9I5X
Porphyromonas gingivalis 70s ribosome (w83 strain)
PDB DOI: 10.2210/pdb9i5x/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: 3.0 Å
Porphyromonas gingivalis 70s ribosome (w83 strain)
Bashan, A. , Hiregange, D.G. , Yonath, A.
Primary Citation of Related Structures: 9I5X
| Proteins | ||||
|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Sequence |
| Large ribosomal subunit protein uL16 | P | 144 | Cellvibrio Japonicus (Strain Ueda107) | MLQPKKTKFRRQQKGRMKGFAQRGNQLSFGSFGIKSLQSKWITGRQIEAARIAVTRYMQRQGQVWVRIFPDKPITKKGEGVRMGKGKGAPEGFVAPITPGRIIFEVEGVPYEIAKEALRLAAQKLPVTTKFVVRHDYDIQNQNA |
| Small ribosomal subunit protein bS6 | B | 117 | Cellvibrio Japonicus (Strain Ueda107) | MNNYETVFILTPVLSDAQMKEAVDKFTGLLKQEGAVIVNEENWGLRKLAYPIQKKSTGFYQLVEFQANPDVIAKLETNFRRDERVIRFLTFRQDKFAAEYAAKRRSLKAKTEEVKEA |
| Small ribosomal subunit protein bS20 | D | 84 | Cellvibrio Japonicus (Strain Ueda107) | MANHISSEKRIRQTNARRLHNRYYARTARNAVKAFRALTDRTEAEKKYPVLASMLDRLAGKNIIHKNKAANLKSKLARRINTLA |
| Small ribosomal subunit protein uS17 | E | 84 | Cellvibrio Japonicus (Strain Ueda107) | MERNLRKERVGVVSSNKMDKTITVAVKWKEKHPIYGKFVNKTKKYHAHDEKNECGIGDTVRIMETRPLSRTKRWRLTEIIERAK |
| Small ribosomal subunit protein uS15 | F | 89 | Cellvibrio Japonicus (Strain Ueda107) | MYLDSAKKAELFEKYGKSVKDTGSPESQIALFTFRIAHLTEHLRQNKKDFATERSLKMLVGKRRRMLDYLIKVDIERYRAIIKELGIRR |
| Small ribosomal subunit protein uS3 | K | 246 | Cellvibrio Japonicus (Strain Ueda107) | MGQKINPVSNRLGIIRGWDSNWYGGRKYGETLLEDSRIRQYLNARLAKASVSRIVIERALKLVTITICTARPGMIIGKAGQEVDKLKEELKRITKKDVQINIYEIRKPELDAAIVAENIARQLEGKIAYRRAVKMAIASAMRMGAEGIKIQVSGRLNGAEMARSEMFKEGRTPLHTLRADIDYALAEALTKVGLLGIKVWICKGEVYEKRDLAPNFAVAKNQSRRPNAQGGNNRGGDRNRRRKGNR |
| Small ribosomal subunit protein uS4 | L | 201 | Cellvibrio Japonicus (Strain Ueda107) | MARYTGPKSKIARKFGDPIFGADKVLSKKNYPPGQHGNNRRRKTSEYGLQLREKQKAKYTYGVLEKQFRHLFHRAQRAKGVTGELLIQFLEARLDNVVFRLGIAPTRSAARQLVSHRHITVDGSVVNIPSYSVKPGQVIGVRERSKSLEVIADALTGFNHSKYPWMEWDQSSLSGKLLHMPDRTDIPENIKEQLIVELYSK |
| Small ribosomal subunit protein uS7 | M | 158 | Cellvibrio Japonicus (Strain Ueda107) | MRKAKPKKRQILPDPVYGDVRVTKFVNHLMYDGKKNTAFSIFYGALDIVKTKHSNEEKSALEIWKAALDNITPQVEVKSRRIGGATFQVPTEIRPERKESISMKNLILYARKRGGKTMADKLAAEIVDAFNNQGAAFKRKEDMHRMAEANRAFAHFRF |
| Small ribosomal subunit protein uS5 | N | 172 | Cellvibrio Japonicus (Strain Ueda107) | MAIVYNRVKSTNDLELKDRLVAINRVTKVTKGGRTFTFAAIVVVGNEDGVIGWGLGKAGEVPAAIAKGVEAAKKNLIRVPVHNGTIPHEQAASYGGASVFLKPATTGTGVKAGGAMRAVLDSVGVTDVLAKSKGSSNPHNLVKATIQALAEMRSPLMVAQNRGISVEKVFKG |
| Small ribosomal subunit protein uS8 | O | 131 | Cellvibrio Japonicus (Strain Ueda107) | MTDPIADYLTRLRNAIMAGHRVVSVPASNIKKEITKILFDKGYILNYKFEENDSQGIIKVALKYDLAHKVNAIKKLKRVSRPGLRKYVGYRDMPRVLNGLGIAIVSTPRGVMTDKEARELKVGGEVLCYVY |
| Large ribosomal subunit protein bL28 | 0 | 79 | Cellvibrio Japonicus (Strain Ueda107) | MSKICQITGKKAMVGNNVSHSKRRTKRVFDVNLFRKKFYWVEQDCWVVLRISAAGLRLINKIGLDAAIKRAAEKGFLNA |
| 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 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 bL27 | Z | 85 | Cellvibrio Japonicus (Strain Ueda107) | MAHKKGVGSSKNGRESESKRLGVKVYGGEMAKAGNILVRQRGTVHHPGENVGIGKDHTLYALKSGVVVFTRKKNDRSYVSIKTES |
| Large ribosomal subunit protein uL29 | 1 | 64 | Cellvibrio Japonicus (Strain Ueda107) | MKIAEIKELATKELQERLDAEVAAYDQMRINHAVSPLDSPAKLKHQRRMIAQMKTVLRQRELNK |
| Small ribosomal subunit protein bS16 | C | 192 | Cellvibrio Japonicus (Strain Ueda107) | MATKIRLQRHGRKGYAFYKIVVADSRAPRDGKFIERIGSYNPNTNPATIDLNFERALYWIGVGAQPTDTARNILSREGVLMMKHLLGGVKKGAFDQAAAENKFEAWLKGKKDALNNMKAKVKEAAVADDKVKLEAEKAVNKARAEAVAEKKAAEAKAKAEAEAAAAAEEAAETEETPVEAAAEEAPAAESAE |
| Small ribosomal subunit protein uS14 | G | 89 | Cellvibrio Japonicus (Strain Ueda107) | MAKESMKAREVKRAKLVAKYAAKRAALKAEGNYEALQLLPKNASPVRLHNRCSMTGRPKGYMRQFGISRIQFREMASAGLIPGVKKASW |
| Large ribosomal subunit protein bL9 | H | 179 | Cellvibrio Japonicus (Strain Ueda107) | MQVILKEDVVNLGYKDDIVTVKDGYGRNFLIPQGKAVIASESAKKVLAENLRQRAHKIAQIKKEAEEKAASMQGISLTIKAKTSSTGTIFGSVTNIQIAEELAKKGVEVDRKIIVLKPAVKEVGNYTAVVRLHKEVTVEIPFEVVSENETIIEAKPEGAPVPVAEEPAAEAEQAEVAAE |
| Small ribosomal subunit protein bS18 | I | 90 | Cellvibrio Japonicus (Strain Ueda107) | MAANNQGEIRYLTPLSVDTKKKKYCRFKKSGIRYIDYKDPEFLKKFLNEQGKILPRRITGTSLKFQRRVAQAVKRARHLALLPYVTDMMK |
| Small ribosomal subunit protein uS9 | J | 128 | Cellvibrio Japonicus (Strain Ueda107) | MDYINAIGRRKAAVARVYLSEGSGKIVINKREIEQYFPSSILQYIVKQPLLKLDVAAKYDIKINLRGGGFKGQSEAARLAIARALVKINPDDKPALRSEGFITRDPRVVERKKPGRPKARKRFQFSKR |
| Large ribosomal subunit protein uL30 | 2 | 58 | Cellvibrio Japonicus (Strain Ueda107) | MAKIKIQQVRSRIRCPKDQKRTLDALGLRKLNQIVEHEATPSILGMVNKVRHLVLIVE |
| Large ribosomal subunit protein bL25 | Y | 192 | Cellvibrio Japonicus (Strain Ueda107) | MKTFQLTGTPRAEFGKKAAKAIRKEDQIPAVLYGGKGEGVNFIVSQDAVRNLIYSPEIFLVELTVEGSGSYKAILKEIQFHPVTDRIIHIDFLQVTDEKPVVMEVPVVLTGHAEGVKAGGKLSLEMRKLKVKALYSEIPEKLDIDVSDLQLGKTIQVGELHFEGLTLMNAKNAVVCAVKLTRAARGAAVKKQ |
| AURKAIP1/COX24 domain-containing protein | 10 | 30 | Cellvibrio Japonicus (Strain Ueda107) | MPNGKKRKRHKMATHKRKKRLKKNRHKKKK |
| Large ribosomal subunit protein bL32 | 4 | 61 | Cellvibrio Japonicus (Strain Ueda107) | MAHPKRRQSKTRTAKRRTHDKAVMPTLAKCPNCGAWHIYHTVCGDCGYYRGKLAIEKEVAV |
| Large ribosomal subunit protein bL33 | 5 | 62 | Cellvibrio Japonicus (Strain Ueda107) | MAKKVKGNRVQVILECTEHKESGMPGISRYITTKNRKNTTQRLELKKYNPILRRMTLHKEIK |
| 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 |
| 16S rRNA | a | 1534 | NA | ACAGUGGAGAGUUUGAUCCUGGCUCAGGAUGAACGCUAGCGAUAGGCUUAACACAUGCAAGUCGAGGGGCAGCAUGAUCUUAGCUUGCUAAGGUUGAUGGCGACCGGCGCACGGGUGCGUAACGCGUAUGCAACUUGCCUUACAGAGGGGGAUAACCCGUUGAAAGACGGACUAAAACCGCAUACACUUGUAUUAUUGCAUGAUAUUACAAGGAAAUAUUUAUAGCUGUAAGAUAGGCAUGCGUCCCAUUAGCUUGUUGGUGAGGUAACGGCUCAXCAAGGCGACGAUGGGUAGGGGAACUGAGAGGUUUAUCCCCCACACUGGUACUGAGACACGGACCAGACUCCUACGGGAGGCAGCAGUGAGGAAUAUUGGUCAAUGGGCGAGAGCCUGAACCAGCCAAGUCGCGUGAAGGAAGACAGUCCUAAGGAUUGUAAACUUCUUUUAUACGGGAAUAACGGGCGAUACGAGUAUUGCAUUGAAUGUACCGUAAGAAACAGCAUCGGCUAACUCCGUGCCAGCAGCCGCGGUAAUACGGAGGAUGCGAGCGUUAUCCGGAUUUAUUGGGUUUAAAGGGUGCGUAGGUUGUUCGGUAAGUCAGCGGUGAAACCUGAGCGCUCAACGUUCAGCCUGCCGUUGAAACUGCCGGGCUUGAGUUCAGUGGCGGCAGGCGGAAUUCGUGGUGUAGCGGUGAAAUGCAUAGAUAUCACGAGGAACUCCGAUUGCGAAGGCAGCUUGCCAUACUGCGACUGACACUGAAGCACGAAGGCGUGGGUAUCAAACAGGAUUAGAUACCCUGGUAGUCCACGCAGUAAACGAUGAUUACUAGGAGUUUGCGAUAUACCGUCAAGCUUCCACAGCGAAAGCGUUAAGUAAUCCACCUGGGGAGUACGCCGGCAACGGUGAAACUCAAAGGAAUUGACGGGGGCCCGCACAAGCGGAGGAACAUGUGGUUUAAUUCGAUGAUACGCGAGGAACCUCAUUUGGGAUUGAAAUGUGGAUGACGGAUGGUGAAAACCGUCUUCCCUUCGGGGCUUCUAUGUAAGGUGCUGCAUGGUUGUCGCCAGCUCGUGCCGUGAGGUUCGGCUUAAGUGCCAUAAACGAGCGAACCCCACAUCGGUAGUUACUACAGUUUUCCGCUGAGGACUCUACCGAGAUGCCGUCGUAAGGCGUGAGGAAGGUGGUGGAUGACGUCAAAUCAGCACGGCCCUUACAUCCGGGGCGACACACGUGUUACAAUGGGAGGGACAAAGGGCAGCUACCGGGCGACCGGAUGCGAAUCUCUAAACCCUUCCCCAGUUCGGAUCGGAGUCUGCAACUCGACUCCGUGAAGCUGGAUUCGCUAGUAAUCGCGCAUCAGCCAUGGCGCGGUGAAUACGUCCCGGGGCCUUGUACACACCGCCCGUCAAGCCAUGGGAGUCGGGGGUACCUGAAGGGCGAACCGCAAGGGGGCGCACUAGGGUAAACCCGGUGACUGGGGCUAAGUCGUAACAAGGUAGCCGUACCGGAAGGUGCGGCUGGAACCCUCCUUUCU |
Experimental Data
Method: ELECTRON MICROSCOPY
Deposited Date: 2025-01-28 Deposition Author(s): Bashan, A. , Hiregange, D.G. , Yonath, A.