1NKW
Crystal structure of the large ribosomal subunit from deinococcus radiodurans
PDB DOI: 10.2210/pdb1nkw/pdb
Classification: RIBOSOME Organism(s): Phytophthora Infestans (Strain T30-4)
Deposited: 2003-01-05 Deposition Author(s): Agmon, I. , Bartels, H. , Bashan, A. , Franceschi, F. , Gat, S. , Harms, J.M. , Schluenzen, F. , Yonath, A. , Zarivach, R.
Experimental Data Snapshot
Method: X-RAY DIFFRACTION Resolution: 3.1 Å
Crystal structure of the large ribosomal subunit from deinococcus radiodurans
Agmon, I. , Bartels, H. , Bashan, A. , Franceschi, F. , Gat, S. , Harms, J.M. , Schluenzen, F. , Yonath, A. , Zarivach, R.
Primary Citation of Related Structures: 1NKW
| Nucleic Acids / Hybrid | ||||
|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Sequence |
| 23S ribosomal RNA | 0 | 2880 | NA | GGUCAAGAUAGUAAGGGUCCACGGUGGAUGCCCUGGCGCUGGAGCCGAUGAAGGACGCGAUUACCUGCGAAAAGCCCCGACGAGCUGGAGAUACGCUUUGACUCGGGGAUGUCCGAAUGGGGAAACCCACCUCGUAAGAGGUAUCCGCAAGGAUGGGAACUCAGGGAACUGAAACAUCUCAGUACCUGAAGGAGAAGAAAGAGAAUUCGAUUCCGUUAGUAGCGGCGAGCGAACCCGGAUCAGCCCAAACCGAAACGCUUGCGUUUCGGGGUUGUAGGACCAGUUUUUAAGAUUCAACCCCUCAAGCCGAAGUGGCUGGAAAGCUACACCUCAGAAGGUGAGAGUCCUGUAGGCGAACGAGCGGUUGACUGUACUGGCACCUGAGUAGGUCGUUGUUCGUGAAACGAUGACUGAAUCCGCGCGGACCACCGCGCAAGGCUAAAUACUCCCAGUGACCGAUAGCGCAUAGUACCGUGAGGGAAAGGUGAAAAGAACCCCGGGAGGGGAGUGAAAGAGAACCUGAAACCGUGGACUUACAAGCAGUCAUGGCACCUUAUGCGUGUUAUGGCGUGCCUAUUGAAGCAUGAGCCGGCGACUUAGACCUGACGUGCGAGCUUAAGUUGAAAAACGGAGGCGGAGCGAAAGCGAGUCCGAAUAGGGCGGCAUUAGUACGUCGGGCUAGACUCGAAACCAGGUGAGCUAAGCAUGACCAGGUUGAAACCCCCGUGACAGGGGGCGGAGGACCGAACCGGUGCCUGCUGAAACAGUCUCGGAUGAGUUGUGUUUAGGAGUGAAAAGCUAACCGAACCUGGAGAUAGCUAGUUCUCCCCGAAAUGUAUUGAGGUACAGCCUCGGAUGUUGACCAUGUCCUGUAGAGCACUCACAAGGCUAGGGGGCCUACCAGCUUACCAAACCUUAUGAAACUCCGAAGGGGCACGCGUUUAGUCCGGGAGUGAGGCUGCGAGAGCUAACUUCCGUAGCCGAGAGGGAAACAACCCAGACCAUCAGCUAAGGUCCCUAAAUGAUCGCUCAGUGGUUAAGGAUGUGUCGUCGCAUAGACAGCCAGGAGGUUGGCUUAGAAGCAGCCACCCUUCAAAGAGUGCGUAAUAGCUCACUGGUCGAGUGACGAUGCGCCGAAAAUGAUCGGGGCUCAAGUGAUCUACCGAAGCUAUGGAUUCAACUCGCGAAGCGAGUUGUCUGGUAGGGGAGCGUUCAGUCCGCGGAGAAGCCAUACCGGAAGGAGUGGUGGAGCCGACUGAAGUGCGGAUGCCGGCAUGAGUAACGAUAAAAGAAGUGAGAAUCUUCUUCGCCGUAAGGACAAGGGUUCCUGGGGAAGGGUCGUCCGCCCAGGGAAAGUCGGGACCUAAGGUGAGGCCGAACGGCGCAGCCGAUGGACAGCAGGUCAAGAUUCCUGCACCGAUCAUGUGGAGUGAUGGAGGGACGCAUUACGCUAUCCAAUGCCAAGCUAUGGCUAUGCUGGUUGGUACGCUCAAGGGCGAUCGGGUCAGAAAAUCUACCGGUCACAUGCCUCAGACGUAUCGGGAGCUUCCUCGGAAGCGAAGUUGGAAACGCGACGGUGCCAAGAAAAGCUUCUAAACGUUGAAACAUGAUUGCCCGUACCGCAAACCGACACAGGUGUCCGAGUGUCAAUGCACUAAGGCGCGCGAGAGAACCCUCGUUAAGGAACUUUGCAAUCUCACCCCGUAACUUCGGAAGAAGGGGUCCCCACGCUUCGCGUGGGGCGCAGUGAAUAGGCCCAGGCGACUGUUUACCAAAAUCACAGCACUCUGCCAACACGAACAGUGGACGUAUAGGGUGUGACGCCUGCCCGGUGCCGGAAGGUCAAGUGGAGCGGUGCAAGCUGCGAAAUGAAGCCCCGGUGAACGGCGGCCGUAACUAUAACGGUCCUAAGGUAGCGAAAUUCCUUGUCGGGUAAGUUCCGACCUGCACGAAAGGCGUAACGAUCUGGGCGCUGUCUCAACGAGGGACUCGGUGAAAUUGAAUUGGCUGUAAAGAUGCGGCCUACCCGUAGCAGGACGAAAAGACCCCGUGGAGCUUUACUAUAGUCUGGCAUUGGGAUUCGGGUUUCUCUGCGUAGGAUAGGUGGGAGCCUGCGAAACUGGCCUUUUGGGGUCGGUGGAGGCAACGGUGAAAUACCACCCUGAGAAACUUGGAUUUCUAACCUGAAAAAUCACUUUCGGGGACCGUGCUUGGCGGGUAGUUUGACUGGGGCGGUCGCCUCCCAAAAUGUAACGGAGGCGCCCAAAGGUCACCUCAAGACGGUUGGAAAUCGUCUGUAGAGCGCAAAGGUAGAAGGUGGCUUGACUGCGAGACUGACACGUCGAGCAGGGAGGAAACUCGGGCUUAGUGAACCGGUGGUACCGUGUGGAAGGGCCAUCGAUCAACGGAUAAAAGUUACCCCGGGGAUAACAGGCUGAUCUCCCCCGAGAGUCCAUAUCGGCGGGGAGGUUUGGCACCUCGAUGUCGGCUCGUCGCAUCCUGGGGCUGAAGAAGGUCCCAAGGGUUGGGCUGUUCGCCCAUUAAAGCGGCACGCGAGCUGGGUUCAGAACGUCGUGAGACAGUUCGGUCUCUAUCCGCUACGGGCGCAGGAGAAUUGAGGGGAGUUGCUCCUAGUACGAGAGGACCGGAGUGAACGGACCGCUGGUCUCCCUGCUGUCGUACCAACGGCACAUGCAGGGUAGCUAUGUCCGGAACGGAUAACCGCUGAAAGCAUCUAAGCGGGAAGCCAGCCCCAAGAUGAGUUCUCCCACUGUUUAUCAGGUAAGACUCCCGGAAGACCACCGGGUUAAGAGGCCAGGCGUGCACGCAUAGCAAUGUGUUCAGCGGACUGGUGCUCAUCAGUCGAGGUCUUGACCACUC |
| 5S ribosomal RNA | 9 | 124 | NA | ACACCCCCGUGCCCAUAGCACUGUGGAACCACCCCACCCCAUGCCGAACUGGGUCGUGAAACACAGCAGCGCCAAUGAUACUCGGACCGCAGGGUCCCGGAAAAGUCGGUCAGCGCGGGGGUUU |
| Proteins | ||||
|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Sequence |
| 50S ribosomal protein L13 | H | 174 | Phytophthora Infestans (Strain T30-4) | MAFPDTDVSPPRGGPSSPAKSPLLRSFKVKTYIPKNDEQNWVVVDASGVPLGRLATLIASRIRGKHRPDFTPNMIQGDFVVVINAAQVALTGKKLDDKVYTRYTGYQGGLKTETAREALSKHPERVIEHAVFGMLPKGRQGRAMHTRLKVYAGETHPHSAQKPQVLKTQPLEVK |
| 50S ribosomal protein L14 | I | 134 | Phytophthora Infestans (Strain T30-4) | MIMPQSRLDVADNSGAREIMCIRVLNSGIGGKGLTTGGGGNKRYAHVGDIIVASVKDAAPRGAVKAGDVVKAVVVRTSHAIKRADGSTIRFDRNAAVIINNQGEPRGTRVFGPVARELRDRRFMKIVSLAPEVL |
| 50S ribosomal protein L15 | J | 156 | Phytophthora Infestans (Strain T30-4) | MKLHDLKPTPGSRKDRKRVGRGPGGTDKTAGRGHKGQKSRSGAGKGAFFEGGRSRLIARLPKRGFNNVGTTYEVVKLSQLQDLEDTTFDRDTLEAYRLVRRKNRPVKLLASGEISRAVTVHVDAASAAAIKAVEAAGGRVVLPEVQTQQDDAQKAE |
| 50S ribosomal protein L16 | K | 142 | Phytophthora Infestans (Strain T30-4) | MMLLPKRTKFRKQFRGRMTGDAKGGDYVAFGDYGLIAMEPAWIKSNQIEACRIVMSRHFRRGGKIYIRIFPDKPVTKKPAETRMGKGKGAVEYWVSVVKPGRVMFEVAGVTEEQAKEAFRLAGHKLPIQTKMVKREVYDEAQ |
| 50S ribosomal protein L17 | L | 116 | Phytophthora Infestans (Strain T30-4) | MRHGKAGRKLNRNSSARVALARAQATALLREGRIQTTLTKAKELRPFVEQLITTAKGGDLHSRRLVAQDIHDKDVVRKVMDEVAPKYAERPGGYTRILRVGTRRGDGVTMALIELV |
| 50S ribosomal protein L18 | M | 114 | Phytophthora Infestans (Strain T30-4) | MATATTIRRKLRTRRKVRTTTAASGRLRLSVYRSSKHIYAQIIDDSRGQTLAAASSAALKSGNKTDTAAAVGKALAAAAAEKGIKQVVFDRGSYKYHGRVKALADAAREGGLDF |
| 50S ribosomal protein L19 | N | 166 | Phytophthora Infestans (Strain T30-4) | MQTHIKINRGELLRGIEQDHTRQLPDFRPGDTVRVDTKVREGNRTRSQAFEGVVIAINGSGSRKSFTVRKISFGEGVERVFPFASPLVNQVTIVERGKVRRAKLYYLRELRGKAARIKSDRSRVMKDAARAQQDKANASASQAAAAQADVTVISAAPEVAPETQGE |
| 50S ribosomal protein L20 | O | 118 | Phytophthora Infestans (Strain T30-4) | MPRAKTGIVRRRRHKKVLKRAKGFWGSRSKQYRNAFQTLLNAATYEYRDRRNKKRDFRRLWIQRINAGARLHGMNYSTFINGLKRANIDLNRKVLADIAAREPEAFKALVDASRNARQ |
| 50S ribosomal protein L21 | P | 100 | Phytophthora Infestans (Strain T30-4) | MFAIIQTGGKQYRVSEGDVIRVESLQGEAGDKVELKALFVGGEQTVFGEDAGKYTVQAEVVEHGRGKKIYIRKYKSGVQYRRRTGHRQNFTAIKILGIQG |
| 50S ribosomal protein L22 | Q | 134 | Phytophthora Infestans (Strain T30-4) | MTAPEQTFRNKKQRKQQVKLRKPGFAVAKYVRMSPRKVRLVVDVIRGKSVQDAEDLLRFIPRSASEPVAKVLNSAKANALHNDEMLEDRLFVKEAYVDAGPTLKRLIPRARGSANIIKKRTSHITIIVAEKGNK |
| 50S ribosomal protein L23 | R | 95 | Phytophthora Infestans (Strain T30-4) | MSHYDILQAPVISEKAYSAMERGVYSFWVSPKATKTEIKDAIQQAFGVRVIGISTMNVPGKRKRVGRFIGQRNDRKKAIVRLAEGQSIEALAGQA |
| 50S ribosomal protein L24 | S | 115 | Phytophthora Infestans (Strain T30-4) | MPRPSAGSHHNDKLHFKKGDTVIVLSGKHKGQTGKVLLALPRDQKVVVEGVNVITKNVKPSMTNPQGGQEQRELALHASKVALVDPETGKATRVRKQIVDGKKVRVAVASGKTID |
| general stress protein CTC | T | 253 | Phytophthora Infestans (Strain T30-4) | MAHTGQTAKSQGDTATMELTAKPRTPKQKLDESMIAAVAYNKENNVSFALDRKAFDRAFRQQSTTGLFDITVEGGETFPALVKAVQMDKRKRAPIHVDFYMVTYGEPVEVSVPVHTTGRSQGEVQGGLVDIVVHNLQIVAPGPRRIPQELVVDVTKMNIGDHITAGDIKLPEGCTLAADPELTVVSVLPPRLTAEELEAEVQAAQVAGLVAAGELSEEAAEAVLEGDASLEEVKAEASEDNAGTDSEDNSDAQ |
| 50S ribosomal protein L27 | U | 91 | Phytophthora Infestans (Strain T30-4) | MAHKKGVGSSKNGRDSNPKYLGVKKFGGEVVKAGNILVRQRGTKFKAGQGVGMGRDHTLFALSDGKVVFINKGKGARFISIEAAQTEVAAD |
| 50S ribosomal protein L29 | W | 67 | Phytophthora Infestans (Strain T30-4) | MKPSEMRNLQATDFAKEIDARKKELMELRFQAAAGQLAQPHRVRQLRREVAQLNTVKAELARKGEQQ |
| 50S ribosomal protein L30 | X | 55 | Phytophthora Infestans (Strain T30-4) | MKIKLVRSVIGRPGNQVKTVQALGLRKIGDSREVSDTPAVRGMVKTVKHLLEVQE |
| 50S ribosomal protein L31 | Y | 73 | Phytophthora Infestans (Strain T30-4) | MQKDLHPKAVPCKIIYQGQVVMETMSTRPEIHVDVWSGVHPFWTGEERFLDTEGRVDKFNKRFGDSYRRGSKK |
| 50S ribosomal protein L32 | Z | 60 | Phytophthora Infestans (Strain T30-4) | MAKHPVPKKKTSKSKRDMRRSHHALTAPNLTECPQCHGKKLSHHICPNCGYYDGRQVLAV |
| 50S ribosomal protein L33 | 1 | 82 | Phytophthora Infestans (Strain T30-4) | MFLLRQALGATFPVPGDQREGCAKESIMAKDGPRIIVKMESSAGTGFYYTTTKNRRNTQAKLELKKYDPVAKKHVVFREKKV |
| 50S ribosomal protein L34 | 2 | 47 | Phytophthora Infestans (Strain T30-4) | MKRTYQPNNRKRAKTHGFRARMKTKSGRNILARRRAKGRHQLTVSDE |
| 50S ribosomal protein L2 | A | 275 | Phytophthora Infestans (Strain T30-4) | MAVKKYRPYTPSRRQMTTADFSGLTKKRPEKALTEALPKTGGRNNRGRITSRFIGGGHKRLYRIIDFKRRDKSGVNAKVAAIEYDPNRSARIALLHYADGEKRYILAPEGLTVGATVNAGPEAEPKLGNALPLRFVPVGAVVHALELVPGKGAQLARSAGTSVQVQGKESDYVIVRLPSGELRRVHSECYATIGAVGNAEHKNIVLGKAGRSRWLGRKPHQRGSAMNPVDHPHGGGEGRTGAGRVPVTPWGKPTKGLKTRRKRKTSDRFIVTRRK |
| 50S ribosomal protein L35 | 3 | 64 | Phytophthora Infestans (Strain T30-4) | MPKMKTHKMAKRRIKITGTGKVMAFKSGKRHQNTGKSGDEIRGKGKGFVLAKAEWARMKLMLPR |
| 50S ribosomal protein L36 | 4 | 36 | Phytophthora Infestans (Strain T30-4) | MKVRSSVKKMCDNCKVVRRHGRVLVICSNVKHKQRQ |
| 50S ribosomal protein L3 | B | 211 | Phytophthora Infestans (Strain T30-4) | MKGILGTKIGMTQIWKNDRAIPVTVVLAGPCPIVQRKTAQTDGYEAVQIGYAPKAERKVNKPMQGHFAKAGVAPTRILREFRGFAPDGDSVNVDIFAEGEKIDATGTSKGKGTQGVMKRWNFAGGPASHGSKKWHRRPGSIGQRKTPGRVYKGKRMAGHMGMERVTVQNLEVVEIRAGENLILVKGAIPGANGGLVVLRSAAKASAAKGGK |
| 50S ribosomal protein L4 | C | 205 | Phytophthora Infestans (Strain T30-4) | MAQINVIGQNGGRTIELPLPEVNSGVLHEVVTWQLASRRRGTASTRTRAQVSKTGRKMYGQKGTGNARHGDRSVPTFVGGGVAFGPKPRSYDYTLPRQVRQLGLAMAIASRQEGGKLVAVDGFDIADAKTKNFISWAKQNGLDGTEKVLLVTDDENTRRAARNVSWVSVLPVAGVNVYDILRHDRLVIDAAALEIVEEEAGEEQQ |
| 50S ribosomal protein L5 | D | 180 | Phytophthora Infestans (Strain T30-4) | MQQLKTKYNDQVRPALMQQFGYSSVMAVPRIEKIVVNEGLGSSKEDSKAIDKAAKELALITLQKPIITKAKKSISNFKLRQGMPVGIKVTLRGERMYVFLEKLINIGLPRIRDFRGINPNAFDGRGNYNLGIKEQLIFPEITYDMVDKTRGMDITIVTTAKTDEEARALLQSMGLPFRKQ |
| 50S ribosomal protein L6 | E | 212 | Phytophthora Infestans (Strain T30-4) | MPQRRRLHHLDLTSAPPRPDLRNKEDNMSRIGKQPIAVPSGVTVNAQDGVFKVKGPKGELTVPYNTELTVRQDGDQLLVERPSDAQKHRALHGLTRTLVANAVKGVSDGYTINLELRGVGFRAKLTGKALEMNIGYSHPVIIEPPAGVTFAVPEPTRIDVSGIDKQLVGQVAANVRKVRKPDAYHGKGVRFVGEQIALKAGKAGATGGKGKK |
| 50S ribosomal protein L9 | F | 146 | Phytophthora Infestans (Strain T30-4) | MQVILLEPSRLGKTGEVVSVKDGYARNWLIPQGLAVSATRTNMKTLEAQLRSIEKRQAQEKAVAEDLASRLNGVAVELSVRAGEGKIYGAVTHQDVANSLDQLGFDVDRRKIDMPKTVKEVGEYDIAYRAHPEVTIPMKLVVHAAK |
| 50S ribosomal protein L11 | G | 144 | Phytophthora Infestans (Strain T30-4) | MKKVAGIVKLQLPAGKATPAPPVGPALGQYGANIMEFTKAFNAQTADKGDAIIPVEITIYADRSFTFITKTPPMSYLIRKAAGIGKGSSTPNKAKVGKLNWDQVLEIAKTKMPDLNAGSVEAAANTVAGTARSMGVTVEGGPNA |
Experimental Data
Method: X-RAY DIFFRACTION
Deposited Date: 2003-01-05 Deposition Author(s): Agmon, I. , Bartels, H. , Bashan, A. , Franceschi, F. , Gat, S. , Harms, J.M. , Schluenzen, F. , Yonath, A. , Zarivach, R.