6MPF
Structure of the thermus thermophilus 30s ribosomal subunit complexed with a 2-thiocytidine (s2c32) and inosine (i34) modified anticodon stem loop (asl) of escherichia coli transfer rna arginine 1 (trnaarg1) bound to an mrna with an cgc-codon in the a-site and paromomycin
PDB DOI: 10.2210/pdb6mpf/pdb
Classification: RIBOSOME Organism(s): Thermus Thermophilus (Strain Hb8 / Atcc 27634 / Dsm 579) , Thermus Thermophilus Hb8 (Strain Hb8 / Atcc 27634 / Dsm 579) , Synthetic Construct
Deposited: 2018-10-05 Deposition Author(s): Agris, P.F. , Cantara, W.A. , Demirci, H.
Experimental Data Snapshot
Method: X-RAY DIFFRACTION Resolution: 3.33 Å
Structure of the thermus thermophilus 30s ribosomal subunit complexed with a 2-thiocytidine (s2c32) and inosine (i34) modified anticodon stem loop (asl) of escherichia coli transfer rna arginine 1 (trnaarg1) bound to an mrna with an cgc-codon in the a-site and paromomycin
Agris, P.F. , Cantara, W.A. , Demirci, H.
Primary Citation of Related Structures: 6MPF
| Nucleic Acids / Hybrid | ||||
|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Sequence |
| 16S rRNA | a | 1508 | NA | UGGAGAGUUUGAUCCUGGCUCAGGGUGAACGCUGGCGGCGUGCCUAAGACAUGCAAGUCGUGCGGGCCGCGGGGUUUUACUCCGUGGUCAGCGGCGGACGGGUGAGUAACGCGUGGGUGACCUACCCGGAAGAGGGGGACAACCCGGGGAAACUCGGGCUAAUCCCCCAUGUGGACCCGCCCCUUGGGGUGUGUCCAAAGGGCUUUGCCCGCUUCCGGAUGGGCCCGCGUCCCAUCAGCUAGUUGGUGGGGUAAUGGCCCACCAAGGCGACGACGGGUAGCCGGUCUGAGAGGAUGGCCGGCCACAGGGGCACUGAGACACGGGCCCCACUCCUACGGGAGGCAGCAGUUAGGAAUCUUCCGCAAUGGGCGCAAGCCUGACGGAGCGACGCCGCUUGGAGGAAGAAGCCCUUCGGGGUGUAAACUCCUGAACCCGGGACGAAACCCCCGACGAGGGGACUGACGGUACCGGGGUAAUAGCGCCGGCCAACUCCGUGCCAGCAGCCGCGGUAAUACGGAGGGCGCGAGCGUUACCCGGAUUCACUGGGCGUAAAGGGCGUGUAGGCGGCCUGGGGCGUCCCAUGUGAAAGACCACGGCUCAACCGUGGGGGAGCGUGGGAUACGCUCAGGCUAGACGGUGGGAGAGGGUGGUGGAAUUCCCGGAGUAGCGGUGAAAUGCGCAGAUACCGGGAGGAACGCCGAUGGCGAAGGCAGCCACCUGGUCCACCCGUGACGCUGAGGCGCGAAAGCGUGGGGAGCAAACCGGAUUAGAUACCCGGGUAGUCCACGCCCUAAACGAUGCGCGCUAGGUCUCUGGGUCUCCUGGGGGCCGAAGCUAACGCGUUAAGCGCGCCGCCUGGGGAGUACGGCCGCAAGGCUGAAACUCAAAGGAAUUGACGGGGGCCCGCACAAGCGGUGGAGCAUGUGGUUUAAUUCGAAGCAACGCGAAGAACCUUACCAGGCCUUGACAUGCUAGGGAACCCGGGUGAAAGCCUGGGGUGCCCCGCGAGGGGAGCCCUAGCACAGGUGCUGCAUGGCCGUCGUCAGCUCGUGCCGUGAGGUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCCCGCCGUUAGUUGCCAGCGGUUCGGCCGGGCACUCUAACGGGACUGCCCGCGAAAGCGGGAGGAAGGAGGGGACGACGUCUGGUCAGCAUGGCCCUUACGGCCUGGGCGACACACGUGCUACAAUGCCCACUACAAAGCGAUGCCACCCGGCAACGGGGAGCUAAUCGCAAAAAGGUGGGCCCAGUUCGGAUUGGGGUCUGCAACCCGACCCCAUGAAGCCGGAAUCGCUAGUAAUCGCGGAUCAGCCAUGCCGCGGUGAAUACGUUCCCGGGCCUUGUACACACCGCCCGUCACGCCAUGGGAGCGGGCUCUACCCGAAGUCGCCGGGAGCCUACGGGCAGGCGCCGAGGGUAGGGCCCGUGACUGGGGCGAAGUCGUAACAAGGUAGCUGUACCGGAAGGUGCGGCUGGAUCAC |
| mRNA A-site fragment | w | 4 | NA | CGCA |
| tRNA ASL Escherichia coli Arg1 | x | 11 | NA | GGCUICGAACC |
| Proteins | ||||
|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Sequence |
| 30S ribosomal protein S10 | J | 98 | Thermus Thermophilus (Strain Hb8 / Atcc 27634 / Dsm 579) , Thermus Thermophilus Hb8 (Strain Hb8 / Atcc 27634 / Dsm 579) , Synthetic Construct | KIRIKLRGFDHKTLDASAQKIVEAARRSGAQVSGPIPLPTRVRRFTVIRGPFKHKDSREHFELRTHNRLVDIINPNRKTIEQLMTLDLPTGVEIEIKT |
| 30S ribosomal protein S11 | K | 119 | Thermus Thermophilus (Strain Hb8 / Atcc 27634 / Dsm 579) , Thermus Thermophilus Hb8 (Strain Hb8 / Atcc 27634 / Dsm 579) , Synthetic Construct | KRQVASGRAYIHASYNNTIVTITDPDGNPITWSSGGVIGYKGSRKGTPYAAQLAALDAAKKAMAYGMQSVDVIVRGTGAGREQAIRALQASGLQVKSIVDDTPVPHNGCRPKKKFRKAS |
| 30S ribosomal protein S12 | L | 124 | Thermus Thermophilus (Strain Hb8 / Atcc 27634 / Dsm 579) , Thermus Thermophilus Hb8 (Strain Hb8 / Atcc 27634 / Dsm 579) , Synthetic Construct | PTINQLVRKGREKVRKKSKVPALKGAPFRRGVCTVVRTVTPKKPNSALRKVAKVRLTSGYEVTAYIPGEGHNLQEHSVVLIRGGRVKDLPGVRYHIVRGVYDAAGVKDRKKSRSKYGTKKPKEA |
| 30S ribosomal protein S13 | M | 125 | Thermus Thermophilus (Strain Hb8 / Atcc 27634 / Dsm 579) , Thermus Thermophilus Hb8 (Strain Hb8 / Atcc 27634 / Dsm 579) , Synthetic Construct | ARIAGVEIPRNKRVDVALTYIYGIGKARAKEALEKTGINPATRVKDLTEAEVVRLREYVENTWKLEGELRAEVAANIKRLMDIGCYRGLRHRRGLPVRGQRTRTNARTRKGPRKTVAGKKKAPRK |
| 30S ribosomal protein S14 type Z | N | 60 | Thermus Thermophilus (Strain Hb8 / Atcc 27634 / Dsm 579) , Thermus Thermophilus Hb8 (Strain Hb8 / Atcc 27634 / Dsm 579) , Synthetic Construct | ARKALIEKAKRTPKFKVRAYTRCVRCGRARSVYRFFGLCRICLRELAHKGQLPGVRKASW |
| 30S ribosomal protein S15 | O | 88 | Thermus Thermophilus (Strain Hb8 / Atcc 27634 / Dsm 579) , Thermus Thermophilus Hb8 (Strain Hb8 / Atcc 27634 / Dsm 579) , Synthetic Construct | PITKEEKQKVIQEFARFPGDTGSTEVQVALLTLRINRLSEHLKVHKKDHHSHRGLLMMVGQRRRLLRYLQREDPERYRALIEKLGIRG |
| 30S ribosomal protein S16 | P | 83 | Thermus Thermophilus (Strain Hb8 / Atcc 27634 / Dsm 579) , Thermus Thermophilus Hb8 (Strain Hb8 / Atcc 27634 / Dsm 579) , Synthetic Construct | MVKIRLARFGSKHNPHYRIVVTDARRKRDGKYIEKIGYYDPRKTTPDWLKVDVERARYWLSVGAQPTDTARRLLRQAGVFRQE |
| 30S ribosomal protein S17 | Q | 104 | Thermus Thermophilus (Strain Hb8 / Atcc 27634 / Dsm 579) , Thermus Thermophilus Hb8 (Strain Hb8 / Atcc 27634 / Dsm 579) , Synthetic Construct | PKKVLTGVVVSDKMQKTVTVLVERQFPHPLYGKVIKRSKKYLAHDPEEKYKLGDVVEIIESRPISKRKRFRVLRLVESGRMDLVEKYLIRRQNYESLSKRGGKA |
| 30S ribosomal protein S18 | R | 73 | Thermus Thermophilus (Strain Hb8 / Atcc 27634 / Dsm 579) , Thermus Thermophilus Hb8 (Strain Hb8 / Atcc 27634 / Dsm 579) , Synthetic Construct | PSRKAKVKATLGEFDLRDYRNVEVLKRFLSETGKILPRRRTGLSAKEQRILAKTIKRARILGLLPFTEKLVRK |
| 30S ribosomal protein S19 | S | 80 | Thermus Thermophilus (Strain Hb8 / Atcc 27634 / Dsm 579) , Thermus Thermophilus Hb8 (Strain Hb8 / Atcc 27634 / Dsm 579) , Synthetic Construct | PRSLKKGVFVDDHLLEKVLELNAKGEKRLIKTWSRRSTIVPEMVGHTIAVYNGKQHVPVYITENMVGHKLGEFAPTRTYR |
| 30S ribosomal protein S2 | B | 234 | Thermus Thermophilus (Strain Hb8 / Atcc 27634 / Dsm 579) , Thermus Thermophilus Hb8 (Strain Hb8 / Atcc 27634 / Dsm 579) , Synthetic Construct | VKELLEAGVHFGHERKRWNPKFARYIYAERNGIHIIDLQKTMEELERTFRFIEDLAMRGGTILFVGTKKQAQDIVRMEAERAGMPYVNQRWLGGMLTNFKTISQRVHRLEELEALFASPEIEERPKKEQVRLKHELERLQKYLSGFRLLKRLPDAIFVVDPTKEAIAVREARKLFIPVIALADTDSDPDLVDYIIPGNDDAIRSIQLILSRAVDLIIQARGGVVEPSPSYALVQ |
| 30S ribosomal protein S20 | T | 99 | Thermus Thermophilus (Strain Hb8 / Atcc 27634 / Dsm 579) , Thermus Thermophilus Hb8 (Strain Hb8 / Atcc 27634 / Dsm 579) , Synthetic Construct | RNLSALKRHRQSLKRRLRNKAKKSAIKTLSKKAIQLAQEGKAEEALKIMRKAESLIDKAAKGSTLHKNAAARRKSRLMRKVRQLLEAAGAPLIGGGLSA |
| 30S ribosomal protein Thx | V | 24 | Thermus Thermophilus (Strain Hb8 / Atcc 27634 / Dsm 579) , Thermus Thermophilus Hb8 (Strain Hb8 / Atcc 27634 / Dsm 579) , Synthetic Construct | GKGDRRTRRGKIWRGTYGKYRPRK |
| 30S ribosomal protein S3 | C | 206 | Thermus Thermophilus (Strain Hb8 / Atcc 27634 / Dsm 579) , Thermus Thermophilus Hb8 (Strain Hb8 / Atcc 27634 / Dsm 579) , Synthetic Construct | GNKIHPIGFRLGITRDWESRWYAGKKQYRHLLLEDQRIRGLLEKELYSAGLARVDIERAADNVAVTVHVAKPGVVIGRGGERIRVLREELAKLTGKNVALNVQEVQNPNLSAPLVAQRVAEQIERRFAVRRAIKQAVQRVMESGAKGAKVIVSGRIGGAEQARTEWAAQGRVPLHTLRANIDYGFALARTTYGVLGVKAYIFLGEV |
| 30S ribosomal protein S4 | D | 208 | Thermus Thermophilus (Strain Hb8 / Atcc 27634 / Dsm 579) , Thermus Thermophilus Hb8 (Strain Hb8 / Atcc 27634 / Dsm 579) , Synthetic Construct | GRYIGPVCRLCRREGVKLYLKGERCYSPKCAMERRPYPPGQHGQKRARRPSDYAVRLREKQKLRRIYGISERQFRNLFEEASKKKGVTGSVFLGLLESRLDNVVYRLGFAVSRRQARQLVRHGHITVNGRRVDLPSYRVRPGDEIAVAEKSRNLELIRQNLEAMKGRKVGPWLSLDVEGMKGKFLRLPDREDLALPVNEQLVIEFYSR |
| 30S ribosomal protein S5 | E | 150 | Thermus Thermophilus (Strain Hb8 / Atcc 27634 / Dsm 579) , Thermus Thermophilus Hb8 (Strain Hb8 / Atcc 27634 / Dsm 579) , Synthetic Construct | DFEEKMILIRRTARMQAGGRRFRFGALVVVGDRQGRVGLGFGKAPEVPLAVQKAGYYARRNMVEVPLQNGTIPHEIEVEFGASKIVLKPAAPGTGVIAGAVPRAILELAGVTDILTKELGSRNPINIAYATMEALRQLRTKADVERLRKG |
| 30S ribosomal protein S6 | F | 101 | Thermus Thermophilus (Strain Hb8 / Atcc 27634 / Dsm 579) , Thermus Thermophilus Hb8 (Strain Hb8 / Atcc 27634 / Dsm 579) , Synthetic Construct | MRRYEVNIVLNPNLDQSQLALEKEIIQRALENYGARVEKVEELGLRRLAYPIAKDPQGYFLWYQVEMPEDRVNDLARELRIRDNVRRVMVVKSQEPFLANA |
| 30S ribosomal protein S7 | G | 155 | Thermus Thermophilus (Strain Hb8 / Atcc 27634 / Dsm 579) , Thermus Thermophilus Hb8 (Strain Hb8 / Atcc 27634 / Dsm 579) , Synthetic Construct | ARRRRAEVRQLQPDLVYGDVLVTAFINKIMRDGKKNLAARIFYDACKIIQEKTGQEPLKVFKQAVENVKPRMEVRSRRVGGANYQVPMEVSPRRQQSLALRWLVQAANQRPERRAAVRIAHELMDAAEGKGGAVKKKEDVERMAEANRAYAHYRW |
| 30S ribosomal protein S8 | H | 138 | Thermus Thermophilus (Strain Hb8 / Atcc 27634 / Dsm 579) , Thermus Thermophilus Hb8 (Strain Hb8 / Atcc 27634 / Dsm 579) , Synthetic Construct | MLTDPIADMLTRIRNATRVYKESTDVPASRFKEEILRILAREGFIKGYERVDVDGKPYLRVYLKYGPRRQGPDPRPEQVIHHIRRISKPGRRVYVGVKEIPRVRRGLGIAILSTSKGVLTDREARKLGVGGELICEVW |
| 30S ribosomal protein S9 | I | 127 | Thermus Thermophilus (Strain Hb8 / Atcc 27634 / Dsm 579) , Thermus Thermophilus Hb8 (Strain Hb8 / Atcc 27634 / Dsm 579) , Synthetic Construct | EQYYGTGRRKEAVARVFLRPGNGKVTVNGQDFNEYFQGLVRAVAALEPLRAVDALGHFDAYITVRGGGKSGQIDAIKLGIARALVQYNPDYRAKLKPLGFLTRDARVVERKKYGKHKARRAPQYSKR |
Experimental Data
Method: X-RAY DIFFRACTION
Deposited Date: 2018-10-05 Deposition Author(s): Agris, P.F. , Cantara, W.A. , Demirci, H.