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FASTA Sequence PDB Format mmCIF Format
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1YIT

Crystal structure of virginiamycin m and s bound to the 50s ribosomal subunit of haloarcula marismortui

PDB DOI: 10.2210/pdb1yit/pdb

Classification: RIBOSOME/ANTIBIOTIC
Organism(s): Haloarcula Marismortui , Streptomyces Virginiae , Synthetic Construct

Deposited: 2005-01-13
Deposition Author(s): Blaha, G. , Moore, P.B. , Steitz, T.A. , Tu, D.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.8 Å

Literature

Crystal structure of virginiamycin m and s bound to the 50s ribosomal subunit of haloarcula marismortui

Blaha, G. , Moore, P.B. , Steitz, T.A. , Tu, D.

Primary Citation of Related Structures: 1YIT


Nucleic Acids / Hybrid
Molecule Chains Sequence Length Organism Sequence
23S RIBOSOMAL RNA 0 2922 NA GUUGGCUACUAUGCCAGCUGGUGGAUUGCUCGGCUCAGGCGCUGAUGAAGGACGUGCCAAGCUGCGAUAAGCUGUGGGGAGCCGCACGGAGGCGAAGAACCACAGAUUUCCGAAUGAGAAUCUCUCUAACAAUUGCUUCGCGCAAUGAGGAACCCCGAGAACUGAAACAUCUCAGUAUCGGGAGGAACAGAAAACGCAACGUGAUGUCGUUAGUAACCGCGAGUGAACGCGAUACAGCCCAAACCGAAGCCCUCACGGGCAAUGUGGUGUCAGGGCUACCUCUCAUCAGCCGACCGUCUUCACGAAGUCUCUUGGAAUAGAGCGUGAUACAGGGUGACAACCCCGUACUGAAGACCAGUACGCUGUGCGGUAGUGCCAGAGUAGCGGGGGUUGGAUAUCCCUCGCGAAUAACGCAGGCAUCGACUGCGAAGGCUAAACACAACCUGAGACCGAUAGUGAACAAGUAGUGUGAACGAACGCUGCAAAGUACCCUCAGAAGGGAGGCGAAAUAGAGCAUGAAAUCAGUUGGCGAUCGAGCGACAGGGCAUACAAGGUCCCUUGACGAAUGACCGAGACGCGAGUCUCCAGUAAGACUCACGGGAAGCCGAUGUUCUGUCGUACGUUUUGAAAAACGAGCCAGGGAGUGUGUCUGUAUGGCAAGUCUAACCGGAGUAUCCGGGGAGGCACAGGGAAACCGACAUGGCCGCAGGGCUUUGCCCGAGGGCCGCCGUCUUCAAGGGCGGGGAGCCAUGUGGACACGACCCGAAUCCGGACGAUCUACGCAUGGACAAGAUGAAGCGUGCCGAAAGGCACGUGGAAGUCUGUUAGAGUUGGUGUCCUACAAUACCCUCUCGUGAUCUAUGUGUAGGGGUGAAAGGCCCAUCGAGUCCGGCAACAGCUGGUUCCAAUCGAAACAUGUCGAAGCAUGACCUCCGCCGAGGUAGUCUGUGAGGUAGAGCGACCGAUUGGUGUGUCCGCCUCCGAGAGGAGUCGGCACACCUGUCAAACUCCAAACUUACAGACGCUGUUUGACGCGGGGAUUCCGGUGCGCGGGGUAAGCCUGUGUACCAGGAGGGGAACAACCCAGAGAUAGGUUAAGGUCCCCAAGUGUGGAUUAAGUGUAAUCCUCUGAAGGUGGUCUCGAGCCCUAGACAGCCGGGAGGUGAGCUUAGAAGCAGCUACCCUCUAAGAAAAGCGUAACAGCUUACCGGCCGAGGUUUGAGGCGCCCAAAAUGAUCGGGACUCAAAUCCACCACCGAGACCUGUCCGUACCACUCAUACUGGUAAUCGAGUAGAUUGGCGCUCUAAUUGGAUGGAAGCAGGGGCGAGAGCUCCUGUGGACCGAUUAGUGACGAAAAUCCUGGCCAUAGUAGCAGCGAUAGUCGGGUGAGAACCCCGACGGCCUAAUGGAUAAGGGUUCCUCAGCACUGCUGAUCAGCUGAGGGUUAGCCGGUCCUAAGUCUCACCGCAACUCGACUGAGACGAAAUGGGAAACAGGUUAAUAUUCCUGUGCCAUCAUGCAGUGAAAGUUGACGCCCUGGGGUCGAUCACGCCGGGCAUUCGCCCGGUCGAACCGUCCAACUCCGUGGAAGCCGUAAUGGCAGGAAGCGGACGAACGGCGGCAUAGGGAAACGUGAUUCAACCUGGGGCCCAUGAAAAGACGAGCAUGAUGUCCGUACCGAGAACCGACACAGGUGUCCAUGGCGGCGAAAGCCAAGGCCUGUCGGGAGCAACCAACGUUAGGGAAUUCGGCAAGUUAGUCCCGUACCUUCGGAAGAAGGGAUGCCUGCUCCGGAACGGAGCAGGUCGCAGUGACUCGGAAGCUCGGACUGUCUAGUAACAACAUAGGUGACCGCAAAUCCGCAAGGACUCGUACGGUCACUGAAUCCUGCCCAGUGCAGGUAUCUGAACACCUCGUACAAGAGGACGAAGGACCUGUCAACGGCGGGGGUAACUAUGACCCUCUUAAGGUAGCGUAGUACCUUGCCGCAUCAGUAGCGGCUUGCAUGAAUGGAUUAACCAGAGCUUCACUGUCCCAACGUUGGGCCCGGUGAACUGUACAUUCCAGUGCGGAGUCUGGAGACACCCAGGGGGAAGCGAAGACCCUAUGGAGCUUUACUGCAGGCUGUCGCUGAGACGUGGUCGCCGAUGUGCAGCAUAGGUAGGAGUCGUUACAGAGGUACCCGCGCUAGCGGGCCACCCAGACAACAGUGAAAUACUACCCGUCGGUGACUGCGACUCUCACUCCGGGAGGAGGACACCGAUAGCCGGGCAGUUUGACUGGGGCGGUACGCGCUCGAAAAGAUAUCGAGCGCGCCCUAUGGUCAUCUCAGCCGGGACAGAGACCCGGCGAAGAGUGCAAGAGCAAAAGAUGACUUGACAGUGUUCUUCCCAACGAGGAACGCUGACGCGAAAGCGUGGUCUAGCGAACCAAUUAGCCUGCUUGAUGCGGGCAAUUGAUGACAGAAAAGCUACCCUAGGGAUAACAGAGUCGUCACUCGCAAGAGCACAUAUCGACCGAGUGGCUUGCUACCUCGAUGUCGGUUCCCUCCAUCCUGCCCGUGCAGAAGCGGGCAAGGGUGAGGUUGUUCGCCUAUUAAAGGAGGUCGUGAGCUGGGUUUAGACCGUCGUGAGACAGGUCGGCUGCUAUCUACUGGGUGUGUAAUGGUGUCUGACAAGAACGACCGUAUAGUACGAGAGGAACUACGGUUGGUGGCCACUGGUGUACCGGUUGUUCGAGAGAGCACGUGCCGGGUAGCCACGCCACACGGGGUAAGAGCUGAACGCAUCUAAGCUCGAAACCCACUUGGAAAAGAGACACCGCCGAGGUCCCGCGUACAAGACGCGGUCGAUAGACUCGGGGUGUGCGCGUCGAGGUAACGAGACGUUAAGCCCACGAGCACUAACAGACCAAAGCCAUCA
5S RIBOSOMAL RNA 9 122 NA UUAGGCGGCCACAGCGGUGGGGUUGCCUCCCGUACCCAUCCCGAACACGGAAGAUAAGCCCACCAGCGUUCCAGGGAGUACUGGAGUGCGCGAGCCUCUGGGAAAUCCGGUUCGCCGCCACC

Proteins
Molecule Chains Sequence Length Organism Sequence
50S RIBOSOMAL PROTEIN L5P D 177 Haloarcula Marismortui , Streptomyces Virginiae , Synthetic Construct MSSESESGGDFHEMREPRIEKVVVHMGIGHGGRDLANAEDILGEITGQMPVRTKAKRTVGEFDIREGDPIGAKVTLRDEMAEEFLQTALPLAELATSQFDDTGNFSFGVEEHTEFPSQEYDPSIGIYGLDVTVNLVRPGYRVAKRDKASRSIPTKHRLNPADAVAFIESTYDVEVSE
50S RIBOSOMAL PROTEIN L6P E 178 Haloarcula Marismortui , Streptomyces Virginiae , Synthetic Construct MPRVELEIPEDVDAEQDHLDITVEGDNGSVTRRLWYPDIDVSVDGDTVVIESDEDNAKTMSTIGTFQSHIENMFHGVTEGWEYGMEVFYSHFPMQVNVEGDEVVIENFLGEKAPRRTTIHGDTDVEIDGEELTVSGPDIEAVGQTAADIEQLTRINDKDVRVFQDGVYITRKPNRGDA
50S RIBOSOMAL PROTEIN L7AE F 120 Haloarcula Marismortui , Streptomyces Virginiae , Synthetic Construct MPVYVDFDVPADLEDDALEALEVARDTGAVKKGTNETTKSIERGSAELVFVAEDVQPEEIVMHIPELADEKGVPFIFVEQQDDLGHAAGLEVGSAAAAVTDAGEADADVEDIADKVEELR
ACIDIC RIBOSOMAL PROTEIN P0 HOMOLOG G 348 Haloarcula Marismortui , Streptomyces Virginiae , Synthetic Construct MSAESERKTETIPEWKQEEVDAIVEMIESYESVGVVNIAGIPSRQLQDMRRDLHGTAELRVSRNTLLERALDDVDDGLEDLNGYITGQVGLIGTDDNPFSLFQELEASKTPAPIGAGEVAPNDIVIPEGDTGVDPGPFVGELQSVGADARIQEGSIQVLSDSTVLDTGEEVSQELSNVLNELGIEPKEVGLDLRAVFADGVLFEPEELELDIDEYRSDIQAAAGRAFNLSVNADYPTATTAPTMLQSDRGNAKSLALQAAIEDPEVVPDLVSKADAQVRALASQIDDEEALPEELQGVEADVATEEPTDDQDDDTASEDDADADDAAEEADDDDDDDEDAGDALGAMF
50S RIBOSOMAL PROTEIN L10E H 177 Haloarcula Marismortui , Streptomyces Virginiae , Synthetic Construct MSDKPASMYRDIDKPAYTRREYITGIPGSKIAQHKMGRKQKDADDYPVQISLIVEETVQLRHGSLEASRLSANRHLIKELGEEGDYKMTLRKFPHQVLRENKQATGAGADRVSDGMRAAFGKIVGTAARVQAGEQLFTAYCNVEDAEHVKEAFRRAYNKITPSCRIKVERGEELLIA
50S RIBOSOMAL PROTEIN L11P I 162 Haloarcula Marismortui , Streptomyces Virginiae , Synthetic Construct MAGTIEVLVPGGEANPGPPLGPELGPTPVDVQAVVQEINDQTAAFDGTEVPVTVKYDDDGSFEIEVGVPPTAELIKDEAGFETGSGEPQEDFVADLSVDQVKQIAEQKHPDLLSYDLTNAAKEVVGTCTSLGVTIEGENPREFKERIDAGEYDDVFAAEAQA
50S RIBOSOMAL PROTEIN L13P J 145 Haloarcula Marismortui , Streptomyces Virginiae , Synthetic Construct MSVAEFDADVIVDARDCIMGRVASQVAEQALDGETVAVVNAERAVITGREEQIVEKYEKRVDIGNDNGYFYPKRPDGIFKRTIRGMLPHKKQRGREAFESVRVYLGNPYDEDGEVLDGTSLDRLSNIKFVTLGEISETLGANKTW
50S RIBOSOMAL PROTEIN L14P K 132 Haloarcula Marismortui , Streptomyces Virginiae , Synthetic Construct MEALGADVTQGLEKGSLITCADNTGARELKVISVHGYSGTKNRLPKAGLGDKITVSVTKGTPEMRRQVLEAVVVRQRKPIRRPDGTRVKFEDNAAVIVDENEDPRGTELKGPIAREVAQRFGSVASAATMIV
50S RIBOSOMAL PROTEIN L15P L 165 Haloarcula Marismortui , Streptomyces Virginiae , Synthetic Construct MTSKKKRQRGSRTHGGGSHKNRRGAGHRGGRGDAGRDKHEFHNHEPLGKSGFKRPQKVQEEAATIDVREIDENVTLLAADDVAEVEDGGFRVDVRDVVEEADDADYVKVLGAGQVRHELTLIADDFSEGAREKVEGAGGSVELTDLGEERQAEAEETEDADADEE
50S RIBOSOMAL PROTEIN L15E M 195 Haloarcula Marismortui , Streptomyces Virginiae , Synthetic Construct MARSAYSYIRDAWENPGDGQLAELQWQRQQEWRNEGAVERIERPTRLDKARSQGYKAKQGVIVARVSVRKGSARKRRHKAGRRSKRQGVTRITRRKDIQRVAEERASRTFPNLRVLNSYSVGQDGRQKWHEVILIDPNHPAIQNDDDLSWICADDQADRVFRGLTGAGRRNRGLSGKGKGSEKTRPSLRSNGGKG
50S RIBOSOMAL PROTEIN L37E 1 57 Haloarcula Marismortui , Streptomyces Virginiae , Synthetic Construct MTGAGTPSQGKKNTTTHTKCRRCGEKSYHTKKKVCSSCGFGKSAKRRDYEWQSKAGE
50S RIBOSOMAL PROTEIN L18P N 187 Haloarcula Marismortui , Streptomyces Virginiae , Synthetic Construct MATGPRYKVPMRRRREARTDYHQRLRLLKSGKPRLVARKSNKHVRAQLVTLGPNGDDTLASAHSSDLAEYGWEAPTGNMPSAYLTGLLAGLRAQEAGVEEAVLDIGLNSPTPGSKVFAIQEGAIDAGLDIPHNDDVLADWQRTRGAHIAEYDEQLEEPLYSGDFDAADLPEHFDELRETLLDGDIEL
50S RIBOSOMAL PROTEIN L18E O 116 Haloarcula Marismortui , Streptomyces Virginiae , Synthetic Construct MSKTNPRLSSLIADLKSAARSSGGAVWGDVAERLEKPRRTHAEVNLGRIERYAQEDETVVVPGKVLGSGVLQKDVTVAAVDFSGTAETKIDQVGEAVSLEQAIENNPEGSHVRVIR
50S RIBOSOMAL PROTEIN L19E P 149 Haloarcula Marismortui , Streptomyces Virginiae , Synthetic Construct MTDLSAQKRLAADVLDVGKNRVWFNPERQGDIADAITREDVRELVDEGAIQAKDKKGNSRGRARERQKKRAYGHQKGAGSRKGKAGARQNSKEDWESRIRAQRTKLRELRDEGTLSSSQYRDLYDKAGGGEFDSVADLERYIDANHGDA
50S RIBOSOMAL PROTEIN L21E Q 96 Haloarcula Marismortui , Streptomyces Virginiae , Synthetic Construct MPSSNGPLEGTRGKLKNKPRDRGTSPPQRAVEEFDDGEKVHLKIDPSVPNGRFHPRFDGQTGTVEGKQGDAYKVDIVDGGKEKTIIVTAAHLRRQE
50S RIBOSOMAL PROTEIN L22P R 155 Haloarcula Marismortui , Streptomyces Virginiae , Synthetic Construct MGISYSVEADPDTTAKAMLRERQMSFKHSKAIAREIKGKTAGEAVDYLEAVIEGDQPVPFKQHNSGVGHKSKVDGWDAGRYPEKASKAFLDLLENAVGNADHQGFDGEAMTIKHVAAHKVGEQQGRKPRAMGRASAWNSPQVDVELILEEPEVED
50S RIBOSOMAL PROTEIN L23P S 85 Haloarcula Marismortui , Streptomyces Virginiae , Synthetic Construct MSWDVIKHPHVTEKAMNDMDFQNKLQFAVDDRASKGEVADAVEEQYDVTVEQVNTQNTMDGEKKAVVRLSEDDDAQEVASRIGVF
50S RIBOSOMAL PROTEIN L24P T 120 Haloarcula Marismortui , Streptomyces Virginiae , Synthetic Construct MSKQPDKQRKSQRRAPLHERHKQVRATLSADLREEYGQRNVRVNAGDTVEVLRGDFAGEEGEVINVDLDKAVIHVEDVTLEKTDGEEVPRPLDTSNVRVTDLDLEDEKREARLESEDDSA
50S RIBOSOMAL PROTEIN L24E U 66 Haloarcula Marismortui , Streptomyces Virginiae , Synthetic Construct PRTRECDYCGTDIEPGTGTMFVHKDGATTHFCSSKCENNADLGREARNLEWTDTARGEAGEAEDEA
50S RIBOSOMAL PROTEIN L29P V 71 Haloarcula Marismortui , Streptomyces Virginiae , Synthetic Construct MTVLHVQEIRDMTPAEREAELDDLKTELLNARAVQAAGGAPENPGRIKELRKAIARIKTIQGEEGDLQENE
50S RIBOSOMAL PROTEIN L30P W 154 Haloarcula Marismortui , Streptomyces Virginiae , Synthetic Construct MHALVQLRGEVNMHTDIQDTLEMLNIHHVNHCTLVPETDAYRGMVAKVNDFVAFGEPSQETLETVLATRAEPLEGDADVDDEWVAEHTDYDDISGLAFALLSEETTLREQGLSPTLRLHPPRGGHDGVKHPVKEGGQLGKHDTEGIDDLLEAMR
50S RIBOSOMAL PROTEIN L39E 2 50 Haloarcula Marismortui , Streptomyces Virginiae , Synthetic Construct MGKKSKATKKRLAKLDNQNSRVPAWVMLKTDREVQRNHKRRHWRRNDTDE
50S RIBOSOMAL PROTEIN L31E X 92 Haloarcula Marismortui , Streptomyces Virginiae , Synthetic Construct MSASDFEERVVTIPLRDARAEPNHKRADKAMILIREHLAKHFSVDEDAVRLDPSINEAAWARGRANTPSKIRVRAARFEEEGEAIVEAETAE
50S RIBOSOMAL PROTEIN L32E Y 241 Haloarcula Marismortui , Streptomyces Virginiae , Synthetic Construct MADNEEDVEAEEEYTELTDISGVGPSKAESLREAGFESVEDVRGADQSALADVSGIGNALAARIKADVGGLEVESETEAEVEEEGGEEAPDEDVETELQARGLTEKTPDLSDEDARLLTQRHRVGKPQFNRQDHHKKKRVSTSWRKPRGQLSKQRRGIKGKGDTVEAGFRSPTAVRGKHPSGFEEVRVHNVDDLEGVDGDTEAVRIASKVGARKRERIEEEAEDAGIRVLNPTYVEVEVSE
50S RIBOSOMAL PROTEIN L37AE Z 83 Haloarcula Marismortui , Streptomyces Virginiae , Synthetic Construct RSGRFGARYGRVSRRRVAEIESEMNEDHACPNCGEDRVDRQGTGIWQCSYCDYKFTGGSYKPETPGGKTVRRSIRAALSEDEE
50S RIBOSOMAL PROTEIN L44E 3 92 Haloarcula Marismortui , Streptomyces Virginiae , Synthetic Construct MQMPRRFNTYCPHCNEHQEHEVEKVRSGRQTGMKWIDRQRERNSGIGNDGKFSKVPGGDKPTKKTDLKYRCGECGKAHLREGWRAGRLEFQE
VIRGINIAMYCIN S1 8 7 Haloarcula Marismortui , Streptomyces Virginiae , Synthetic Construct XTXPFXX
50S RIBOSOMAL PROTEIN L2P A 240 Haloarcula Marismortui , Streptomyces Virginiae , Synthetic Construct MGRRIQGQRRGRGTSTFRAPSHRYKADLEHRKVEDGDVIAGTVVDIEHDPARSAPVAAVEFEDGDRRLILAPEGVGVGDELQVGVSAEIAPGNTLPLAEIPEGVPVCNVESSPGDGGKFARASGVNAQLLTHDRNVAVVKLPSGEMKRLDPQCRATIGVVAGGGRTDKPFVKAGNKHHKMKARGTKWPNVRGVAMNAVDHPFGGGGRQHPGKPKSISRNAPPGRKVGDIASKRTGRGGNE
50S RIBOSOMAL PROTEIN L3P B 338 Haloarcula Marismortui , Streptomyces Virginiae , Synthetic Construct MPQPSRPRKGSLGFGPRKRSTSETPRFNSWPSDDGQPGVQGFAGYKAGMTHVVLVNDEPNSPREGMEETVPVTVIETPPMRAVALRAYEDTPYGQRPLTEVWTDEFHSELDRTLDVPEDHDPDAAEEQIRDAHEAGDLGDLRLITHTVPDAVPSVPKKKPDVMETRVGGGSVSDRLDHALDIVEDGGEHAMNDIFRAGEYADVAGVTKGKGTQGPVKRWGVQKRKGKHARQGWRRRIGNLGPWNPSRVRSTVPQQGQTGYHQRTELNKRLIDIGEGDEPTVDGGFVNYGEVDGPYTLVKGSVPGPDKRLVRFRPAVRPNDQPRLDPEVRYVSNESNQG
50S RIBOSOMAL PROTEIN L4E C 246 Haloarcula Marismortui , Streptomyces Virginiae , Synthetic Construct MQATIYDLDGNTDGEVDLPDVFETPVRSDLIGKAVRAAQANRKQDYGSDEYAGLRTPAESFGSGRGQAHVPKLDGRARRVPQAVKGRSAHPPKTEKDRSLDLNDKERQLAVRSALAATADADLVADRGHEFDRDEVPVVVSDDFEDLVKTQEVVSLLEALDVHADIDRADETKIKAGQGSARGRKYRRPASILFVTSDEPSTAARNLAGADVATASEVNTEDLAPGGAPGRLTVFTESALAEVAER
Experimental Data

Method: X-RAY DIFFRACTION

Deposited Date: 2005-01-13
Deposition Author(s): Blaha, G. , Moore, P.B. , Steitz, T.A. , Tu, D.