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9I5T
50s subunit of p. gingivalis ribosome with lefamulin
PDB DOI: 10.2210/pdb9i5t/pdb
Classification: RIBOSOME Organism(s): Cellvibrio Japonicus (Strain Ueda107)
Deposited: 2025-01-28 Deposition Author(s): Bashan, A. , Hiregange, D.G. , Yonath, A.
Experimental Data Snapshot
Method: ELECTRON MICROSCOPY Resolution: 2.6 Å
50s subunit of p. gingivalis ribosome with lefamulin
Bashan, A. , Hiregange, D.G. , Yonath, A.
Primary Citation of Related Structures: 9I5T
| Proteins | ||||
|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Sequence |
| Large ribosomal subunit protein bL28 | 0 | 79 | Cellvibrio Japonicus (Strain Ueda107) | MSKICQITGKKAMVGNNVSHSKRRTKRVFDVNLFRKKFYWVEQDCWVVLRISAAGLRLINKIGLDAAIKRAAEKGFLNA |
| Large ribosomal subunit protein uL2 | D | 274 | Cellvibrio Japonicus (Strain Ueda107) | MGIRKLKPTTPGQRHKVIGAFDKITASTPEKSLVVGKKKTGGRNNTGKMTMRYIGGGHKQKYRFIDFKRTKDGIPATVKTIEYDPNRSSRIALLYYADGAKAYIIAPDGLEVGHTVMSGSEAAPEVGNALPLANIPVGTIIHNIELRPGQGAKMVRSAGSFAQLTSREGTYVVIKMPSGEVRRILSTCKATIGSVGNSDHALEKSGKAGRSRWLGRRPHNRGVVMNPVDHPMGGGEGRQSGGHPRSRKGLYAKGLKTRAPKKHSSKYIIERRKK |
| Large ribosomal subunit protein uL3 | E | 205 | Cellvibrio Japonicus (Strain Ueda107) | MPGLLGKKIGMTSVFSAEGKNLPCTVIEVGPCVVTQVKTLEKDGYSALQLGFVDAKEKHTTKPLAGHFKKANVAPKRHLAEFKNFEGEHKLGDVLNVEFFSDADFVDVVGTSKGKGFQGVVKRHGFGGVGQATHGQHNRLRAPGAVGACSYPAKVFKGTRMAGQMGNERVTVQNLEVIKVMPEHNLLLVKGSVPGAKGSILLIEK |
| Large ribosomal subunit protein uL4 | F | 209 | Cellvibrio Japonicus (Strain Ueda107) | MELSVYNIKGEDTGKKVVLDDSIFAIEPNDHAIYLDVKQYMANQRQGTHKAKERSELSGSTRKLIRQKGSGGARRGDINSPLLSGGARVFGPRPRNYSFKLNKKLKALARRSALSYKAKNNEIIVVEDFNFDAPKTKAFKAISAALKVGEKKVLYVLPEVNKNVYLSARNLPNTNLILANLINTYTVLASKNLVLTERSVAVVNELFKA |
| Large ribosomal subunit protein uL13 | M | 151 | Cellvibrio Japonicus (Strain Ueda107) | MDTLSFKTISANKATVTKEWVIVDAEGQTLGRMCAKVAKLLRGKYKPNFTPHVDCGDNVIVINADKIVLSGNKWDGRIYLRHTGYPGGQRQFTPRDFMNKGPEYLFRKVVKGMLPKNRLGAKIIGNLYVYAGTEHKHEAQQPRQLDINSLK |
| Large ribosomal subunit protein uL15 | O | 148 | Cellvibrio Japonicus (Strain Ueda107) | MNLSSLKPAEGAVKSRKRIGRGPGSGLGGTSTRGHKGAKSRSGYSKKIGFEGGQMPIQRRLPKFGFKNINRVEYKPINLSVLQTLSEANSLTKISVEDLIAAGLVSRNSLVKILANGTVTTALTVEAHAFSKTAEEAIVRAGGSVVKL |
| Large ribosomal subunit protein uL16 | P | 144 | Cellvibrio Japonicus (Strain Ueda107) | MLQPKKTKFRRQQKGRMKGFAQRGNQLSFGSFGIKSLQSKWITGRQIEAARIAVTRYMQRQGQVWVRIFPDKPITKKGEGVRMGKGKGAPEGFVAPITPGRIIFEVEGVPYEIAKEALRLAAQKLPVTTKFVVRHDYDIQNQNA |
| Large ribosomal subunit protein bL17 | Q | 160 | Cellvibrio Japonicus (Strain Ueda107) | MRHNKKFNHLGRKAAHRKAMLSNMAASLILHKRIFTTVAKAKALRIYVEPLLTKTKEDTTHSRRIAFSYLQNKYALKELFGDVAAKIADRPGGYTRILKTGYRLGDNAAMCFIELVDYNENMLGEAAKKATKTRRSRKRKSADVVVEAAPAEETPKAAEE |
| Large ribosomal subunit protein uL18 | R | 114 | Cellvibrio Japonicus (Strain Ueda107) | MVTKEQRRQKIKARVRGKISGTQEKPRLTVFRSNKQIYAQLIDDIAGRTLASASSLKLEMTGSKKEIAAKVGDEIAKAATEAGISTVVFDRNGYLFHGRIKELADAARKGGLKF |
| Large ribosomal subunit protein uL29 | 1 | 64 | Cellvibrio Japonicus (Strain Ueda107) | MKIAEIKELATKELQERLDAEVAAYDQMRINHAVSPLDSPAKLKHQRRMIAQMKTVLRQRELNK |
| Large ribosomal subunit protein bL19 | S | 121 | Cellvibrio Japonicus (Strain Ueda107) | MDFIKIVNEEFKSGKEHPKFNSGDTITVEYRIKEGNKERIQKYRGVVIRISGHGDKKRFTVRKISDGIGVERIFPIESPFIENITVEKYGKVRRAKLYYLRGLTGKKARIKERRVALSSKD |
| Large ribosomal subunit protein bL20 | T | 115 | Cellvibrio Japonicus (Strain Ueda107) | MPRSVNHVASRAKRKRILKLTRGYFGARKNVWTVAKNTWEKGLTYAYRDRKSKKRNFRALWIQRINAAARLEGMSYSRLMGALHANGIEINRKVLADLAMNHPEAFRAIVAKVKN |
| Large ribosomal subunit protein bL21 | U | 105 | Cellvibrio Japonicus (Strain Ueda107) | MYVIVDIQGQQMKVEQGRRLFVHHIKDVESGASVEFDKVLLVDNNGAITVGSPLVEGAKVVCEVLTPLVKGDKVLIFHKKRRKGYRKLNGHRQQFTEILVKEVVA |
| Large ribosomal subunit protein uL22 | V | 134 | Cellvibrio Japonicus (Strain Ueda107) | MGARKHNSAEARKEALKQMYFAKLRNVPTSPRKMRLVADMIRGMEVNRALGVLKFSNKEASARVEKLLRSAVANWEEKNERKAEEGELFVSRICVDGASTLKRLRPAPQGRGYRIRKRSNHVTIYVDTLNNDNN |
| Large ribosomal subunit protein uL23 | W | 97 | Cellvibrio Japonicus (Strain Ueda107) | MGIIIKPIISEKMTAVTEKMSERYGFRVSPNANKIEIKKAVEAMYNVKVEDVNTMRYDGKRKNRYTKSGLIRGKEASFKKAIVTLKKGETIDFFSNI |
| Large ribosomal subunit protein uL24 | X | 106 | Cellvibrio Japonicus (Strain Ueda107) | MSKLHIKKGDTVMVISGEDKGHSGRVLEVLVKEQRAIVEGLNMIKKHAKPSAKNPQGGIISKEAPIHISNLNVVDPKTGKATRIGRRLNENGKLVRYAKKSGEEIK |
| Large ribosomal subunit protein bL25 | Y | 192 | Cellvibrio Japonicus (Strain Ueda107) | MKTFQLTGTPRAEFGKKAAKAIRKEDQIPAVLYGGKGEGVNFIVSQDAVRNLIYSPEIFLVELTVEGSGSYKAILKEIQFHPVTDRIIHIDFLQVTDEKPVVMEVPVVLTGHAEGVKAGGKLSLEMRKLKVKALYSEIPEKLDIDVSDLQLGKTIQVGELHFEGLTLMNAKNAVVCAVKLTRAARGAAVKKQ |
| Large ribosomal subunit protein bL27 | Z | 85 | Cellvibrio Japonicus (Strain Ueda107) | MAHKKGVGSSKNGRESESKRLGVKVYGGEMAKAGNILVRQRGTVHHPGENVGIGKDHTLYALKSGVVVFTRKKNDRSYVSIKTES |
| Large ribosomal subunit protein bL9 | H | 179 | Cellvibrio Japonicus (Strain Ueda107) | MQVILKEDVVNLGYKDDIVTVKDGYGRNFLIPQGKAVIASESAKKVLAENLRQRAHKIAQIKKEAEEKAASMQGISLTIKAKTSSTGTIFGSVTNIQIAEELAKKGVEVDRKIIVLKPAVKEVGNYTAVVRLHKEVTVEIPFEVVSENETIIEAKPEGAPVPVAEEPAAEAEQAEVAAE |
| DUF4295 domain-containing protein | 15 | 49 | Cellvibrio Japonicus (Strain Ueda107) | MAKKSVATFKKGDGRTYSKVIKMVKSPKTGAYTFQEEMVPNEAVKDFFK |
| Large ribosomal subunit protein uL5 | 11 | 186 | Cellvibrio Japonicus (Strain Ueda107) | MSATANLKKDYQERIVPALMKQFGYTSVMQVPVLKKIVINQGLGMATGDKKIIDVAVSELTAITGQKAVPTVSKKDISNFKLRKKMPIGVMVTLRREQMYEFLERLVRIALPRIRDFKGIESKLDGRGNYTLGINEQIIFPEINIDAITKILGMNITFVTSAQSDEEGYALLKEFGLPFKNAKKQN |
| Large ribosomal subunit protein uL6 | 13 | 183 | Cellvibrio Japonicus (Strain Ueda107) | MSRIGKLPISIPAGVTVSHKDEIVTVKGPKGELSQYVDPRITVVIEGGMIHLERKTDDRIERSLHGLYRSLINNMVQGVSAGFKRELELVGVGYRASNQGQLLELSLGFTHSIFMQLPKEVTVETKSERNKNPLIILESADKQLLGQVCMKIRSFRKPEPYKGKGVKFVGEQIRRKSGKSAGK |
| Large ribosomal subunit protein uL14 | N | 121 | Cellvibrio Japonicus (Strain Ueda107) | MIQQESRLVVADNSGAKEALCIRVLGGTRRRYASVGDIIVVSVKSVIPSSDIKKGAVSKAVIVRTKKEVRRPDGSYIRFDDNACVLLNAAGDIRGSRIFGPVARELRGTNMKIVSLAPEVL |
| Large ribosomal subunit protein bL33 | 5 | 62 | Cellvibrio Japonicus (Strain Ueda107) | MAKKVKGNRVQVILECTEHKESGMPGISRYITTKNRKNTTQRLELKKYNPILRRMTLHKEIK |
| Large ribosomal subunit protein bL31B | 12 | 85 | Cellvibrio Japonicus (Strain Ueda107) | MKKGIHPENYRPVVFKDMSNEDIFITRSTMEAKETIEIDGVTYPLIKVEISNTSHPFFTGKAKLVDTAGRVDKFMSRYGDRNKKK |
| Large ribosomal subunit protein uL30 | 2 | 58 | Cellvibrio Japonicus (Strain Ueda107) | MAKIKIQQVRSRIRCPKDQKRTLDALGLRKLNQIVEHEATPSILGMVNKVRHLVLIVE |
| Large ribosomal subunit protein bL32 | 4 | 61 | Cellvibrio Japonicus (Strain Ueda107) | MAHPKRRQSKTRTAKRRTHDKAVMPTLAKCPNCGAWHIYHTVCGDCGYYRGKLAIEKEVAV |
| Large ribosomal subunit protein bL34 | 6 | 50 | Cellvibrio Japonicus (Strain Ueda107) | MKRTYQPSNRKRLNKHGFRSRMATANGRRVLAARRAKGRAKLTVSDEFVG |
| Large ribosomal subunit protein bL35 | 7 | 65 | Cellvibrio Japonicus (Strain Ueda107) | MPKLKTNSGAKKRFALTGTGKIKRKHAFKSHILTKKTKKQKRNLTYFSTVHKVDENAVKQLLCLR |
| Large ribosomal subunit protein bL36 | 8 | 38 | Cellvibrio Japonicus (Strain Ueda107) | MKVRASVKKRTPECKIVRRKGRLYVINKKNPKYKQRQG |
| Nucleic Acids / Hybrid | ||||
|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Sequence |
| 23S rRNA | a | 2882 | NA | UAAGGGCAGACGGUGGAUGCCUAGGCUCUCGGAGGCGAAGAAGGACGUGAUAAGCUGCGAAAAGCUGCGGGAAUCGGCACAUACGAAUUGAUCCGCAGAUAUCCGAAUGGGGCAACCCGUCAGGCCAAGGCCUGACACAUGAAUUGAUUUCAUGAGCGAACGCGGGGAACUGAAACAUCUCAUUACCCGUAGGAGAAGAAAACAAAAGUGAUUCCCUCAGUAGUGGCGAGCGAACGGGGAUUAGCCCAAACCGGCUUUGUUUCGGCAAAGUCGGGGUAAUAGGACUUCGACAAAAGUUUAAUGAUAGAUAUAGGAGAACCUACUGGAAAGUAUGGCCGAAGAGCAUGAAAGCUGCGUAUCCGACAUAUCGAACAAUAGACGACGGAGCACCUGAGUAGCGCGGGACACGAGACAUCCUGUGUGAAUUGGCGGGGCCCAUCCCGUAAGGCUAAAUACUCCCGAGAGACCGAUAGUGAACCAGUACCGUGAGGGAAAGGUGAAAAGAACCUCGAACAGAGGAGUGCAAUAGACCCUGAACCCGUCUGCCUACAAGCGGUAGGAGCGCCAUUAAGGUGUGACUGCGUGCCUUUUGCAUAAUGAACCUACGAGUUACUGUUUGUGGCAAGGUUAAUUGUUAUAAUCAAGACAAGGAGCCGAAGCGAAAGCGAGUCUUAAAAGGGCGCCCAUUUAGUCACGAGCAGUAGACGCGAAACCAAGUGAUCUACCCUUGGUCAGGUUGAAGGUUAGGUAACACUAACUGGAGGACCGAAUCGGUAAGCGUUGAAAAGCUUUCGAAUGAACUGAGGGUAGGGGUGAAAGGCUAAUCAAACUUGGAGAUAGCUCGUACUCCCCGAAAUGCAUUUAGGUGCAGCCUGUUGGAUGUUAUCAUGAGGUAGAGCGACUGAUUGGAUGCGAGGGUUUCACCGCCUAUCAAGUCCAGAUAAACUCCGAAUGCAUGAUAAUUGACCGAUGGAGUGAGGGCAUGGGUGCUAAGGUCCAUGUCCGAGAGGAGAAGAAUCCGGACCACCGGCUAAGGUCCCGAAAUAAUUGCUAAGUUGUAAAAACGAAGUCAAGAAGCAGAGACAGCUAGGAUGUUGGCUUGGAAGCAGCCAUUCAUUUAAAGAGUGCGUAACAGCUCACUAGUCGAGGAUUUUGGCAUGGAUAAUACACGGGCAUAAGCAAUUUACCGAAGCCGUGGGAUAUAGUUAAUAUAUCGGUAGGGGAGCAUUCCAGCGACGUAGAAGGGAAAAGGGCGACUUUUUCUGGAGUUUCUGGAAAAGCAAAUGUAGGUAUAAGUAACGAUAAAGGGGGCGAGAACCCCCCUCGCCGAAAGACCAAGGUUUCCUGAUCAACGCUAAUCGGAUCAGGGUUAGUCGGGGCCUAAGGAUAAGCCGAAUGGCGAUUCCGAUGGAAGAACCGGUUAAUAUUCCGGUACUGAUACUAGAGGCGAUGUGGUGACGGAGAAGUGACAGUCCGGCCGUCUGACGGAUUAGGCGGUUAAAGGGUGUAGAUGUUAUUCGGGGUAGGCAAAUCCGCCCUCAGAGUGCAACCUGACAGUACCGGAGUACAAGUACGAAGGGAUAAAGGACGUAACCCGGCUCCCAAGAAAACCCGCUAAGAUAUUUCUUGUGUUACCCGUACCGUAAACCGACACAGGUGGUUGGGUUGAGUAUACUAAGGCGCUCGAGAGAUUCGCGGUUAAGGAACUAGGCAAAAUGGUCCUGUAACUUCGGGAGAAAGGACGCCUGUCCCGGGACAGGCCGCAGAAACCAGGCCCAGGCGACUGUUUAACAAAAACACAAGGCUAUGCAAAAAAGCAAUUUGAGGUAUAUAGUCUGACACCUGCCCGGUGCUGGAAGGUUAAGAGGAGGAGUCAUGUCAAGGAGAAGCUCUGAAUUGAAGCCCCAGUAAACGGCGCCGUAACUAUAACGGUCCCUAAGGUAGCGAAAUUCCUUGUCGGGUAAGUUCCGACCUGCACGAAUGGUGUAACGAUCUGGGCACUGUCUCAACCGCGAUCUCGGUGAAAUUGUAGUAUCGGUGAAGAUGCCGAUUACCCGCAACGGGACGAAAAGACCCCGUGAACCUUUACUAUAGCUUUACAUUGUAUUGGGCAUCAGAUGUGUAGGAUAGGCCGGAGGCAGAGAAGCGGGUACGCCAGUAUUCGUGGAGUCGAUGUUGAAAUACGGCCCUUUUGAUGUUUGGGAUACUAACUCGCGGGUGGCGAGGACAGUGUAUGGUGGGUAGUUUGACUGGGGUGGUCGCCUCCAAAAGCGUAACGGAGGCUUCUAAAGGUACCCUCAGGCCGAUUGUAAACCGGUCGCAGAGUGUAAUGGCACAAGGGUGCUUGACUGGGAGACAAACAAGUCGCACAGGUAGGAAACUAGAGCAUAGUGAUCCGGUGGUCCCGCAUGGAAGGGCCAUCGCUCAAAGGAUAAAAGGUACUCCGGGGAUAACAGGCUGAUCACUCCCAAGAGUCCAUAUCGACGGAGUGGUUUGGCACCUXGAUGUCGGCUCGUCACAUCCUGGGGCUGGAGAAGGUCCCAAGGGUUGGGCUGUUCGCCCAUUAAAGUGGCACGCGAGCUGGGUUCAGAACGUCGUGAGACAGUUCGGUCUCUAUCUGUUGUGGGCGCAGGAAAUUUGCGAGGGUCUGACACUAGUACGAGAGGACCGUGUUGGACAGACCCCUGGUUUACCGGUUGUACCGCCAGGUGCACCGCCGGGUAUCCACGUCUGGUAAGGAUAAGUGCUGAAAGCAUCUAAGCACGAAGCCGGCCUCAAGAUAAGAUUUCCAUAAAUAGGGUGGUUAAAGACUAUGACCUUGAUAGGCUGCAGGUGUAUGAUUGGUAACAAUUAAGCCGAGCAGUACUAAUAGCCCGAACUUU |
| 5S rRNA | b | 109 | NA | UCAGGUGGUUAUAACGUUGGGGAUCCACCUCUUCCCAUUCCGAACAGAGAAGUUAAGCCCAACGGUGCCGAUGGUACUGCGUCACAGUGGGAGAGUAGGACGCCGCCGA |
Experimental Data
Method: ELECTRON MICROSCOPY
Deposited Date: 2025-01-28 Deposition Author(s): Bashan, A. , Hiregange, D.G. , Yonath, A.