9RJA
Manikomycin bound to the escherichia coli 70s ribosome
PDB DOI: 10.2210/pdb9rja/pdb
Classification: ANTIBIOTIC Organism(s): Escherichia Coli Bw25113 , Streptomyces Rimosus
Deposited: 2025-06-12 Deposition Author(s): Berger, M.J. , Chen, X. , Guitor, A.K. , Jangra, M. , Kaur, M. , Koteva, K. , Mankin, A.S. , Morici, M. , Safdari, H.A. , Travin, D. , Vazquez-Laslop, N. , Wilson, D.N. , Wright, G. , Xu, M.
Experimental Data Snapshot
Method: ELECTRON MICROSCOPY Resolution: 2.45 Å
Manikomycin bound to the escherichia coli 70s ribosome
Berger, M.J. , Chen, X. , Guitor, A.K. , Jangra, M. , Kaur, M. , Koteva, K. , Mankin, A.S. , Morici, M. , Safdari, H.A. , Travin, D. , Vazquez-Laslop, N. , Wilson, D.N. , Wright, G. , Xu, M.
Primary Citation of Related Structures: 9RJA
| Proteins | ||||
|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Sequence |
| Large ribosomal subunit protein bL33 | 0 | 55 | Escherichia Coli Bw25113 , Streptomyces Rimosus | MAKGIREKIKLVSSAGTGHFYTTTKNKRTKPEKLELKKFDPVVRQHVIYKEAKIK |
| 50S ribosomal protein L15 | K | 144 | Escherichia Coli Bw25113 , Streptomyces Rimosus | MRLNTLSPAEGSKKAGKRLGRGIGSGLGKTGGRGHKGQKSRSGGGVRRGFEGGQMPLYRRLPKFGFTSRKAAITAEIRLSDLAKVEGGVVDLNTLKAANIIGIQIEFAKVILAGEVTTPVTVRGLRVTKGARAAIEAAGGKIEE |
| Large ribosomal subunit protein uL16 | L | 136 | Escherichia Coli Bw25113 , Streptomyces Rimosus | MLQPKRTKFRKMHKGRNRGLAQGTDVSFGSFGLKAVGRGRLTARQIEAARRAMTRAVKRQGKIWIRVFPDKPITEKPLAVXXGKGKGNVEYWVALIQPGKVLYEMDGVPEELAREAFKLAAAKLPIKTTFVTKTVM |
| Large ribosomal subunit protein bL17 | M | 127 | Escherichia Coli Bw25113 , Streptomyces Rimosus | MRHRKSGRQLNRNSSHRQAMFRNMAGSLVRHEIIKTTLPKAKELRRVVEPLITLAKTDSVANRRLAFARTRDNEIVAKLFNELGPRFASRAGGYTRILKCGFRAGDNAPMAYIELVDRSEKAEAAAE |
| Large ribosomal subunit protein uL18 | N | 117 | Escherichia Coli Bw25113 , Streptomyces Rimosus | MDKKSARIRRATRARRKLQELGATRLVVHRTPRHIYAQVIAPNGSEVLVAASTVEKAIAEQLKYTGNKDAAAAVGKAVAERALEKGIKDVSFDRSGFQYHGRVQALADAAREAGLQF |
| Large ribosomal subunit protein bL19 | O | 115 | Escherichia Coli Bw25113 , Streptomyces Rimosus | MSNIIKQLEQEQMKQDVPSFRPGDTVEVKVWVVEGSKKRLQAFEGVVIAIRNRGLHSAFTVRKISNGEGVERVFQTHSPVVDSISVKRRGAVRKAKLYYLRERTGKAARIKERLN |
| Large ribosomal subunit protein bL20 | P | 118 | Escherichia Coli Bw25113 , Streptomyces Rimosus | MARVKRGVIARARHKKILKQAKGYYGARSRVYRVAFQAVIKAGQYAYRDRRQRKRQFRQLWIARINAAARQNGISYSKFINGLKKASVEIDRKILADIAVFDKVAFTALVEKAKAALA |
| Large ribosomal subunit protein bL21 | Q | 103 | Escherichia Coli Bw25113 , Streptomyces Rimosus | MYAVFQSGGKQHRVSEGQTVRLEKLDIATGETVEFAEVLMIANGEEVKIGVPFVDGGVIKAEVVAHGRGEKVKIVKFRRRKHYRKQQGHRQWFTDVKITGISA |
| Large ribosomal subunit protein uL22 | R | 110 | Escherichia Coli Bw25113 , Streptomyces Rimosus | METIAKHRHARSSAQKVRLVADLIRGKKVSQALDILTYTNKKAAVLVKKVLESAIANAEHNDGADIDDLKVTKIFVDEGPSMKRIMPRAKGRADRILKRTSHITVVVSDR |
| Large ribosomal subunit protein uL29 | X | 63 | Escherichia Coli Bw25113 , Streptomyces Rimosus | MKAKELREKSVEELNTELLNLLREQFNLRMQAASGQLQQSHLLKQVRRDVARVKTLLNEKAGA |
| Small ribosomal subunit protein uS3 | C | 233 | Escherichia Coli Bw25113 , Streptomyces Rimosus | MGQKVHPNGIRLGIVKPWNSTWFANTKEFADNLDSDFKVRQYLTKELAKASVSRIVIERPAKSIRVTIHTARPGIVIGKKGEDVEKLRKVVADIAGVPAQINIAEVRKPELDAKLVADSITSQLERRVMFRRAMKRAVQNAMRLGAKGIKVEVSGRLGGAEIARTEWYREGRVPLHTLRADIDYNTSEAHTTYGVIGVKVWIFKGEILGGMAAVEQPEKPAAQPKKQQRKGRK |
| Large ribosomal subunit protein bL34 | 1 | 46 | Escherichia Coli Bw25113 , Streptomyces Rimosus | MKRTFQPSVLKRNRSHGFRARMATKNGRQVLARRRAKGRARLTVSK |
| Small ribosomal subunit protein uS4 | D | 206 | Escherichia Coli Bw25113 , Streptomyces Rimosus | MARYLGPKLKLSRREGTDLFLKSGVRAIDTKCKIEQAPGQHGARKPRLSDYGVQLREKQKVRRIYGVLERQFRNYYKEAARLKGNTGENLLALLEGRLDNVVYRMGFGATRAEARQLVSHKAIMVNGRVVNIASYQVSPNDVVSIREKAKKQSRVKAALELAEQREKPTWLEVDAGKMEGTFKRKPERSDLSADINEHLIVELYSK |
| 30S ribosomal protein S6, fully modified isoform | F | 135 | Escherichia Coli Bw25113 , Streptomyces Rimosus | MRHYEIVFMVHPDQSEQVPGMIERYTAAITGAEGKIHRLEDWGRRQLAYPINKLHKAHYVLMNVEAPQEVIDELETTFRFNDAVIRSMVMRTKHAVTEASPMVKAKDERRERRDDFANETADDAEAGDSEEEEEE |
| Small ribosomal subunit protein uS8 | H | 130 | Escherichia Coli Bw25113 , Streptomyces Rimosus | MSMQDPIADMLTRIRNGQAANKAAVTMPSSKLKVAIANVLKEEGFIEDFKVEGDTKPELELTLKYFQGKAVVESIQRVSRPGLRIYKRKDELPKVMAGLGIAVVSTSKGVMTDRAARQAGLGGEIICYVA |
| Small ribosomal subunit protein uS9 | I | 130 | Escherichia Coli Bw25113 , Streptomyces Rimosus | MAENQYYGTGRRKSSAARVFIKPGNGKIVINQRSLEQYFGRETARMVVRQPLELVDMVEKLDLYITVKGGGISGQAGAIRHGITRALMEYDESLRSELRKAGFVTRDARQVERKKVGLRKARRRPQFSKR |
| Small ribosomal subunit protein uS10 | J | 103 | Escherichia Coli Bw25113 , Streptomyces Rimosus | MQNQRIRIRLKAFDHRLIDQATAEIVETAKRTGAQVRGPIPLPTRKERFTVLISPHVNKDARDQYEIRTHLRLVDIVEPTEKTVDALMRLDLAAGVDVQISLG |
| Large ribosomal subunit protein bL35 | 2 | 65 | Escherichia Coli Bw25113 , Streptomyces Rimosus | MPKIKTVRGAAKRFKKTGKGGFKHKHANLRHILTKKATKRKRHLRPKAMVSKGDLGLVIACLPYA |
| Small ribosomal subunit protein bS21 | U | 71 | Escherichia Coli Bw25113 , Streptomyces Rimosus | MPVIKVRENEPFDVALRRFKRSCEKAGVLAEVRRREFYEKPTTERKRAKASAVKRHAKKLARENARRTRLY |
| Manikomycin | V | 9 | Escherichia Coli Bw25113 , Streptomyces Rimosus | RXFTNRRTH |
| Manikomycin | W | 9 | Escherichia Coli Bw25113 , Streptomyces Rimosus | RXFTNRRTH |
| Large ribosomal subunit protein bL31A | 4 | 70 | Escherichia Coli Bw25113 , Streptomyces Rimosus | MKKDIHPKYEEITASCSCGNVMKIRSTVGHDLNLDVCSKCHPFFTGKQRDVATGGRVDRFNKRFNIPGSK |
| Large ribosomal subunit protein bL36A | 3 | 38 | Escherichia Coli Bw25113 , Streptomyces Rimosus | MKVRASVKKLCRNCKIVKRDGVIRVICSAEPKHKQRQG |
| 30S ribosomal protein S2 | B | 241 | Escherichia Coli Bw25113 , Streptomyces Rimosus | MATVSMRDMLKAGVHFGHQTRYWNPKMKPFIFGARNKVHIINLEKTVPMFNEALAELNKIASRKGKILFVGTKRAASEAVKDAALSCDQFFVNHRWLGGMLTNWKTVRQSIKRLKDLETQSQDGTFDKLTKKEALMRTRELEKLENSLGGIKDMGGLPDALFVIDADHEHIAIKEANNLGIPVFAIVDTNSDPDGVDFVIPGNDDAIRAVTLYLGAVAATVREGRSQDLASQAEESFVEAE |
| Large ribosomal subunit protein uL6 | G | 177 | Escherichia Coli Bw25113 , Streptomyces Rimosus | MSRVAKAPVVVPAGVDVKINGQVITIKGKNGELTRTLNDAVEVKHADNTLTFGPRDGYADGWAQAGTARALLNSMVIGVTEGFTKKLQLVGVGYRAAVKGNVINLSLGFSHPVDHQLPAGITAECPTQTEIVLKGADKQVIGQVAADLRAYRRPEPYKGKGVRYADEVVRTKEAKKK |
| Large ribosomal subunit protein uL23 | S | 100 | Escherichia Coli Bw25113 , Streptomyces Rimosus | MIREERLLKVLRAPHVSEKASTAMEKSNTIVLKVAKDATKAEIKAAVQKLFEVEVEVVNTLVVKGKVKRHGQRIGRRSDWKKAYVTLKEGQNLDFVGGAE |
| Large ribosomal subunit protein uL24 | T | 104 | Escherichia Coli Bw25113 , Streptomyces Rimosus | MAAKIRRDDEVIVLTGKDKGKRGKVKNVLSSGKVIVEGINLVKKHQKPVPALNQPGGIVEKEAAIQVSNVAIFNAATGKADRVGFRFEDGKKVRFFKSNSETIK |
| Small ribosomal subunit protein uS5 | E | 167 | Escherichia Coli Bw25113 , Streptomyces Rimosus | MAHIEKQAGELQEKLIAVNRVSKTVKGGRIFSFTALTVVGDGNGRVGFGYGKAREVPAAIQKAMEKARRNMINVALNNGTLQHPVKGVHTGSRVFMQPASEGTGIIAGGAMRAVLEVAGVHNVLAKAYGSTNPINVVRATIDGLENMNSPEMVAAKRGKSVEEILGK |
| Nucleic Acids / Hybrid | ||||
|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Sequence |
| A-site Phe-tRNA | y | 76 | NA | GCCCGGAUAGCUCAGUAGGUAGAGCAGGGGAUUGAAAAUCCCCGUGUCCUUGGUUCGAUUCCGAGUCCGCGCACCA |
| P-Site Val-tRNA | z | 76 | NA | GGGUGAUUAGCUCAGCUGGGAGAGCACCUCCCUUACAAGGAGGGGGUCGGCGGUUCGAUCCCGUCAUCACCCACCA |
| 16S rRNA | a | 1542 | NA | AAAUUGAAGAGUUUGAUCAUGGCUCAGAUUGAACGCUGGCGGCAGGCCUAACACAUGCAAGUCGAACGGUAACAGGAAGAAGCUUGCUUCUUUGCUGACGAGUGGCGGACGGGUGAGUAAUGUCUGGGAAACUGCCUGAUGGAGGGGGAUAACUACUGGAAACGGUAGCUAAUACCGCAUAACGUCGCAAGACCAAAGAGGGGGACCUUCGGGCCUCUUGCCAUCGGAUGUGCCCAGAUGGGAUUAGCUAGUAGGUGGGGUAACGGCUCACCUAGGCGACGAUCCCUAGCUGGUCUGAGAGGAUGACCAGCCACACUGGAACUGAGACACGGUCCAGACUCCUACGGGAGGCAGCAGUGGGGAAUAUUGCACAAUGGGCGCAAGCCUGAUGCAGCCAUGCCGCGUGUAUGAAGAAGGCCUUCGGGUUGUAAAGUACUUUCAGCGGGGAGGAAGGGAGUAAAGUUAAUACCUUUGCUCAUUGACGUUACCCGCAGAAGAAGCACCGGCUAACUCCGUGCCAGCAGCCGCGGUAAUACGGAGGGUGCAAGCGUUAAUCGGAAUUACUGGGCGUAAAGCGCACGCAGGCGGUUUGUUAAGUCAGAUGUGAAAUCCCCGGGCUCAACCUGGGAACUGCAUCUGAUACUGGCAAGCUUGAGUCUCGUAGAGGGGGGUAGAAUUCCAGGUGUAGCGGUGAAAUGCGUAGAGAUCUGGAGGAAUACCGGUGGCGAAGGCGGCCCCCUGGACGAAGACUGACGCUCAGGUGCGAAAGCGUGGGGAGCAAACAGGAUUAGAUACCCUGGUAGUCCACGCCGUAAACGAUGUCGACUUGGAGGUUGUGCCCUUGAGGCGUGGCUUCCGGAGCUAACGCGUUAAGUCGACCGCCUGGGGAGUACGGCCGCAAGGUUAAAACUCAAAUGAAUUGACGGGGGCCCGCACAAGCGGUGGAGCAUGUGGUUUAAUUCGAUGCAACGCGAAGAACCUUACCUGGUCUUGACAUCCACGGAAGUUUUCAGAGAUGAGAAUGUGCCUUCGGGAACCGUGAGACAGGUGCUGCAUGGCUGUCGUCAGCUCGUGUUGUGAAAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUUAUCCUUUGUUGCCAGCGGUCCGGCCGGGAACUCAAAGGAGACUGCCAGUGAUAAACUGGAGGAAGGUGGGGAUGACGUCAAGUCAUCAUGGCCCUUACGACCAGGGCUACACACGUGCUACAAUGGCGCAUACAAAGAGAAGCGACCUCGCGAGAGCAAGCGGACCUCAUAAAGUGCGUCGUAGUCCGGAUUGGAGUCUGCAACUCGACUCCAUGAAGUCGGAAUCGCUAGUAAUCGUGGAUCAGAAUGCCACGGUGAAUACGUUCCCGGGCCUUGUACACACCGCCCGUCACACCAUGGGAGUGGGUUGCAAAAGAAGUAGGUAGCUUAACCUUCGGGAGGGCGCUUACCACUUUGUGAUUCAUGACUGGGGUGAAGUCGUAACAAGGUAACCGUAGGGGAACCUGCGGUUGGAUCACCUCCUUA |
Experimental Data
Method: ELECTRON MICROSCOPY
Deposited Date: 2025-06-12 Deposition Author(s): Berger, M.J. , Chen, X. , Guitor, A.K. , Jangra, M. , Kaur, M. , Koteva, K. , Mankin, A.S. , Morici, M. , Safdari, H.A. , Travin, D. , Vazquez-Laslop, N. , Wilson, D.N. , Wright, G. , Xu, M.