4B3R
Crystal structure of the 30s ribosome in complex with compound 30
PDB DOI: 10.2210/pdb4b3r/pdb
Classification: RIBOSOME Organism(s): Saccharopolyspora Erythraea (Strain Atcc 11635 / Dsm 40517 / Jcm 4748 / Nbrc 13426 / Ncimb 8594 / Nrrl 2338)
Deposited: 2012-07-26 Deposition Author(s): Akbergenov, R. , Bottger, E.C. , Boukari, H. , Duscha, S. , Freihofer, P. , Kudyba, I. , Lang, K. , Matt, T. , Meyer, M. , Nandurikar, R.S. , Ng, C.L. , Patak, R. , Perez-Fernandez, D. , Ramakrishnan, V. , Reddy, M.S.K. , Shcherbakov, D. , Vasella, A.
Experimental Data Snapshot
Method: X-RAY DIFFRACTION Resolution: 3 Å
Crystal structure of the 30s ribosome in complex with compound 30
Akbergenov, R. , Bottger, E.C. , Boukari, H. , Duscha, S. , Freihofer, P. , Kudyba, I. , Lang, K. , Matt, T. , Meyer, M. , Nandurikar, R.S. , Ng, C.L. , Patak, R. , Perez-Fernandez, D. , Ramakrishnan, V. , Reddy, M.S.K. , Shcherbakov, D. , Vasella, A.
Primary Citation of Related Structures: 4B3R
| Nucleic Acids / Hybrid | ||||
|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Sequence |
| 16S RIBOSOMAL RNA | a | 1521 | NA | UUGUUGGAGAGUUUGAUCCUGGCUCAGGGUGAACGCUGGCGGCGUGCCUAAGACAUGCAAGUCGUGCGGGCCGCGGGGUUUUACUCCGUGGUCAGCGGCGGACGGGUGAGUAACGCGUGGGUGACCUACCCGGAAGAGGGGGACAACCCGGGGAAACUCGGGCUAAUCCCCCAUGUGGACCCGCCCCUUGGGGUGUGUCCAAAGGGCUUUGCCCGCUUCCGGAUGGGCCCGCGUCCCAUCAGCUAGUUGGUGGGGUAAUGGCCCACCAAGGCGACGACGGGUAGCCGGUCUGAGAGGAUGGCCGGCCACAGGGGCACUGAGACACGGGCCCCACUCCUACGGGAGGCAGCAGUUAGGAAUCUUCCGCAAUGGGCGCAAGCCUGACGGAGCGACGCCGCUUGGAGGAAGAAGCCCUUCGGGGUGUAAACUCCUGAACCCGGGACGAAACCCCCGACGAGGGGACUGACGGUACCGGGGUAAUAGCGCCGGCCAACUCCGUGCCAGCAGCCGCGGUAAUACGGAGGGCGCGAGCGUUACCCGGAUUCACUGGGCGUAAAGGGCGUGUAGGCGGCCUGGGGCGUCCCAUGUGAAAGACCACGGCUCAACCGUGGGGGAGCGUGGGAUACGCUCAGGCUAGACGGUGGGAGAGGGUGGUGGAAUUCCCGGAGUAGCGGUGAAAUGCGCAGAUACCGGGAGGAACGCCGAUGGCGAAGGCAGCCACCUGGUCCACCCGUGACGCUGAGGCGCGAAAGCGUGGGGAGCAAACCGGAUUAGAUACCCGGGUAGUCCACGCCCUAAACGAUGCGCGCUAGGUCUCUGGGUCUCCUGGGGGCCGAAGCUAACGCGUUAAGCGCGCCGCCUGGGGAGUACGGCCGCAAGGCUGAAACUCAAAGGAAUUGACGGGGGCCCGCACAAGCGGUGGAGCAUGUGGUUUAAUUCGAAGCAACGCGAAGAACCUUACCAGGCCUUGACAUGCUAGGGAACCCGGGUGAAAGCCUGGGGUGCCCCGCGAGGGGAGCCCUAGCACAGGUGCUGCAUGGCCGUCGUCAGCUCGUGCCGUGAGGUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCCCGCCGUUAGUUGCCAGCGGUUCGGCCGGGCACUCUAACGGGACUGCCCGCGAAAGCGGGAGGAAGGAGGGGACGACGUCUGGUCAGCAUGGCCCUUACGGCCUGGGCGACACACGUGCUACAAUGCCCACUACAAAGCGAUGCCACCCGGCAACGGGGAGCUAAUCGCAAAAAGGUGGGCCCAGUUCGGAUUGGGGUCUGCAACCCGACCCCAUGAAGCCGGAAUCGCUAGUAAUCGCGGAUCAGCCAUGCCGCGGUGAAUACGUUCCCGGGCCUUGUACACACCGCCCGUCACGCCAUGGGAGCGGGCUCUACCCGAAGUCGCCGGGAGCCUACGGGCAGGCGCCGAGGGUAGGGCCCGUGACUGGGGCGAAGUCGUAACAAGGUAGCUGUACCGGAAGGUGCGGCUGGAUCACCUCCUUUCU |
| 5'-R(*UP*UP*CP*AP*AP*AP)-3' | w | 6 | NA | UUCAAA |
| 5'-R(*GP*GP*GP*AP*UP*UP*GP*AP*AP*AP*AP*UP*CP*CP*CP-3' | z | 16 | NA | GGGGAUUGAAAAUCCC |
| Proteins | ||||
|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Sequence |
| 30S RIBOSOMAL PROTEIN S10 | J | 104 | Saccharopolyspora Erythraea (Strain Atcc 11635 / Dsm 40517 / Jcm 4748 / Nbrc 13426 / Ncimb 8594 / Nrrl 2338) | PKIRIKLRGFDHKTLDASAQKIVEAARRSGAQVSGPIPLPTRVRRFTVIRGPFKHKDSREHFELRTHNRLVDIINPNRKTIEQLMTLDLPTGVEIEIKTVGGGR |
| 30S RIBOSOMAL PROTEIN S11 | K | 129 | Saccharopolyspora Erythraea (Strain Atcc 11635 / Dsm 40517 / Jcm 4748 / Nbrc 13426 / Ncimb 8594 / Nrrl 2338) | MAKKPSKKKVKRQVASGRAYIHASYNNTIVTITDPDGNPITWSSGGVIGYKGSRKGTPYAAQLAALDAAKKAMAYGMQSVDVIVRGTGAGREQAIRALQASGLQVKSIVDDTPVPHNGCRPKKKFRKAS |
| 30S RIBOSOMAL PROTEIN S12 | L | 132 | Saccharopolyspora Erythraea (Strain Atcc 11635 / Dsm 40517 / Jcm 4748 / Nbrc 13426 / Ncimb 8594 / Nrrl 2338) | MPTINQLVRKGREKVRKKSKVPALKGAPFRRGVCTVVRTVTPKKPNSALRKVAKVRLTSGYEVTAYIPGEGHNLQEHSVVLIRGGRVKDLPGVRYHIVRGVYDAAGVKDRKKSRSKYGTKKPKEAAKTAAKK |
| 30S RIBOSOMAL PROTEIN S13 | M | 126 | Saccharopolyspora Erythraea (Strain Atcc 11635 / Dsm 40517 / Jcm 4748 / Nbrc 13426 / Ncimb 8594 / Nrrl 2338) | MARIAGVEIPRNKRVDVALTYIYGIGKARAKEALEKTGINPATRVKDLTEAEVVRLREYVENTWKLEGELRAEVAANIKRLMDIGCYRGLRHRRGLPVRGQRTRTNARTRKGPRKTVAGKKKAPRK |
| 30S RIBOSOMAL PROTEIN S14 TYPE Z | N | 60 | Saccharopolyspora Erythraea (Strain Atcc 11635 / Dsm 40517 / Jcm 4748 / Nbrc 13426 / Ncimb 8594 / Nrrl 2338) | ARKALIEKAKRTPKFKVRAYTRCVRCGRARSVYRFFGLCRICLRELAHKGQLPGVRKASW |
| 30S RIBOSOMAL PROTEIN S15 | O | 88 | Saccharopolyspora Erythraea (Strain Atcc 11635 / Dsm 40517 / Jcm 4748 / Nbrc 13426 / Ncimb 8594 / Nrrl 2338) | PITKEEKQKVIQEFARFPGDTGSTEVQVALLTLRINRLSEHLKVHKKDHHSHRGLLMMVGQRRRLLRYLQREDPERYRALIEKLGIRG |
| 30S RIBOSOMAL PROTEIN S16 | P | 88 | Saccharopolyspora Erythraea (Strain Atcc 11635 / Dsm 40517 / Jcm 4748 / Nbrc 13426 / Ncimb 8594 / Nrrl 2338) | MVKIRLARFGSKHNPHYRIVVTDARRKRDGKYIEKIGYYDPRKTTPDWLKVDVERARYWLSVGAQPTDTARRLLRQAGVFRQEAREGA |
| 30S RIBOSOMAL PROTEIN S17 | Q | 104 | Saccharopolyspora Erythraea (Strain Atcc 11635 / Dsm 40517 / Jcm 4748 / Nbrc 13426 / Ncimb 8594 / Nrrl 2338) | PKKVLTGVVVSDKMQKTVTVLVERQFPHPLYGKVIKRSKKYLAHDPEEKYKLGDVVEIIESRPISKRKRFRVLRLVESGRMDLVEKYLIRRQNYQSLSKRGGKA |
| 30S RIBOSOMAL PROTEIN S18 | R | 88 | Saccharopolyspora Erythraea (Strain Atcc 11635 / Dsm 40517 / Jcm 4748 / Nbrc 13426 / Ncimb 8594 / Nrrl 2338) | MSTKNAKPKKEAQRRPSRKAKVKATLGEFDLRDYRNVEVLKRFLSETGKILPRRRTGLSGKEQRILAKTIKRARILGLLPFTEKLVRK |
| 30S RIBOSOMAL PROTEIN S19 | S | 92 | Saccharopolyspora Erythraea (Strain Atcc 11635 / Dsm 40517 / Jcm 4748 / Nbrc 13426 / Ncimb 8594 / Nrrl 2338) | PRSLKKGVFVDDHLLEKVLELNAKGEKRLIKTWSRRSTIVPEMVGHTIAVYNGKQHVPVYITENMVGHKLGEFAPTRTYRGHGKEAKATKKK |
| 30S RIBOSOMAL PROTEIN S2 | B | 256 | Saccharopolyspora Erythraea (Strain Atcc 11635 / Dsm 40517 / Jcm 4748 / Nbrc 13426 / Ncimb 8594 / Nrrl 2338) | MPVEITVKELLEAGVHFGHERKRWNPKFARYIYAERNGIHIIDLQKTMEELERTFRFIEDLAMRGGTILFVGTKKQAQDIVRMEAERAGMPYVNQRWLGGMLTNFKTISQRVHRLEELEALFASPEIEERPKKEQVRLKHELERLQKYLSGFRLLKRLPDAIFVVDPTKEAIAVREARKLFIPVIALADTDSDPDLVDYIIPGNDDAIRSIQLILSRAVDLIIQARGGVVEPSPSYALVQEAEATETPEGESEVEA |
| 30S RIBOSOMAL PROTEIN S20 | T | 106 | Saccharopolyspora Erythraea (Strain Atcc 11635 / Dsm 40517 / Jcm 4748 / Nbrc 13426 / Ncimb 8594 / Nrrl 2338) | MAQKKPKRNLSALKRHRQSLKRRLRNKAKKSAIKTLSKKAVQLAQEGKAEEALKIMRKAESLIDKAAKGSTLHKNAAARRKSRLMRKVRQLLEAAGAPLIGGGLSA |
| 30S RIBOSOMAL PROTEIN THX | V | 26 | Saccharopolyspora Erythraea (Strain Atcc 11635 / Dsm 40517 / Jcm 4748 / Nbrc 13426 / Ncimb 8594 / Nrrl 2338) | GKGDRRTRRGKIWRGTYGKYRPRKKK |
| 30S RIBOSOMAL PROTEIN S3 | C | 239 | Saccharopolyspora Erythraea (Strain Atcc 11635 / Dsm 40517 / Jcm 4748 / Nbrc 13426 / Ncimb 8594 / Nrrl 2338) | MGNKIHPIGFRLGITRDWESRWYAGKKQYRHLLLEDQRIRGLLEKELYSAGLARVDIERAADNVAVTVHVAKPGVVIGRGGERIRVLREELAKLTGKNVALNVQEVQNPNLSAPLVAQRVAEQIERRFAVRRAIKQAVQRVMESGAKGAKVIVSGRIGGAEQARTEWAAQGRVPLHTLRANIDYGFALARTTYGVLGVKAYIFLGEVIGGQKPKARPELPKAEERPRRRRPAVRVKKEE |
| 30S RIBOSOMAL PROTEIN S4 | D | 208 | Saccharopolyspora Erythraea (Strain Atcc 11635 / Dsm 40517 / Jcm 4748 / Nbrc 13426 / Ncimb 8594 / Nrrl 2338) | GRYIGPVCRLCRREGVKLYLKGERCYSPKCAMERRPYPPGQHGQKRARRPSDYAVRLREKQKLRRIYGISERQFRNLFEEASKKKGVTGSVFLGLLESRLDNVVYRLGFAVSRRQARQLVRHGHITVNGRRVDLPSYRVRPGDEIAVAEKSRNLELIRQNLEAMKGRKVGPWLSLDVEGMKGKFLRLPDREDLALPVNEQLVIEFYSR |
| 30S RIBOSOMAL PROTEIN S5 | E | 161 | Saccharopolyspora Erythraea (Strain Atcc 11635 / Dsm 40517 / Jcm 4748 / Nbrc 13426 / Ncimb 8594 / Nrrl 2338) | PETDFEEKMILIRRTARMQAGGRRFRFGALVVVGDRQGRVGLGFGKAPEVPLAVQKAGYYARRNMVEVPLQNGTIPHEIEVEFGASKIVLKPAAPGTGVIAGAVPRAILELAGVTDILTKELGSRNPINIAYATMEALRQLRTKADVERLRKGEAHAQAQG |
| 30S RIBOSOMAL PROTEIN S6 | F | 101 | Saccharopolyspora Erythraea (Strain Atcc 11635 / Dsm 40517 / Jcm 4748 / Nbrc 13426 / Ncimb 8594 / Nrrl 2338) | MRRYEVNIVLNPNLDQSQLALEKEIIQRALENYGARVEKVEELGLRRLAYPIAKDPQGYFLWYQVEMPEDRVNDLARELRIRDNVRRVMVVKSQEPFLANA |
| 30S RIBOSOMAL PROTEIN S7 | G | 155 | Saccharopolyspora Erythraea (Strain Atcc 11635 / Dsm 40517 / Jcm 4748 / Nbrc 13426 / Ncimb 8594 / Nrrl 2338) | ARRRRAEVRQLQPDLVYGDVLVTAFINKIMRDGKKNLAARIFYDACKIIQEKTGQEPLKVFKQAVENVKPRMEVRSRRVGGANYQVPMEVSPRRQQSLALRWLVQAANQRPERRAAVRIAHELMDAAEGKGGAVKKKEDVERMAEANRAYAHYRW |
| 30S RIBOSOMAL PROTEIN S8 | H | 138 | Saccharopolyspora Erythraea (Strain Atcc 11635 / Dsm 40517 / Jcm 4748 / Nbrc 13426 / Ncimb 8594 / Nrrl 2338) | MLTDPIADMLTRIRNATRVYKESTDVPASRFKEEILRILAREGFIKGYERVDVDGKPYLRVYLKYGPRRQGPDPRPEQVIHHIRRISKPGRRVYVGVKEIPRVRRGLGIAILSTSKGVLTDREARKLGVGGELICEVW |
| 30S RIBOSOMAL PROTEIN S9 | I | 128 | Saccharopolyspora Erythraea (Strain Atcc 11635 / Dsm 40517 / Jcm 4748 / Nbrc 13426 / Ncimb 8594 / Nrrl 2338) | MEQYYGTGRRKEAVARVFLRPGNGKVTVNGQDFNEYFQGLVRAVAALEPLRAVDALGRFDAYITVRGGGKSGQIDAIKLGIARALVQYNPDYRAKLKPLGFLTRDARVVERKKYGKHKARRAPQYSKR |
Experimental Data
Method: X-RAY DIFFRACTION
Deposited Date: 2012-07-26 Deposition Author(s): Akbergenov, R. , Bottger, E.C. , Boukari, H. , Duscha, S. , Freihofer, P. , Kudyba, I. , Lang, K. , Matt, T. , Meyer, M. , Nandurikar, R.S. , Ng, C.L. , Patak, R. , Perez-Fernandez, D. , Ramakrishnan, V. , Reddy, M.S.K. , Shcherbakov, D. , Vasella, A.