCCAGGC |
Experimental Data
Method: ELECTRON MICROSCOPY
Deposited Date: 2025-03-10 Deposition Author(s): Rivalta, A. , Yonath, A.