Advanced Search:
9NO7
Cryo-em structure of the wild-type thermus thermophilus 70s ribosome in complex with mrna, a-site q230-n5-methylated release factor 1, and p-site 2'-deoxy-a76-fmeaaakc-peptidyl-trnacys at 2.13a resolution
PDB DOI: 10.2210/pdb9no7/pdb
Classification: RIBOSOME Organism(s): Thermus Thermophilus Hb8
Deposited: 2025-03-08 Deposition Author(s): Aleksandrova, E.V. , Basu, R.S. , Gagnon, M.G. , Polikanov, Y.S. , Syroegin, E.A. , Vassilevski, A.A.
Experimental Data Snapshot
Method: ELECTRON MICROSCOPY Resolution: 2.13 Å
Cryo-em structure of the wild-type thermus thermophilus 70s ribosome in complex with mrna, a-site q230-n5-methylated release factor 1, and p-site 2'-deoxy-a76-fmeaaakc-peptidyl-trnacys at 2.13a resolution
Aleksandrova, E.V. , Basu, R.S. , Gagnon, M.G. , Polikanov, Y.S. , Syroegin, E.A. , Vassilevski, A.A.
Primary Citation of Related Structures: 9NO7
| Nucleic Acids / Hybrid | ||||
|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Sequence |
| 16S Ribosomal RNA | a | 1521 | NA | UUGUUGGAGAGUUUGAUCCUGGCUCAGGGUGAACGCUGGCGGCGUGCCUAAGACAUGCAAGUCGUGCGGGCCGCGGGGUUUUACUCCGUGGUCAGCGGCGGACGGGUGAGUAACGCGUGGGUGACCUACCCGGAAGAGGGGGACAACCCGGGGAAACUCGGGCUAAUCCCCCAUGUGGACCCGCCCCUUGGGGUGUGUCCAAAGGGCUUUGCCCGCUUCCGGAUGGGCCCGCGUCCCAUCAGCUAGUUGGUGGGGUAAUGGCCCACCAAGGCGACGACGGGUAGCCGGUCUGAGAGGAUGGCCGGCCACAGGGGCACUGAGACACGGGCCCCACUCCUACGGGAGGCAGCAGUUAGGAAUCUUCCGCAAUGGGCGCAAGCCUGACGGAGCGACGCCGCUUGGAGGAAGAAGCCCUUCGGGGUGUAAACUCCUGAACCCGGGACGAAACCCCCGACGAGGGGACUGACGGUACCGGGGUAAUAGCGCCGGCCAACUCCGUGCCAGCAGCCGCGGUAAUACGGAGGGCGCGAGCGUUACCCGGAUUCACUGGGCGUAAAGGGCGUGUAGGCGGCCUGGGGCGUCCCAUGUGAAAGACCACGGCUCAACCGUGGGGGAGCGUGGGAUACGCUCAGGCUAGACGGUGGGAGAGGGUGGUGGAAUUCCCGGAGUAGCGGUGAAAUGCGCAGAUACCGGGAGGAACGCCGAUGGCGAAGGCAGCCACCUGGUCCACCCGUGACGCUGAGGCGCGAAAGCGUGGGGAGCAAACCGGAUUAGAUACCCGGGUAGUCCACGCCCUAAACGAUGCGCGCUAGGUCUCUGGGUCUCCUGGGGGCCGAAGCUAACGCGUUAAGCGCGCCGCCUGGGGAGUACGGCCGCAAGGCUGAAACUCAAAGGAAUUGACGGGGGCCCGCACAAGCGGUGGAGCAUGUGGUUUAAUUCGAAGCAACGCGAAGAACCUUACCAGGCCUUGACAUGCUAGGGAACCCGGGUGAAAGCCUGGGGUGCCCCGCGAGGGGAGCCCUAGCACAGGUGCUGCAUGGCCGUCGUCAGCUCGUGCCGUGAGGUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCCCGCCGUUAGUUGCCAGCGGUUCGGCCGGGCACUCUAACGGGACUGCCCGCGAAAGCGGGAGGAAGGAGGGGACGACGUCUGGUCAGCAUGGCCCUUACGGCCUGGGCGACACACGUGCUACAAUGCCCACUACAAAGCGAUGCCACCCGGCAACGGGGAGCUAAUCGCAAAAAGGUGGGCCCAGUUCGGAUUGGGGUCUGCAACCCGACCCCAUGAAGCCGGAAUCGCUAGUAAUCGCGGAUCAGCCAUGCCGCGGUGAAUACGUUCCCGGGCCUUGUACACACCGCCCGUCACGCCAUGGGAGCGGGCUCUACCCGAAGUCGCCGGGAGCCUACGGGCAGGCGCCGAGGGUAGGGCCCGUGACUGGGGCGAAGUCGUAACAAGGUAGCUGUACCGGAAGGUGCGGCUGGAUCACCUCCUUUCU |
| CYS-Stop mRNA | v | 24 | NA | GGCAAGGAGGUAAAAUGCUAAUAA |
| P-site Peptidyl-tRNA fMEAAAKC-tRNAcys RNA-part | x | 74 | NA | GGCGCGUUAACAAAGCGGUUAUGUAGCGGAUUGCAAAUCCGUCUAGUCCGGUUCGACUCCGGAACGCGCCUCCA |
| Proteins | ||||
|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Sequence |
| 30S ribosomal protein S15 | O | 89 | Thermus Thermophilus Hb8 | MPITKEEKQKVIQEFARFPGDTGSTEVQVALLTLRINRLSEHLKVHKKDHHSHRGLLMMVGQRRRLLRYLQREDPERYRALIEKLGIRG |
| 30S ribosomal protein S16 | P | 88 | Thermus Thermophilus Hb8 | MVKIRLARFGSKHNPHYRIVVTDARRKRDGKYIEKIGYYDPRKTTPDWLKVDVERARYWLSVGAQPTDTARRLLRQAGVFRQEAREGA |
| 30S ribosomal protein S17 | Q | 105 | Thermus Thermophilus Hb8 | MPKKVLTGVVVSDKMQKTVTVLVERQFPHPLYGKVIKRSKKYLAHDPEEKYKLGDVVEIIESRPISKRKRFRVLRLVESGRMDLVEKYLIRRQNYESLSKRGGKA |
| 30S ribosomal protein S18 | R | 88 | Thermus Thermophilus Hb8 | MSTKNAKPKKEAQRRPSRKAKVKATLGEFDLRDYRNVEVLKRFLSETGKILPRRRTGLSAKEQRILAKTIKRARILGLLPFTEKLVRK |
| 30S ribosomal protein S19 | S | 93 | Thermus Thermophilus Hb8 | MPRSLKKGVFVDDHLLEKVLELNAKGEKRLIKTWSRRSTIVPEMVGHTIAVYNGKQHVPVYITENMVGHKLGEFAPTRTYRGHGKEAKATKKK |
| 30S ribosomal protein S20 | T | 106 | Thermus Thermophilus Hb8 | MAQKKPKRNLSALKRHRQSLKRRLRNKAKKSAIKTLSKKAIQLAQEGKAEEALKIMRKAESLIDKAAKGSTLHKNAAARRKSRLMRKVRQLLEAAGAPLIGGGLSA |
| 30S ribosomal protein Thx | U | 27 | Thermus Thermophilus Hb8 | MGKGDRRTRRGKIWRGTYGKYRPRKKK |
| Peptide chain release factor 1 | W | 354 | Thermus Thermophilus Hb8 | MLDKLDRLEEEYRELEALLSDPEVLKDKGRYQSLSRRYAEMGEVIGLIREYRKVLEDLEQAESLLDDPELKEMAKAEREALLARKEALEKELERHLLPKDPMDERDAIVEIRAGTGGEEAALFARDLFNMYLRFAEEMGFETEVLDSHPTDLGGFSKVVFEVRGPGAYGTFKYESGVHRVQRVPVTETQGRIHTSTATVAVLPKAEEEDFALNMDEIRIDVMRASGPGGQGVNTTDSAVRVVHLPTGIMVTCQDSRSQIKNREKALMILRSRLLEMKRAEEAERLRKTRLAQIGTGERSEKIRTYNFPQSRVTDHRIGFTTHDLEGVLSGHLTPILEALKRADQERQLAALAEG |
| 30S ribosomal protein S2 | B | 256 | Thermus Thermophilus Hb8 | MPVEITVKELLEAGVHFGHERKRWNPKFARYIYAERNGIHIIDLQKTMEELERTFRFIEDLAMRGGTILFVGTKKQAQDIVRMEAERAGMPYVNQRWLGGMLTNFKTISQRVHRLEELEALFASPEIEERPKKEQVRLKHELERLQKYLSGFRLLKRLPDAIFVVDPTKEAIAVREARKLFIPVIALADTDSDPDLVDYIIPGNDDAIRSIQLILSRAVDLIIQARGGVVEPSPSYALVQEAEATETPEGESEVEA |
| 50S ribosomal protein L24 | Y | 110 | Thermus Thermophilus Hb8 | MRVKMHVKKGDTVLVASGKYKGRVGKVKEVLPKKYAVIVEGVNIVKKAVRVSPKYPQGGFIEKEAPLHASKVRPICPACGKPTRVRKKFLENGKKIRVCAKCGGALDTEE |
| P-site Peptidyl-tRNA fMEAAAKC-tRNAcys Peptide-part | Z | 7 | Thermus Thermophilus Hb8 | MEAAAKC |
| 50S ribosomal protein L27 | 0 | 85 | Thermus Thermophilus Hb8 | MAHKKGLGSTRNGRDSQAKRLGVKRYEGQVVRAGNILVRQRGTRFKPGKNVGMGRDFTLFALVDGVVEFQDRGRLGRYVHVRPLA |
| 50S ribosomal protein L28 | 1 | 98 | Thermus Thermophilus Hb8 | MSKVCEISGKRPIVANSIQRRGKAKREGGVGKKTTGISKRRQYPNLQKVRVRVAGQEITFRVAASHIPKVYELVERAKGLKLEGLSPKEIKKELLKLL |
| 50S ribosomal protein L29 | 2 | 72 | Thermus Thermophilus Hb8 | MKLSEVRKQLEEARKLSPVELEKLVREKKRELMELRFQASIGQLSQNHKIRDLKRQIARLLTVLNEKRRQNA |
| 50S ribosomal protein L30 | 3 | 60 | Thermus Thermophilus Hb8 | MPRLKVKLVKSPIGYPKDQKAALKALGLRRLQQERVLEDTPAIRGNVEKVAHLVRVEVVE |
| 50S ribosomal protein L31 | 4 | 71 | Thermus Thermophilus Hb8 | MKEGIHPKLVPARIICGCGNVIETYSTKPEIYVEVCSKCHPFYTGQQRFVDTEGRVERFQRRYGDSYRKGR |
| 50S ribosomal protein L32 | 5 | 60 | Thermus Thermophilus Hb8 | MAKHPVPKKKTSKARRDARRSHHALTPPTLVPCPECKAMKPPHTVCPECGYYAGRKVLEV |
| 50S ribosomal protein L33 | 6 | 54 | Thermus Thermophilus Hb8 | MASEVRIKLLLECTECKRRNYATEKNKRNTPNKLELRKYCPWCRKHTVHREVKI |
| 50S ribosomal protein L34 | 7 | 49 | Thermus Thermophilus Hb8 | MKRTWQPNRRKRAKTHGFRARMRTPGGRKVLKRRRQKGRWRLTPAVRKR |
| 30S ribosomal protein S4 | D | 209 | Thermus Thermophilus Hb8 | MGRYIGPVCRLCRREGVKLYLKGERCYSPKCAMERRPYPPGQHGQKRARRPSDYAVRLREKQKLRRIYGISERQFRNLFEEASKKKGVTGSVFLGLLESRLDNVVYRLGFAVSRRQARQLVRHGHITVNGRRVDLPSYRVRPGDEIAVAEKSRNLELIRQNLEAMKGRKVGPWLSLDVEGMKGKFLRLPDREDLALPVNEQLVIEFYSR |
| 50S ribosomal protein L35 | 8 | 65 | Thermus Thermophilus Hb8 | MPKMKTHKGAKKRVKITASGKVVAMKTGKRHLNWQKSGKEIRQKGRKFVLAKPEAERIKLLLPYE |
| 50S ribosomal protein L36 | 9 | 37 | Thermus Thermophilus Hb8 | MKVRASVKRICDKCKVIRRHGRVYVICENPKHKQRQG |
| 30S ribosomal protein S3 | C | 239 | Thermus Thermophilus Hb8 | MGNKIHPIGFRLGITRDWESRWYAGKKQYRHLLLEDQRIRGLLEKELYSAGLARVDIERAADNVAVTVHVAKPGVVIGRGGERIRVLREELAKLTGKNVALNVQEVQNPNLSAPLVAQRVAEQIERRFAVRRAIKQAVQRVMESGAKGAKVIVSGRIGGAEQARTEWAAQGRVPLHTLRANIDYGFALARTTYGVLGVKAYIFLGEVIGGQKPKARPELPKAEERPRRRRPAVRVKKEE |
| 50S ribosomal protein L3 | E | 206 | Thermus Thermophilus Hb8 | MKGILGVKVGMTRIFRDDRAVPVTVILAGPCPVVQRRTPEKDGYTAVQLGFLPQNPKRVNRPLKGHFAKAGVEPVRILREIRDFNPEGDTVTVEIFKPGERVDVTGTSKGRGFAGVMKRWNFAGGPDSHGAHKIHRHPGSIGNRKTPGRVYKGKKMAGHYGAERVTVMNLEVVDVIPEENLLLVKGAVPGPNGGLVIVRETKKAAK |
| 50S ribosomal protein L4 | F | 210 | Thermus Thermophilus Hb8 | MKEVAVYQIPVLSPSGRRELAADLPAEINPHLLWEVVRWQLAKRRRGTASTKTRGEVAYSGRKIWPQKHTGRARHGDIGAPIFVGGGVVFGPKPRDYSYTLPKKVRKKGLAMAVADRAREGKLLLVEAFAGVNGKTKEFLAWAKEAGLDGSESVLLVTGNELVRRAARNLPWVVTLAPEGLNVYDIVRTERLVMDLDAWEVFQNRIGGEA |
| 50S ribosomal protein L5 | G | 182 | Thermus Thermophilus Hb8 | MPLDVALKRKYYEEVRPELIRRFGYQNVWEVPRLEKVVINQGLGEAKEDARILEKAAQELALITGQKPAVTRAKKSISNFKLRKGMPIGLRVTLRRDRMWIFLEKLLNVALPRIRDFRGLNPNSFDGRGNYNLGLREQLIFPEITYDMVDALRGMDIAVVTTAETDEEARALLELLGFPFRK |
| 50S ribosomal protein L6 | H | 180 | Thermus Thermophilus Hb8 | MSRIGRLPIPVPKGVSVEVAPGRVKVKGPKGELEVPVSPEMRVVVEEGVVRVERPSDERRHKSLHGLTRTLIANAVKGVSEGYSKELLIKGIGYRARLVGRALELTVGFSHPVVVEPPEGITFEVPEPTRVRVSGIDKQKVGQVAANIRAIRKPSAYHEKGIYYAGEPVRLKPGKAGAKK |
| 50S ribosomal protein L9 | I | 148 | Thermus Thermophilus Hb8 | MKVILLEPLENLGDVGQVVDVKPGYARNYLLPRGLAVLATESNLKALEARIRAQAKRLAERKAEAERLKEILENLTLTIPVRAGETKIYGSVTAKDIAEALSRQHGVTIDPKRLALEKPIKELGEYVLTYKPHPEVPIQLKVSVVAQE |
| 30S ribosomal protein S10 | J | 105 | Thermus Thermophilus Hb8 | MPKIRIKLRGFDHKTLDASAQKIVEAARRSGAQVSGPIPLPTRVRRFTVIRGPFKHKDSREHFELRTHNRLVDIINPNRKTIEQLMTLDLPTGVEIEIKTVGGGR |
| 30S ribosomal protein S11 | K | 129 | Thermus Thermophilus Hb8 | MAKKPSKKKVKRQVASGRAYIHASYNNTIVTITDPDGNPITWSSGGVIGYKGSRKGTPYAAQLAALDAAKKAMAYGMQSVDVIVRGTGAGREQAIRALQASGLQVKSIVDDTPVPHNGCRPKKKFRKAS |
| 30S ribosomal protein S12 | L | 132 | Thermus Thermophilus Hb8 | MPTINQLVRKGREKVRKKSKVPALKGAPFRRGVCTVVRTVTPKKPNSALRKVAKVRLTSGYEVTAYIPGEGHNLQEHSVVLIRGGRVKXLPGVRYHIVRGVYDAAGVKDRKKSRSKYGTKKPKEAAKTAAKK |
| 30S ribosomal protein S13 | M | 126 | Thermus Thermophilus Hb8 | MARIAGVEIPRNKRVDVALTYIYGIGKARAKEALEKTGINPATRVKDLTEAEVVRLREYVENTWKLEGELRAEVAANIKRLMDIGCYRGLRHRRGLPVRGQRTRTNARTRKGPRKTVAGKKKAPRK |
| 50S ribosomal protein L13 | N | 140 | Thermus Thermophilus Hb8 | MKTYVPKQVEPRWVLIDAEGKTLGRLATKIATLLRGKHRPDWTPNVAMGDFVVVVNADKIRVTGKKLEQKIYTRYSGYPGGLKKIPLEKMLATHPERVLEHAVKGMLPKGPLGRRLFKRLKVYAGPDHPHQAQRPEKLEV |
Experimental Data
Method: ELECTRON MICROSCOPY
Deposited Date: 2025-03-08 Deposition Author(s): Aleksandrova, E.V. , Basu, R.S. , Gagnon, M.G. , Polikanov, Y.S. , Syroegin, E.A. , Vassilevski, A.A.