NDB ID: RR0201 PDB ID: 3CF5 
NAKB(beta): RR0201
Title:
THIOPEPTIDE ANTIBIOTIC THIOSTREPTON BOUND TO THE LARGE RIBOSOMAL SUBUNIT OF DEINOCOCCUS RADIODURANS
Molecular Description:
50S RIBOSOMAL PROTEIN L33
50S RIBOSOMAL PROTEIN L34
50S RIBOSOMAL PROTEIN L35
50S RIBOSOMAL PROTEIN L36
THIOSTREPTON
50S RIBOSOMAL PROTEIN L2
50S RIBOSOMAL PROTEIN L4
50S RIBOSOMAL PROTEIN L5
50S RIBOSOMAL PROTEIN L6
50S RIBOSOMAL PROTEIN L11
50S RIBOSOMAL PROTEIN L13
50S RIBOSOMAL PROTEIN L14
50S RIBOSOMAL PROTEIN L15
50S RIBOSOMAL PROTEIN L16
50S RIBOSOMAL PROTEIN L17
50S RIBOSOMAL PROTEIN L18
50S RIBOSOMAL PROTEIN L19
50S RIBOSOMAL PROTEIN L20
50S RIBOSOMAL PROTEIN L21
50S RIBOSOMAL PROTEIN L22
50S RIBOSOMAL PROTEIN L23
50S RIBOSOMAL PROTEIN L24
50S RIBOSOMAL PROTEIN L25
50S RIBOSOMAL PROTEIN L27
50S RIBOSOMAL PROTEIN L28
50S RIBOSOMAL PROTEIN L29
50S RIBOSOMAL PROTEIN L30
50S RIBOSOMAL PROTEIN L32
Deposited:
2008-03-02
Released:
2008-06-17
Structural Keywords:
SINGLE STRAND, LOOPS, HAIRPIN LOOPS
Nucleic Acid Sequence:
Click to show/hide 2 nucleic acid sequences
Chain X
GGUCAAGAUAGUAAGGGUCCACGGUGGAUGCCCUGGCGCUGGAGCCGAUGAAGGACGCGAUUACCUGCGAAAAGCCCCGA CGAGCUGGA
GAUACGCUUUGACUCGGGGAUGUCCGAAUGGGGAAACCCACCUCGUAAGAGGUAUCCGCAAGGAUGGGAAC UCAGGGAACUGAAACAUC
UCAGUACCUGAAGGAGAAGAAAGAGAAUUCGAUUCCGUUAGUAGCGGCGAGCGAACCCGGAU CAGCCCAAACCGAAACGCUUGCGUUUC
GGGGUUGUAGGACCAGUUUUUAAGAUUCAACCCCUCAAGCCGAAGUGGCUGGA AAGCUACACCUCAGAAGGUGAGAGUCCUGUAGGCGA
ACGAGCGGUUGACUGUACUGGCACCUGAGUAGGUCGUUGUUCGU GAAACGAUGACUGAAUCCGCGCGGACCACCGCGCAAGGCUAAAUA
CUCCCAGUGACCGAUAGCGCAUAGUACCGUGAGGG AAAGGUGAAAAGAACCCCGGGAGGGGAGUGAAAGAGAACCUGAAACCGUGGACU
UACAAGCAGUCAUGGCACCUUAUGCG UGUUAUGGCGUGCCUAUUGAAGCAUGAGCCGGCGACUUAGACCUGACGUGCGAGCUUAAGUUG
AAAAACGGAGGCGGAGC GAAAGCGAGUCCGAAUAGGGCGGCAUUAGUACGUCGGGCUAGACUCGAAACCAGGUGAGCUAAGCAUGACCA
GGUUGAAA CCCCCGUGACAGGGGGCGGAGGACCGAACCGGUGCCUGCUGAAACAGUCUCGGAUGAGUUGUGUUUAGGAGUGAAAAGCU
AACCGAACCUGGAGAUAGCUAGUUCUCCCCGAAAUGUAUUGAGGUACAGCCUCGGAUGUUGACCAUGUCCUGUAGAGCAC UCACAAGGC
UAGGGGGCCUACCAGCUUACCAAACCUUAUGAAACUCCGAAGGGGCACGCGUUUAGUCCGGGAGUGAGGCU GCGAGAGCUAACUUCCGU
AGCCGAGAGGGAAACAACCCAGACCAUCAGCUAAGGUCCCUAAAUGAUCGCUCAGUGGUUAA GGAUGUGUCGUCGCAUAGACAGCCAGG
AGGUUGGCUUAGAAGCAGCCACCCUUCAAAGAGUGCGUAAUAGCUCACUGGUC GAGUGACGAUGCGCCGAAAAUGAUCGGGGCUCAAGU
GAUCUACCGAAGCUAUGGAUUCAACUCGCGAAGCGAGUUGUCUG GUAGGGGAGCGUUCAGUCCGCGGAGAAGCCAUACCGGAAGGAGUG
GUGGAGCCGACUGAAGUGCGGAUGCCGGCAUGAGU AACGAUAAAAGAAGUGAGAAUCUUCUUCGCCGUAAGGACAAGGGUUCCUGGGGA
AGGGUCGUCCGCCCAGGGAAAGUCGG GACCUAAGGUGAGGCCGAACGGCGCAGCCGAUGGACAGCAGGUCAAGAUUCCUGCACCGAUCA
UGUGGAGUGAUGGAGGG ACGCAUUACGCUAUCCAAUGCCAAGCUAUGGCUAUGCUGGUUGGUACGCUCAAGGGCGAUCGGGUCAGAAAA
UCUACCGG UCACAUGCCUCAGACGUAUCGGGAGCUUCCUCGGAAGCGAAGUUGGAAACGCGACGGUGCCAAGAAAAGCUUCUAAACGU
UGAAACAUGAUUGCCCGUACCGCAAACCGACACAGGUGUCCGAGUGUCAAUGCACUAAGGCGCGCGAGAGAACCCUCGUU AAGGAACUU
UGCAAUCUCACCCCGUAACUUCGGAAGAAGGGGUCCCCACGCUUCGCGUGGGGCGCAGUGAAUAGGCCCAG GCGACUGUUUACCAAAAU
CACAGCACUCUGCCAACACGAACAGUGGACGUAUAGGGUGUGACGCCUGCCCGGUGCCGGAA GGUCAAGUGGAGCGGUGCAAGCUGCGA
AAUGAAGCCCCGGUGAACGGCGGCCGUAACUAUAACGGUCCUAAGGUAGCGAA AUUCCUUGUCGGGUAAGUUCCGACCUGCACGAAAGG
CGUAACGAUCUGGGCGCUGUCUCAACGAGGGACUCGGUGAAAUU GAAUUGGCUGUAAAGAUGCGGCCUACCCGUAGCAGGACGAAAAGA
CCCCGUGGAGCUUUACUAUAGUCUGGCAUUGGGAU UCGGGUUUCUCUGCGUAGGAUAGGUGGGAGCCUGCGAAACUGGCCUUUUGGGGU
CGGUGGAGGCAACGGUGAAAUACCAC CCUGAGAAACUUGGAUUUCUAACCUGAAAAAUCACUUUCGGGGACCGUGCUUGGCGGGUAGUU
UGACUGGGGCGGUCGCC UCCCAAAAUGUAACGGAGGCGCCCAAAGGUCACCUCAAGACGGUUGGAAAUCGUCUGUAGAGCGCAAAGGUA
GAAGGUGG CUUGACUGCGAGACUGACACGUCGAGCAGGGAGGAAACUCGGGCUUAGUGAACCGGUGGUACCGUGUGGAAGGGCCAUCG
AUCAACGGAUAAAAGUUACCCCGGGGAUAACAGGCUGAUCUCCCCCGAGAGUCCAUAUCGGCGGGGAGGUUUGGCACCUC GAUGUCGGC
UCGUCGCAUCCUGGGGCUGAAGAAGGUCCCAAGGGUUGGGCUGUUCGCCCAUUAAAGCGGCACGCGAGCUG GGUUCAGAACGUCGUGAG
ACAGUUCGGUCUCUAUCCGCUACGGGCGCAGGAGAAUUGAGGGGAGUUGCUCCUAGUACGAG AGGACCGGAGUGAACGGACCGCUGGUC
UCCCUGCUGUCGUACCAACGGCACAUGCAGGGUAGCUAUGUCCGGAACGGAUA ACCGCUGAAAGCAUCUAAGCGGGAAGCCAGCCCCAA
GAUGAGUUCUCCCACUGUUUAUCAGGUAAGACUCCCGGAAGACC ACCGGGUUAAGAGGCCAGGCGUGCACGCAUAGCAAUGUGUUCAGC
GGACUGGUGCUCAUCAGUCGAGGUCUUGACCACUC
Chain Z
ACACCCCCGUGCCCAUAGCACUGUGGAACCACCCCACCCCAUGCCGAACUGGGUCGUGAAACACAGCAGCGCCAAUGAUA CUCGGACCG
CAGGGUCCCGGAAAAGUCGGUCAGCGCGGGGGUU
Protein Sequence:
Click to show/hide 29 protein sequences
Chain S
MELTAKPRTPKQKLDESMIAAVAYNKENNVSFALDRKAFDRAFRQQSTTGLFDITVEGGETFPALVKAVQMDKRKRAPIH VDFYMVTYG
EPVEVSVPVHTTGRSQGEVQGGLVDIVVHNLQIVAPGPRRIPQELVVDVTKMNIGDHITAGDIKLPEGCTL AADPELTVVSVLPPRLTA
EELEAEVQAAQVAGLVAAGELSEEAAEAVLEGDASLEEVKAEASEDNAGTDSEDNSDAQ
Chain T
MAHKKGVGSSKNGRDSNPKYLGVKKFGGEVVKAGNILVRQRGTKFKAGQGVGMGRDHTLFALSDGKVVFINKGKGARFIS IEAAQTEVA
AD
Chain U
MSRECYLTGKKNLVVNSVIRRGKARADGGVGRKTTGITKRVQRANLHKKAIRENGQVKTVWLSANALRTLSKGPYKGIEL I
Chain V
MKPSEMRNLQATDFAKEIDARKKELMELRFQAAAGQLAQPHRVRQLRREVAQLNTVKAELARKGEQQ
Chain O
MFAIIQTGGKQYRVSEGDVIRVESLQGEAGDKVELKALFVGGEQTVFGEDAGKYTVQAEVVEHGRGKKIYIRKYKSGVQY RRRTGHRQN
FTAIKILGIQG
Chain P
MTAPEQTFRNKKQRKQQVKLRKPGFAVAKYVRMSPRKVRLVVDVIRGKSVQDAEDLLRFIPRSASEPVAKVLNSAKANAL HNDEMLEDR
LFVKEAYVDAGPTLKRLIPRARGSANIIKKRTSHITIIVAEKGNK
Chain Q
MSHYDILQAPVISEKAYSAMERGVYSFWVSPKATKTEIKDAIQQAFGVRVIGISTMNVPGKRKRVGRFIGQRNDRKKAIV RLAEGQSIE
ALAGQA
Chain R
MPRPSAGSHHNDKLHFKKGDTVIVLSGKHKGQTGKVLLALPRDQKVVVEGVNVITKNVKPSMTNPQGGQEQRELALHASK VALVDPETG
KATRVRKQIVDGKKVRVAVASGKTID
Chain W
MKIKLVRSVIGRPGNQVKTVQALGLRKIGDSREVSDTPAVRGMVKTVKHLLEVQE
Chain 1
MAKDGPRIIVKMESSAGTGFYYTTTKNRRNTQAKLELKKYDPVAKKHVVFREKKV
Chain 3
MPKMKTHKMAKRRIKITGTGKVMAFKSGKRHQNTGKSGDEIRGKGKGFVLAKAEWARMKLMLPRGK
Chain 2
MKRTYQPNNRKRAKTHGFRARMKTKSGRNILARRRAKGRHQLTVSDE
Chain 5
(QUA)IA(DHA)AS(BB9)T(DBU)(DCY)(TS9)(BB9)T(BB9)(MH6)(BB9)(DHA)(DHA)(NH2)
Chain 4
MKVRSSVKKMCDNCKVVRRHGRVLVICSNVKHKQRQG
Chain B
MKGILGTKIGMTQIWKNDRAIPVTVVLAGPCPIVQRKTAQTDGYEAVQIGYAPKAERKVNKPMQGHFAKAGVAPTRILRE FRGFAPDGD
SVNVDIFAEGEKIDATGTSKGKGTQGVMKRWNFAGGPASHGSKKWHRRPGSIGQRKTPGRVYKGKRMAGHM GMERVTVQNLEVVEIRAG
ENLILVKGAIPGANGGLVVLRSAAKASAAKGGK
Chain A
AVKKYRPYTPSRRQMTTADFSGLTKKRPEKALTEALPKTGGRNNRGRITSRFIGGGHKRLYRIIDFKRRDKSGVNAKVAA IEYDPNRSA
RIALLHYADGEKRYILAPEGLTVGATVNAGPEAEPKLGNALPLRFVPVGAVVHALELVPGKGAQLARSAGT SVQVQGKESDYVIVRLPS
GELRRVHSECYATIGAVGNAEHKNIVLGKAGRSRWLGRKPHQRGSAMNPVDHPHGGGEGRTG AGRVPVTPWGKPTKGLKTRRKRKTSDR
FIVTRRK
Chain D
MQQLKTKYNDQVRPALMQQFGYSSVMAVPRIEKIVVNEGLGSSKEDSKAIDKAAKELALITLQKPIITKAKKSISNFKLR QGMPVGIKV
TLRGERMYVFLEKLINIGLPRIRDFRGINPNAFDGRGNYNLGIKEQLIFPEITYDMVDKTRGMDITIVTTA KTDEEARALLQSMGLPFR
KQ
Chain C
MAQINVIGQNGGRTIELPLPEVNSGVLHEVVTWQLASRRRGTASTRTRAQVSKTGRKMYGQKGTGNARHGDRSVPTFVGG GVAFGPKPR
SYDYTLPRQVRQLGLAMAIASRQEGGKLVAVDGFDIADAKTKNFISWAKQNGLDGTEKVLLVTDDENTRRA ARNVSWVSVLPVAGVNVY
DILRHDRLVIDAAALEIVEEEAGEEQQ
Chain F
MKKVAGIVKLQLPAGKATPAPPVGPALGQYGANIMEFTKAFNAQTADKGDAIIPVEITIYADRSFTFITKTPPMSYLIRK AAGIGKGSS
TPNKAKVGKLNWDQVLEIAKTKMPDLNAGSVEAAANTVAGTARSMGVTVEGGPNA
Chain E
MSRIGKQPIAVPSGVTVNAQDGVFKVKGPKGELTVPYNTELTVRQDGDQLLVERPSDAQKHRALHGLTRTLVANAVKGVS DGYTINLEL
RGVGFRAKLTGKALEMNIGYSHPVIIEPPAGVTFAVPEPTRIDVSGIDKQLVGQVAANVRKVRKPDAYHGK GVRFVGEQIALKAGKAGA
TGGKGKK
Chain H
MIMPQSRLDVADNSGAREIMCIRVLNSGIGGKGLTTGGGGNKRYAHVGDIIVASVKDAAPRGAVKAGDVVKAVVVRTSHA IKRADGSTI
RFDRNAAVIINNQGEPRGTRVFGPVARELRDRRFMKIVSLAPEVL
Chain G
MAFPDTDVSPPRGGPSSPAKSPLLRSFKVKTYIPKNDEQNWVVVDASGVPLGRLATLIASRIRGKHRPDFTPNMIQGDFV VVINAAQVA
LTGKKLDDKVYTRYTGYQGGLKTETAREALSKHPERVIEHAVFGMLPKGRQGRAMHTRLKVYAGETHPHSA QKPQVLKTQPLEVK
Chain J
MMLLPKRTKFRKQFRGRMTGDAKGGDYVAFGDYGLIAMEPAWIKSNQIEACRIVMSRHFRRGGKIYIRIFPDKPVTKKPA ETRMGKGKG
AVEYWVSVVKPGRVMFEVAGVTEEQAKEAFRLAGHKLPIQTKMVKREVYDEAQ
Chain I
MKLHDLKPTPGSRKDRKRVGRGPGGTDKTAGRGHKGQKSRSGAGKGAFFEGGRSRLIARLPKRGFNNVGTTYEVVKLSQL QDLEDTTFD
RDTLEAYRLVRRKNRPVKLLASGEISRAVTVHVDAASAAAIKAVEAAGGRVVLPEVQTQQDDAQKAE
Chain L
MATATTIRRKLRTRRKVRTTTAASGRLRLSVYRSSKHIYAQIIDDSRGQTLAAASSAALKSGNKTDTAAAVGKALAAAAA EKGIKQVVF
DRGSYKYHGRVKALADAAREGGLDF
Chain K
MRHGKAGRKLNRNSSARVALARAQATALLREGRIQTTLTKAKELRPFVEQLITTAKGGDLHSRRLVAQDIHDKDVVRKVM DEVAPKYAE
RPGGYTRILRVGTRRGDGVTMALIELV
Chain N
MPRAKTGIVRRRRHKKVLKRAKGFWGSRSKQYRNAFQTLLNAATYEYRDRRNKKRDFRRLWIQRINAGARLHGMNYSTFI NGLKRANID
LNRKVLADIAAREPEAFKALVDASRNARQ
Chain M
MQTHIKINRGELLRGIEQDHTRQLPDFRPGDTVRVDTKVREGNRTRSQAFEGVVIAINGSGSRKSFTVRKISFGEGVERV FPFASPLVN
QVTIVERGKVRRAKLYYLRELRGKAARIKSDRSRVMKDAARAQQDKANASASQAAAAQADVTVISAAPEVA PETQGE
Chain Y
MAKHPVPKKKTSKSKRDMRRSHHALTAPNLTECPQCHGKKLSHHICPNCGYYDGRQVLAV
Primary Citation:
Harms, J.M., Wilson, D.N., Schluenzen, F., Connell, S.R., Stachelhaus, T., Zaborowska, Z., Spahn, C.M., Fucini, P.
Translational Regulation Via L11: Molecular Switches on the Ribosome Turned on and Off by Thiostrepton and Micrococcin.
Mol.Cell, 30, pp. 26 - , 2008.
Experimental Information:
X-RAY DIFFRACTION
Space Group:
I 2 2 2
Cell Constants:
a = 169.9 b = 408.9 c = 694.5 (Ångstroms)
α = 90.0 β = 90.0 γ = 90.0 (degrees)
Refinement:
The structure was refined using the CNS program.
The R value is 0.276 for 342617 reflections in
the resolution range 30.0 to 3.3 Ångstroms
with Fobs > 2.0 sigma(Fobs) and with I > 0.0 sigma(I)
