5BR8
Ambient-temperature crystal structure of 30s ribosomal subunit from thermus thermophilus in complex with paromomycin
PDB DOI: 10.2210/pdb5br8/pdb
Classification: RIBOSOME Organism(s): Thermus Thermophilus , Thermus Thermophilus (Strain Hb8 / Atcc 27634 / Dsm 579)
Deposited: 2015-05-29 Deposition Author(s): Aquila, A. , Bogan, M.J. , Boutet, S. , Brewster, A. , Chatterjee, R. , Dao, E.H. , Demirci, H. , Fuller, F. , Gati, C. , Gul, S. , Hampton, C.Y. , Hayes, B. , Hunter, M.S. , Ibrahim, M. , Junco, E.A. , Kern, J. , Koglin, J.E. , Laksmono, H. , Mengning, L. , Michels-Clark, T. , Puglisi, E.V. , Puglisi, J.D. , Sauter, N.K. , Sierra, R.G. , Soltis, S.M. , Stan, C.A. , Yachandra, V.K. , Yano, J. , Young, I.D. , Zouni, A.
Experimental Data Snapshot
Method: X-RAY DIFFRACTION Resolution: 3.4 Å
Ambient-temperature crystal structure of 30s ribosomal subunit from thermus thermophilus in complex with paromomycin
Aquila, A. , Bogan, M.J. , Boutet, S. , Brewster, A. , Chatterjee, R. , Dao, E.H. , Demirci, H. , Fuller, F. , Gati, C. , Gul, S. , Hampton, C.Y. , Hayes, B. , Hunter, M.S. , Ibrahim, M. , Junco, E.A. , Kern, J. , Koglin, J.E. , Laksmono, H. , Mengning, L. , Michels-Clark, T. , Puglisi, E.V. , Puglisi, J.D. , Sauter, N.K. , Sierra, R.G. , Soltis, S.M. , Stan, C.A. , Yachandra, V.K. , Yano, J. , Young, I.D. , Zouni, A.
Primary Citation of Related Structures: 5BR8
| Nucleic Acids / Hybrid | ||||
|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Sequence |
| 16S ribosomal RNA | a | 1522 | NA | UUUGUUGGAGAGUUUGAUCCUGGCUCAGGGUGAACGCUGGCGGCGUGCCUAAGACAUGCAAGUCGUGCGGGCCGCGGGGUUUUACUCCGUGGUCAGCGGCGGACGGGUGAGUAACGCGUGGGUGACCUACCCGGAAGAGGGGGACAACCCGGGGAAACUCGGGCUAAUCCCCCAUGUGGACCCGCCCCUUGGGGUGUGUCCAAAGGGCUUUGCCCGCUUCCGGAUGGGCCCGCGUCCCAUCAGCUAGUUGGUGGGGUAAUGGCCCACCAAGGCGACGACGGGUAGCCGGUCUGAGAGGAUGGCCGGCCACAGGGGCACUGAGACACGGGCCCCACUCCUACGGGAGGCAGCAGUUAGGAAUCUUCCGCAAUGGGCGCAAGCCUGACGGAGCGACGCCGCUUGGAGGAAGAAGCCCUUCGGGGUGUAAACUCCUGAACCCGGGACGAAACCCCCGACGAGGGGACUGACGGUACCGGGGUAAUAGCGCCGGCCAACUCCGUGCCAGCAGCCGCGGUAAUACGGAGGGCGCGAGCGUUACCCGGAUUCACUGGGCGUAAAGGGCGUGUAGGCGGCCUGGGGCGUCCCAUGUGAAAGACCACGGCUCAACCGUGGGGGAGCGUGGGAUACGCUCAGGCUAGACGGUGGGAGAGGGUGGUGGAAUUCCCGGAGUAGCGGUGAAAUGCGCAGAUACCGGGAGGAACGCCGAUGGCGAAGGCAGCCACCUGGUCCACCCGUGACGCUGAGGCGCGAAAGCGUGGGGAGCAAACCGGAUUAGAUACCCGGGUAGUCCACGCCCUAAACGAUGCGCGCUAGGUCUCUGGGUCUCCUGGGGGCCGAAGCUAACGCGUUAAGCGCGCCGCCUGGGGAGUACGGCCGCAAGGCUGAAACUCAAAGGAAUUGACGGGGGCCCGCACAAGCGGUGGAGCAUGUGGUUUAAUUCGAAGCAACGCGAAGAACCUUACCAGGCCUUGACAUGCUAGGGAACCCGGGUGAAAGCCUGGGGUGCCCCGCGAGGGGAGCCCUAGCACAGGUGCUGCAUGGCCGUCGUCAGCUCGUGCCGUGAGGUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCCCGCCGUUAGUUGCCAGCGGUUCGGCCGGGCACUCUAACGGGACUGCCCGCGAAAGCGGGAGGAAGGAGGGGACGACGUCUGGUCAGCAUGGCCCUUACGGCCUGGGCGACACACGUGCUACAAUGCCCACUACAAAGCGAUGCCACCCGGCAACGGGGAGCUAAUCGCAAAAAGGUGGGCCCAGUUCGGAUUGGGGUCUGCAACCCGACCCCAUGAAGCCGGAAUCGCUAGUAAUCGCGGAUCAGCCAUGCCGCGGUGAAUACGUUCCCGGGCCUUGUACACACCGCCCGUCACGCCAUGGGAGCGGGCUCUACCCGAAGUCGCCGGGAGCCUACGGGCAGGCGCCGAGGGUAGGGCCCGUGACUGGGGCGAAGUCGUAACAAGGUAGCUGUACCGGAAGGUGCGGCUGGAUCCACUCCUUUCU |
| Proteins | ||||
|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Sequence |
| 30S ribosomal protein S10 | J | 105 | Thermus Thermophilus , Thermus Thermophilus (Strain Hb8 / Atcc 27634 / Dsm 579) | MPKIRIKLRGFDHKTLDASAQKIVEAARRSGAQVSGPIPLPTRVRRFTVIRGPFKHKDSREHFELRTHNRLVDIINPNRKTIEQLMTLDLPTGVEIEIKTVGGGR |
| 30S ribosomal protein S11 | K | 129 | Thermus Thermophilus , Thermus Thermophilus (Strain Hb8 / Atcc 27634 / Dsm 579) | MAKKPSKKKVKRQVASGRAYIHASYNNTIVTITDPDGNPITWSSGGVIGYKGSRKGTPYAAQLAALDAAKKAMAYGMQSVDVIVRGTGAGREQAIRALQASGLQVKSIVDDTPVPHNGCRPKKKFRKAS |
| 30S ribosomal protein S12 | L | 135 | Thermus Thermophilus , Thermus Thermophilus (Strain Hb8 / Atcc 27634 / Dsm 579) | MVALPTINQLVRKGREKVRKKSKVPALKGAPFRRGVCTVVRTVTPKKPNSALRKVAKVRLTSGYEVTAYIPGEGHNLQEHSVVLIRGGRVKXLPGVRYHIVRGVYDAAGVKDRKKSRSKYGTKKPKEAAKTAAKK |
| 30S ribosomal protein S13 | M | 126 | Thermus Thermophilus , Thermus Thermophilus (Strain Hb8 / Atcc 27634 / Dsm 579) | MARIAGVEIPRNKRVDVALTYIYGIGKARAKEALEKTGINPATRVKDLTEAEVVRLREYVENTWKLEGELRAEVAANIKRLMDIGCYRGLRHRRGLPVRGQRTRTNARTRKGPRKTVAGKKKAPRK |
| 30S ribosomal protein S14 type Z | N | 61 | Thermus Thermophilus , Thermus Thermophilus (Strain Hb8 / Atcc 27634 / Dsm 579) | MARKALIEKAKRTPKFKVRAYTRCVRCGRARSVYRFFGLCRICLRELAHKGQLPGVRKASW |
| 30S ribosomal protein S15 | O | 89 | Thermus Thermophilus , Thermus Thermophilus (Strain Hb8 / Atcc 27634 / Dsm 579) | MPITKEEKQKVIQEFARFPGDTGSTEVQVALLTLRINRLSEHLKVHKKDHHSHRGLLMMVGQRRRLLRYLQREDPERYRALIEKLGIRG |
| 30S ribosomal protein S16 | P | 88 | Thermus Thermophilus , Thermus Thermophilus (Strain Hb8 / Atcc 27634 / Dsm 579) | MVKIRLARFGSKHNPHYRIVVTDARRKRDGKYIEKIGYYDPRKTTPDWLKVDVERARYWLSVGAQPTDTARRLLRQAGVFRQEAREGA |
| 30S ribosomal protein S17 | Q | 105 | Thermus Thermophilus , Thermus Thermophilus (Strain Hb8 / Atcc 27634 / Dsm 579) | MPKKVLTGVVVSDKMQKTVTVLVERQFPHPLYGKVIKRSKKYLAHDPEEKYKLGDVVEIIESRPISKRKRFRVLRLVESGRMDLVEKYLIRRQNYQSLSKRGGKA |
| 30S ribosomal protein S18 | R | 88 | Thermus Thermophilus , Thermus Thermophilus (Strain Hb8 / Atcc 27634 / Dsm 579) | MSTKNAKPKKEAQRRPSRKAKVKATLGEFDLRDYRNVEVLKRFLSETGKILPRRRTGLSAKEQRILAKTIKRARILGLLPFTEKLVRK |
| 30S ribosomal protein S19 | S | 93 | Thermus Thermophilus , Thermus Thermophilus (Strain Hb8 / Atcc 27634 / Dsm 579) | MPRSLKKGVFVDDHLLEKVLELNAKGEKRLIKTWSRRSTIVPEMVGHTIAVYNGKQHVPVYITENMVGHKLGEFAPTRTYRGHGKEAKATKKK |
| 30S ribosomal protein S2 | B | 256 | Thermus Thermophilus , Thermus Thermophilus (Strain Hb8 / Atcc 27634 / Dsm 579) | MPVEITVKELLEAGVHFGHERKRWNPKFARYIYAERNGIHIIDLQKTMEELERTFRFIEDLAMRGGTILFVGTKKQAQDIVRMEAERAGMPYVNQRWLGGMLTNFKTISQRVHRLEELEALFASPEIEERPKKEQVRLKHELERLQKYLSGFRLLKRLPDAIFVVDPTKEAIAVREARKLFIPVIALADTDSDPDLVDYIIPGNDDAIRSIQLILSRAVDLIIQARGGVVEPSPSYALVQEAEATETPEGESEVEA |
| 30S ribosomal protein S20 | T | 106 | Thermus Thermophilus , Thermus Thermophilus (Strain Hb8 / Atcc 27634 / Dsm 579) | MAQKKPKRNLSALKRHRQSLKRRLRNKAKKSAIKTLSKKAIQLAQEGKAEEALKIMRKAESLIDKAAKGSTLHKNAAARRKSRLMRKVRQLLEAAGAPLIGGGLSA |
| 30S ribosomal protein Thx | U | 27 | Thermus Thermophilus , Thermus Thermophilus (Strain Hb8 / Atcc 27634 / Dsm 579) | MGKGDRRTRRGKIWRGTYGKYRPRKKK |
| 30S ribosomal protein S3 | C | 239 | Thermus Thermophilus , Thermus Thermophilus (Strain Hb8 / Atcc 27634 / Dsm 579) | MGNKIHPIGFRLGITRDWESRWYAGKKQYRHLLLEDQRIRGLLEKELYSAGLARVDIERAADNVAVTVHVAKPGVVIGRGGERIRVLREELAKLTGKNVALNVQEVQNPNLSAPLVAQRVAEQIERRFAVRRAIKQAVQRVMESGAKGAKVIVSGRIGGAEQARTEWAAQGRVPLHTLRANIDYGFALARTTYGVLGVKAYIFLGEVIGGQKPKARPELPKAEERPRRRRPAVRVKKEE |
| 30S ribosomal protein S4 | D | 209 | Thermus Thermophilus , Thermus Thermophilus (Strain Hb8 / Atcc 27634 / Dsm 579) | MGRYIGPVCRLCRREGVKLYLKGERCYSPKCAMERRPYPPGQHGQKRARRPSDYAVRLREKQKLRRIYGISERQFRNLFEEASKKKGVTGSVFLGLLESRLDNVVYRLGFAVSRRQARQLVRHGHITVNGRRVDLPSYRVRPGDEIAVAEKSRNLELIRQNLEAMKGRKVGPWLSLDVEGMKGKFLRLPDREDLALPVNEQLVIEFYSR |
| 30S ribosomal protein S5 | E | 162 | Thermus Thermophilus , Thermus Thermophilus (Strain Hb8 / Atcc 27634 / Dsm 579) | MPETDFEEKMILIRRTARMQAGGRRFRFGALVVVGDRQGRVGLGFGKAPEVPLAVQKAGYYARRNMVEVPLQNGTIPHEIEVEFGASKIVLKPAAPGTGVIAGAVPRAILELAGVTDILTKELGSRNPINIAYATMEALRQLRTKADVERLRKGEAHAQAQG |
| 30S ribosomal protein S6 | F | 101 | Thermus Thermophilus , Thermus Thermophilus (Strain Hb8 / Atcc 27634 / Dsm 579) | MRRYEVNIVLNPNLDQSQLALEKEIIQRALENYGARVEKVEELGLRRLAYPIAKDPQGYFLWYQVEMPEDRVNDLARELRIRDNVRRVMVVKSQEPFLANA |
| 30S ribosomal protein S7 | G | 156 | Thermus Thermophilus , Thermus Thermophilus (Strain Hb8 / Atcc 27634 / Dsm 579) | MARRRRAEVRQLQPDLVYGDVLVTAFINKIMRDGKKNLAARIFYDACKIIQEKTGQEPLKVFKQAVENVKPRMEVRSRRVGGANYQVPMEVSPRRQQSLALRWLVQAANQRPERRAAVRIAHELMDAAEGKGGAVKKKEDVERMAEANRAYAHYRW |
| 30S ribosomal protein S8 | H | 138 | Thermus Thermophilus , Thermus Thermophilus (Strain Hb8 / Atcc 27634 / Dsm 579) | MLTDPIADMLTRIRNATRVYKESTDVPASRFKEEILRILAREGFIKGYERVDVDGKPYLRVYLKYGPRRQGPDPRPEQVIHHIRRISKPGRRVYVGVKEIPRVRRGLGIAILSTSKGVLTDREARKLGVGGELICEVW |
| 30S ribosomal protein S9 | I | 128 | Thermus Thermophilus , Thermus Thermophilus (Strain Hb8 / Atcc 27634 / Dsm 579) | MEQYYGTGRRKEAVARVFLRPGNGKVTVNGQDFNEYFQGLVRAVAALEPLRAVDALGHFDAYITVRGGGKSGQIDAIKLGIARALVQYNPDYRAKLKPLGFLTRDARVVERKKYGKHKARRAPQYSKR |
Experimental Data
Method: X-RAY DIFFRACTION
Deposited Date: 2015-05-29 Deposition Author(s): Aquila, A. , Bogan, M.J. , Boutet, S. , Brewster, A. , Chatterjee, R. , Dao, E.H. , Demirci, H. , Fuller, F. , Gati, C. , Gul, S. , Hampton, C.Y. , Hayes, B. , Hunter, M.S. , Ibrahim, M. , Junco, E.A. , Kern, J. , Koglin, J.E. , Laksmono, H. , Mengning, L. , Michels-Clark, T. , Puglisi, E.V. , Puglisi, J.D. , Sauter, N.K. , Sierra, R.G. , Soltis, S.M. , Stan, C.A. , Yachandra, V.K. , Yano, J. , Young, I.D. , Zouni, A.