3PIO
Crystal structure of the synergistic antibiotic pair lankamycin and lankacidin in complex with the large ribosomal subunit
PDB DOI: 10.2210/pdb3pio/pdb
Classification: RIBOSOME/ANTIBIOTIC Organism(s): Deinococcus Radiodurans , Deinococcus Radiodurans R1
Deposited: 2010-11-07 Deposition Author(s): Arakawa, K. , Bashan, A. , Belousoff, M.J. , Kinashi, H. , Rozenberg, H. , Shapira, T. , Yonath, A. , Zimmerman, E.
Experimental Data Snapshot
Method: X-RAY DIFFRACTION Resolution: 3.2473 Å
Crystal structure of the synergistic antibiotic pair lankamycin and lankacidin in complex with the large ribosomal subunit
Arakawa, K. , Bashan, A. , Belousoff, M.J. , Kinashi, H. , Rozenberg, H. , Shapira, T. , Yonath, A. , Zimmerman, E.
Primary Citation of Related Structures: 3PIO
| Nucleic Acids / Hybrid | ||||
|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Sequence |
| RIBOSOMAL 23S RNA | x | 2880 | NA | GGUCAAGAUAGUAAGGGUCCACGGUGGAUGCCCUGGCGCUGGAGCCGAUGAAGGACGCGAUUACCUGCGAAAAGCCCCGACGAGCUGGAGAUACGCUUUGACUCGGGGAUGUCCGAAUGGGGAAACCCACCUCGUAAGAGGUAUCCGCAAGGAUGGGAACUCAGGGAACUGAAACAUCUCAGUACCUGAAGGAGAAGAAAGAGAAUUCGAUUCCGUUAGUAGCGGCGAGCGAACCCGGAUCAGCCCAAACCGAAACGCUUGCGUUUCGGGGUUGUAGGACCAGUUUUUAAGAUUCAACCCCUCAAGCCGAAGUGGCUGGAAAGCUACACCUCAGAAGGUGAGAGUCCUGUAGGCGAACGAGCGGUUGACUGUACUGGCACCUGAGUAGGUCGUUGUUCGUGAAACGAUGACUGAAUCCGCGCGGACCACCGCGCAAGGCUAAAUACUCCCAGUGACCGAUAGCGCAUAGUACCGUGAGGGAAAGGUGAAAAGAACCCCGGGAGGGGAGUGAAAGAGAACCUGAAACCGUGGACUUACAAGCAGUCAUGGCACCUUAUGCGUGUUAUGGCGUGCCUAUUGAAGCAUGAGCCGGCGACUUAGACCUGACGUGCGAGCUUAAGUUGAAAAACGGAGGCGGAGCGAAAGCGAGUCCGAAUAGGGCGGCAUUAGUACGUCGGGCUAGACUCGAAACCAGGUGAGCUAAGCAUGACCAGGUUGAAACCCCCGUGACAGGGGGCGGAGGACCGAACCGGUGCCUGCUGAAACAGUCUCGGAUGAGUUGUGUUUAGGAGUGAAAAGCUAACCGAACCUGGAGAUAGCUAGUUCUCCCCGAAAUGUAUUGAGGUACAGCCUCGGAUGUUGACCAUGUCCUGUAGAGCACUCACAAGGCUAGGGGGCCUACCAGCUUACCAAACCUUAUGAAACUCCGAAGGGGCACGCGUUUAGUCCGGGAGUGAGGCUGCGAGAGCUAACUUCCGUAGCCGAGAGGGAAACAACCCAGACCAUCAGCUAAGGUCCCUAAAUGAUCGCUCAGUGGUUAAGGAUGUGUCGUCGCAUAGACAGCCAGGAGGUUGGCUUAGAAGCAGCCACCCUUCAAAGAGUGCGUAAUAGCUCACUGGUCGAGUGACGAUGCGCCGAAAAUGAUCGGGGCUCAAGUGAUCUACCGAAGCUAUGGAUUCAACUCGCGAAGCGAGUUGUCUGGUAGGGGAGCGUUCAGUCCGCGGAGAAGCCAUACCGGAAGGAGUGGUGGAGCCGACUGAAGUGCGGAUGCCGGCAUGAGUAACGAUAAAAGAAGUGAGAAUCUUCUUCGCCGUAAGGACAAGGGUUCCUGGGGAAGGGUCGUCCGCCCAGGGAAAGUCGGGACCUAAGGUGAGGCCGAACGGCGCAGCCGAUGGACAGCAGGUCAAGAUUCCUGCACCGAUCAUGUGGAGUGAUGGAGGGACGCAUUACGCUAUCCAAUGCCAAGCUAUGGCUAUGCUGGUUGGUACGCUCAAGGGCGAUCGGGUCAGAAAAUCUACCGGUCACAUGCCUCAGACGUAUCGGGAGCUUCCUCGGAAGCGAAGUUGGAAACGCGACGGUGCCAAGAAAAGCUUCUAAACGUUGAAACAUGAUUGCCCGUACCGCAAACCGACACAGGUGUCCGAGUGUCAAUGCACUAAGGCGCGCGAGAGAACCCUCGUUAAGGAACUUUGCAAUCUCACCCCGUAACUUCGGAAGAAGGGGUCCCCACGCUUCGCGUGGGGCGCAGUGAAUAGGCCCAGGCGACUGUUUACCAAAAUCACAGCACUCUGCCAACACGAACAGUGGACGUAUAGGGUGUGACGCCUGCCCGGUGCCGGAAGGUCAAGUGGAGCGGUGCAAGCUGCGAAAUGAAGCCCCGGUGAACGGCGGCCGUAACUAUAACGGUCCUAAGGUAGCGAAAUUCCUUGUCGGGUAAGUUCCGACCUGCACGAAAGGCGUAACGAUCUGGGCGCUGUCUCAACGAGGGACUCGGUGAAAUUGAAUUGGCUGUAAAGAUGCGGCCUACCCGUAGCAGGACGAAAAGACCCCGUGGAGCUUUACUAUAGUCUGGCAUUGGGAUUCGGGUUUCUCUGCGUAGGAUAGGUGGGAGCCUGCGAAACUGGCCUUUUGGGGUCGGUGGAGGCAACGGUGAAAUACCACCCUGAGAAACUUGGAUUUCUAACCUGAAAAAUCACUUUCGGGGACCGUGCUUGGCGGGUAGUUUGACUGGGGCGGUCGCCUCCCAAAAUGUAACGGAGGCGCCCAAAGGUCACCUCAAGACGGUUGGAAAUCGUCUGUAGAGCGCAAAGGUAGAAGGUGGCUUGACUGCGAGACUGACACGUCGAGCAGGGAGGAAACUCGGGCUUAGUGAACCGGUGGUACCGUGUGGAAGGGCCAUCGAUCAACGGAUAAAAGUUACCCCGGGGAUAACAGGCUGAUCUCCCCCGAGAGUCCAUAUCGGCGGGGAGGUUUGGCACCUCGAUGUCGGCUCGUCGCAUCCUGGGGCUGAAGAAGGUCCCAAGGGUUGGGCUGUUCGCCCAUUAAAGCGGCACGCGAGCUGGGUUCAGAACGUCGUGAGACAGUUCGGUCUCUAUCCGCUACGGGCGCAGGAGAAUUGAGGGGAGUUGCUCCUAGUACGAGAGGACCGGAGUGAACGGACCGCUGGUCUCCCUGCUGUCGUACCAACGGCACAUGCAGGGUAGCUAUGUCCGGAACGGAUAACCGCUGAAAGCAUCUAAGCGGGAAGCCAGCCCCAAGAUGAGUUCUCCCACUGUUUAUCAGGUAAGACUCCCGGAAGACCACCGGGUUAAGAGGCCAGGCGUGCACGCAUAGCAAUGUGUUCAGCGGACUGGUGCUCAUCAGUCGAGGUCUUGACCACUC |
| 5S ribosomal RNA | y | 123 | NA | ACACCCCCGUGCCCAUAGCACUGUGGAACCACCCCACCCCAUGCCGAACUGGGUCGUGAAACACAGCAGCGCCAAUGAUACUCGGACCGCAGGGUCCCGGAAAAGUCGGUCAGCGCGGGGGUU |
| Proteins | ||||
|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Sequence |
| 50S ribosomal protein L14 | H | 134 | Deinococcus Radiodurans , Deinococcus Radiodurans R1 | MIMPQSRLDVADNSGAREIMCIRVLNSGIGGKGLTTGGGGNKRYAHVGDIIVASVKDAAPRGAVKAGDVVKAVVVRTSHAIKRADGSTIRFDRNAAVIINNQGEPRGTRVFGPVARELRDRRFMKIVSLAPEVL |
| 50S ribosomal protein L15 | I | 156 | Deinococcus Radiodurans , Deinococcus Radiodurans R1 | MKLHDLKPTPGSRKDRKRVGRGPGGTDKTAGRGHKGQKSRSGAGKGAFFEGGRSRLIARLPKRGFNNVGTTYEVVKLSQLQDLEDTTFDRDTLEAYRLVRRKNRPVKLLASGEISRAVTVHVDAASAAAIKAVEAAGGRVVLPEVQTQQDDAQKAE |
| 50S ribosomal protein L16 | J | 141 | Deinococcus Radiodurans , Deinococcus Radiodurans R1 | MLLPKRTKFRKQFRGRMTGDAKGGDYVAFGDYGLIAMEPAWIKSNQIEACRIVMSRHFRRGGKIYIRIFPDKPVTKKPAETRMGKGKGAVEYWVSVVKPGRVMFEVAGVTEEQAKEAFRLAGHKLPIQTKMVKREVYDEAQ |
| 50S ribosomal protein L17 | K | 116 | Deinococcus Radiodurans , Deinococcus Radiodurans R1 | MRHGKAGRKLNRNSSARVALARAQATALLREGRIQTTLTKAKELRPFVEQLITTAKGGDLHSRRLVAQDIHDKDVVRKVMDEVAPKYAERPGGYTRILRVGTRRGDGVTMALIELV |
| 50S ribosomal protein L18 | L | 114 | Deinococcus Radiodurans , Deinococcus Radiodurans R1 | MATATTIRRKLRTRRKVRTTTAASGRLRLSVYRSSKHIYAQIIDDSRGQTLAAASSAALKSGNKTDTAAAVGKALAAAAAEKGIKQVVFDRGSYKYHGRVKALADAAREGGLDF |
| 50S ribosomal protein L19 | M | 166 | Deinococcus Radiodurans , Deinococcus Radiodurans R1 | MQTHIKINRGELLRGIEQDHTRQLPDFRPGDTVRVDTKVREGNRTRSQAFEGVVIAINGSGSRKSFTVRKISFGEGVERVFPFASPLVNQVTIVERGKVRRAKLYYLRELRGKAARIKSDRSRVMKDAARAQQDKANASASQAAAAQADVTVISAAPEVAPETQGE |
| 50S ribosomal protein L20 | N | 118 | Deinococcus Radiodurans , Deinococcus Radiodurans R1 | MPRAKTGIVRRRRHKKVLKRAKGFWGSRSKQYRNAFQTLLNAATYEYRDRRNKKRDFRRLWIQRINAGARLHGMNYSTFINGLKRANIDLNRKVLADIAAREPEAFKALVDASRNARQ |
| 50S ribosomal protein L21 | O | 100 | Deinococcus Radiodurans , Deinococcus Radiodurans R1 | MFAIIQTGGKQYRVSEGDVIRVESLQGEAGDKVELKALFVGGEQTVFGEDAGKYTVQAEVVEHGRGKKIYIRKYKSGVQYRRRTGHRQNFTAIKILGIQG |
| 50S ribosomal protein L22 | P | 134 | Deinococcus Radiodurans , Deinococcus Radiodurans R1 | MTAPEQTFRNKKQRKQQVKLRKPGFAVAKYVRMSPRKVRLVVDVIRGKSVQDAEDLLRFIPRSASEPVAKVLNSAKANALHNDEMLEDRLFVKEAYVDAGPTLKRLIPRARGSANIIKKRTSHITIIVAEKGNK |
| 50S ribosomal protein L23 | Q | 95 | Deinococcus Radiodurans , Deinococcus Radiodurans R1 | MSHYDILQAPVISEKAYSAMERGVYSFWVSPKATKTEIKDAIQQAFGVRVIGISTMNVPGKRKRVGRFIGQRNDRKKAIVRLAEGQSIEALAGQA |
| 50S ribosomal protein L24 | R | 115 | Deinococcus Radiodurans , Deinococcus Radiodurans R1 | MPRPSAGSHHNDKLHFKKGDTVIVLSGKHKGQTGKVLLALPRDQKVVVEGVNVITKNVKPSMTNPQGGQEQRELALHASKVALVDPETGKATRVRKQIVDGKKVRVAVASGKTID |
| 50S ribosomal protein L25 | S | 237 | Deinococcus Radiodurans , Deinococcus Radiodurans R1 | MELTAKPRTPKQKLDESMIAAVAYNKENNVSFALDRKAFDRAFRQQSTTGLFDITVEGGETFPALVKAVQMDKRKRAPIHVDFYMVTYGEPVEVSVPVHTTGRSQGEVQGGLVDIVVHNLQIVAPGPRRIPQELVVDVTKMNIGDHITAGDIKLPEGCTLAADPELTVVSVLPPRLTAEELEAEVQAAQVAGLVAAGELSEEAAEAVLEGDASLEEVKAEASEDNAGTDSEDNSDAQ |
| 50S ribosomal protein L27 | T | 91 | Deinococcus Radiodurans , Deinococcus Radiodurans R1 | MAHKKGVGSSKNGRDSNPKYLGVKKFGGEVVKAGNILVRQRGTKFKAGQGVGMGRDHTLFALSDGKVVFINKGKGARFISIEAAQTEVAAD |
| 50S ribosomal protein L28 | U | 81 | Deinococcus Radiodurans , Deinococcus Radiodurans R1 | MSRECYLTGKKNLVVNSVIRRGKARADGGVGRKTTGITKRVQRANLHKKAIRENGQVKTVWLSANALRTLSKGPYKGIELI |
| 50S ribosomal protein L29 | V | 67 | Deinococcus Radiodurans , Deinococcus Radiodurans R1 | MKPSEMRNLQATDFAKEIDARKKELMELRFQAAAGQLAQPHRVRQLRREVAQLNTVKAELARKGEQQ |
| 50S ribosomal protein L30 | W | 55 | Deinococcus Radiodurans , Deinococcus Radiodurans R1 | MKIKLVRSVIGRPGNQVKTVQALGLRKIGDSREVSDTPAVRGMVKTVKHLLEVQE |
| 50S ribosomal protein L32 | Z | 60 | Deinococcus Radiodurans , Deinococcus Radiodurans R1 | MAKHPVPKKKTSKSKRDMRRSHHALTAPNLTECPQCHGKKLSHHICPNCGYYDGRQVLAV |
| 50S ribosomal protein L33 | 1 | 55 | Deinococcus Radiodurans , Deinococcus Radiodurans R1 | MAKDGPRIIVKMESSAGTGFYYTTTKNRRNTQAKLELKKYDPVAKKHVVFREKKV |
| 50S ribosomal protein L34 | 2 | 47 | Deinococcus Radiodurans , Deinococcus Radiodurans R1 | MKRTYQPNNRKRAKTHGFRARMKTKSGRNILARRRAKGRHQLTVSDE |
| 50S ribosomal protein L35 | 3 | 66 | Deinococcus Radiodurans , Deinococcus Radiodurans R1 | MPKMKTHKMAKRRIKITGTGKVMAFKSGKRHQNTGKSGDEIRGKGKGFVLAKAEWARMKLMLPRGK |
| 50S ribosomal protein L2 | A | 274 | Deinococcus Radiodurans , Deinococcus Radiodurans R1 | AVKKYRPYTPSRRQMTTADFSGLTKKRPEKALTEALPKTGGRNNRGRITSRFIGGGHKRLYRIIDFKRRDKSGVNAKVAAIEYDPNRSARIALLHYADGEKRYILAPEGLTVGATVNAGPEAEPKLGNALPLRFVPVGAVVHALELVPGKGAQLARSAGTSVQVQGKESDYVIVRLPSGELRRVHSECYATIGAVGNAEHKNIVLGKAGRSRWLGRKPHQRGSAMNPVDHPHGGGEGRTGAGRVPVTPWGKPTKGLKTRRKRKTSDRFIVTRRK |
| 50S ribosomal protein L36 | 4 | 37 | Deinococcus Radiodurans , Deinococcus Radiodurans R1 | MKVRSSVKKMCDNCKVVRRHGRVLVICSNVKHKQRQG |
| 50S ribosomal protein L3 | B | 211 | Deinococcus Radiodurans , Deinococcus Radiodurans R1 | MKGILGTKIGMTQIWKNDRAIPVTVVLAGPCPIVQRKTAQTDGYEAVQIGYAPKAERKVNKPMQGHFAKAGVAPTRILREFRGFAPDGDSVNVDIFAEGEKIDATGTSKGKGTQGVMKRWNFAGGPASHGSKKWHRRPGSIGQRKTPGRVYKGKRMAGHMGMERVTVQNLEVVEIRAGENLILVKGAIPGANGGLVVLRSAAKASAAKGGK |
| 50S ribosomal protein L4 | C | 205 | Deinococcus Radiodurans , Deinococcus Radiodurans R1 | MAQINVIGQNGGRTIELPLPEVNSGVLHEVVTWQLASRRRGTASTRTRAQVSKTGRKMYGQKGTGNARHGDRSVPTFVGGGVAFGPKPRSYDYTLPRQVRQLGLAMAIASRQEGGKLVAVDGFDIADAKTKNFISWAKQNGLDGTEKVLLVTDDENTRRAARNVSWVSVLPVAGVNVYDILRHDRLVIDAAALEIVEEEAGEEQQ |
| 50S ribosomal protein L5 | D | 180 | Deinococcus Radiodurans , Deinococcus Radiodurans R1 | MQQLKTKYNDQVRPALMQQFGYSSVMAVPRIEKIVVNEGLGSSKEDSKAIDKAAKELALITLQKPIITKAKKSISNFKLRQGMPVGIKVTLRGERMYVFLEKLINIGLPRIRDFRGINPNAFDGRGNYNLGIKEQLIFPEITYDMVDKTRGMDITIVTTAKTDEEARALLQSMGLPFRKQ |
| 50S ribosomal protein L6 | E | 185 | Deinococcus Radiodurans , Deinococcus Radiodurans R1 | MSRIGKQPIAVPSGVTVNAQDGVFKVKGPKGELTVPYNTELTVRQDGDQLLVERPSDAQKHRALHGLTRTLVANAVKGVSDGYTINLELRGVGFRAKLTGKALEMNIGYSHPVIIEPPAGVTFAVPEPTRIDVSGIDKQLVGQVAANVRKVRKPDAYHGKGVRFVGEQIALKAGKAGATGGKGKK |
| 50S ribosomal protein L11 | F | 144 | Deinococcus Radiodurans , Deinococcus Radiodurans R1 | MKKVAGIVKLQLPAGKATPAPPVGPALGQYGANIMEFTKAFNAQTADKGDAIIPVEITIYADRSFTFITKTPPMSYLIRKAAGIGKGSSTPNKAKVGKLNWDQVLEIAKTKMPDLNAGSVEAAANTVAGTARSMGVTVEGGPNA |
| 50S ribosomal protein L13 | G | 174 | Deinococcus Radiodurans , Deinococcus Radiodurans R1 | MAFPDTDVSPPRGGPSSPAKSPLLRSFKVKTYIPKNDEQNWVVVDASGVPLGRLATLIASRIRGKHRPDFTPNMIQGDFVVVINAAQVALTGKKLDDKVYTRYTGYQGGLKTETAREALSKHPERVIEHAVFGMLPKGRQGRAMHTRLKVYAGETHPHSAQKPQVLKTQPLEVK |
Experimental Data
Method: X-RAY DIFFRACTION
Deposited Date: 2010-11-07 Deposition Author(s): Arakawa, K. , Bashan, A. , Belousoff, M.J. , Kinashi, H. , Rozenberg, H. , Shapira, T. , Yonath, A. , Zimmerman, E.