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5UQ7

70s ribosome complex with dnax mrna stemloop and e-site trna (""in"" conformation)

PDB DOI: 10.2210/pdb5uq7/pdb

Classification: RIBOSOME
Organism(s): Sphingobium Sp. (Strain Nbrc 103272 / Syk-6) , Haementeria Ghilianii , Rhodobacter Sphaeroides (Strain Atcc 17023 / Dsm 158 / Jcm 6121 / Nbrc 12203 / Ncimb 8253 / Ath 2.4.1.)

Deposited: 2017-02-07
Deposition Author(s): Dunham, C.M. , Hong, S. , Skiniotis, G. , Zhang, Y.

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.5 Å

5uq7
Literature

70s ribosome complex with dnax mrna stemloop and e-site trna (""in"" conformation)

Dunham, C.M. , Hong, S. , Skiniotis, G. , Zhang, Y.

Primary Citation of Related Structures: 5UQ7


Nucleic Acids / Hybrid
Molecule Chains Sequence Length Organism Sequence
16S rRNA a 1521 NA UUGUUGGAGAGUUUGAUCCUGGCUCAGGGUGAACGCUGGCGGCGUGCCUAAGACAUGCAAGUCGUGCGGGCCGCGGGGUUUUACUCCGUGGUCAGCGGCGGACGGGUGAGUAACGCGUGGGUGACCUACCCGGAAGAGGGGGACAACCCGGGGAAACUCGGGCUAAUCCCCCAUGUGGACCCGCCCCUUGGGGUGUGUCCAAAGGGCUUUGCCCGCUUCCGGAUGGGCCCGCGUCCCAUCAGCUAGUUGGUGGGGUAAUGGCCCACCAAGGCGACGACGGGUAGCCGGUCUGAGAGGAUGGCCGGCCACAGGGGCACUGAGACACGGGCCCCACUCCUACGGGAGGCAGCAGUUAGGAAUCUUCCGCAAUGGGCGCAAGCCUGACGGAGCGACGCCGCUUGGAGGAAGAAGCCCUUCGGGGUGUAAACUCCUGAACCCGGGACGAAACCCCCGACGAGGGGACUGACGGUACCGGGGUAAUAGCGCCGGCCAACUCCGUGCCAGCAGCCGCGGUAAUACGGAGGGCGCGAGCGUUACCCGGAUUCACUGGGCGUAAAGGGCGUGUAGGCGGCCUGGGGCGUCCCAUGUGAAAGACCACGGCUCAACCGUGGGGGAGCGUGGGAUACGCUCAGGCUAGACGGUGGGAGAGGGUGGUGGAAUUCCCGGAGUAGCGGUGAAAUGCGCAGAUACCGGGAGGAACGCCGAUGGCGAAGGCAGCCACCUGGUCCACCCGUGACGCUGAGGCGCGAAAGCGUGGGGAGCAAACCGGAUUAGAUACCCGGGUAGUCCACGCCCUAAACGAUGCGCGCUAGGUCUCUGGGUCUCCUGGGGGCCGAAGCUAACGCGUUAAGCGCGCCGCCUGGGGAGUACGGCCGCAAGGCUGAAACUCAAAGGAAUUGACGGGGGCCCGCACAAGCGGUGGAGCAUGUGGUUUAAUUCGAAGCAACGCGAAGAACCUUACCAGGCCUUGACAUGCUAGGGAACCCGGGUGAAAGCCUGGGGUGCCCCGCGAGGGGAGCCCUAGCACAGGUGCUGCAUGGCCGUCGUCAGCUCGUGCCGUGAGGUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCCCGCCGUUAGUUGCCAGCGGUUCGGCCGGGCACUCUAACGGGACUGCCCGCGAAAGCGGGAGGAAGGAGGGGACGACGUCUGGUCAGCAUGGCCCUUACGGCCUGGGCGACACACGUGCUACAAUGCCCACUACAAAGCGAUGCCACCCGGCAACGGGGAGCUAAUCGCAAAAAGGUGGGCCCAGUUCGGAUUGGGGUCUGCAACCCGACCCCAUGAAGCCGGAAUCGCUAGUAAUCGCGGAUCAGCCAUGCCGCGGUGAAUACGUUCCCGGGCCUUGUACACACCGCCCGUCACGCCAUGGGAGCGGGCUCUACCCGAAGUCGCCGGGAGCCUACGGGCAGGCGCCGAGGGUAGGGCCCGUGACUGGGGCGAAGUCGUAACAAGGUAGCUGUACCGGAAGGUGCGGCUGGAUCACCUCCUUGCU
messenger RNA x 55 NA UAAGGAAAUAAAAAUGUUUAGUGAACCGGCAGCCGCUACCCGCGCGCGGCCGGUA
P-site tRNA fMet y 77 NA CGCGGGGUGGAGCAGCCCGGUAGCUCGUCGGGCUCAUAACCCGAAGGUCGUCGGUUCAAAUCCGGCCCCCGCAACCA
E-site tRNA Phe z 76 NA GCCCGGAUAGCUCAGUCGGUAGAGCAGGGGAUUGAAAAUCCCCGUGUCCUUGGUUCGAUUCCGAGUCCGGGCACCA

Proteins
Molecule Chains Sequence Length Organism Sequence
30S ribosomal protein S15 O 88 Sphingobium Sp. (Strain Nbrc 103272 / Syk-6) , Haementeria Ghilianii , Rhodobacter Sphaeroides (Strain Atcc 17023 / Dsm 158 / Jcm 6121 / Nbrc 12203 / Ncimb 8253 / Ath 2.4.1.) PITKEEKQKVIQEFARFPGDTGSTEVQVALLTLRINRLSEHLKVHKKDHHSHRGLLMMVGQRRRLLRYLQREDPERYRALIEKLGIRG
30S ribosomal protein S16 P 82 Sphingobium Sp. (Strain Nbrc 103272 / Syk-6) , Haementeria Ghilianii , Rhodobacter Sphaeroides (Strain Atcc 17023 / Dsm 158 / Jcm 6121 / Nbrc 12203 / Ncimb 8253 / Ath 2.4.1.) MVKIRLARFGSKHNPHYRIVVTDARRKRDGKYIEKIGYYDPRKTTPDWLKVDVERARYWLSVGAQPTDTARRLLRQAGVFRQ
30S ribosomal protein S17 Q 99 Sphingobium Sp. (Strain Nbrc 103272 / Syk-6) , Haementeria Ghilianii , Rhodobacter Sphaeroides (Strain Atcc 17023 / Dsm 158 / Jcm 6121 / Nbrc 12203 / Ncimb 8253 / Ath 2.4.1.) PKKVLTGVVVSDKMQKTVTVLVERQFPHPLYGKVIKRSKKYLAHDPEEKYKLGDVVEIIESRPISKRKRFRVLRLVESGRMDLVEKYLIRRQNYESLSK
30S ribosomal protein S18 R 68 Sphingobium Sp. (Strain Nbrc 103272 / Syk-6) , Haementeria Ghilianii , Rhodobacter Sphaeroides (Strain Atcc 17023 / Dsm 158 / Jcm 6121 / Nbrc 12203 / Ncimb 8253 / Ath 2.4.1.) AKVKATLGEFDLRDYRNVEVLKRFLSETGKILPRRRTGLSAKEQRILAKTIKRARILGLLPFTEKLVR
30S ribosomal protein S19 S 83 Sphingobium Sp. (Strain Nbrc 103272 / Syk-6) , Haementeria Ghilianii , Rhodobacter Sphaeroides (Strain Atcc 17023 / Dsm 158 / Jcm 6121 / Nbrc 12203 / Ncimb 8253 / Ath 2.4.1.) PRSLKKGVFVDDHLLEKVLELNAKGEKRLIKTWSRRSTIVPEMVGHTIAVYNGKQHVPVYITENMVGHKLGEFAPTRTYRGHG
30S ribosomal protein S20 T 98 Sphingobium Sp. (Strain Nbrc 103272 / Syk-6) , Haementeria Ghilianii , Rhodobacter Sphaeroides (Strain Atcc 17023 / Dsm 158 / Jcm 6121 / Nbrc 12203 / Ncimb 8253 / Ath 2.4.1.) PKRNLSALKRHRQSLKRRLRNKAKKSAIKTLSKKAIQLAQEGKAEEALKIMRKAESLIDKAAKGSTLHKNAAARRKSRLMRKVRQLLEAAGAPLIGGG
30S ribosomal protein Thx U 23 Sphingobium Sp. (Strain Nbrc 103272 / Syk-6) , Haementeria Ghilianii , Rhodobacter Sphaeroides (Strain Atcc 17023 / Dsm 158 / Jcm 6121 / Nbrc 12203 / Ncimb 8253 / Ath 2.4.1.) GKGDRRTRRGKIWRGTYGKYRPR
50S ribosomal protein L21 V 101 Sphingobium Sp. (Strain Nbrc 103272 / Syk-6) , Haementeria Ghilianii , Rhodobacter Sphaeroides (Strain Atcc 17023 / Dsm 158 / Jcm 6121 / Nbrc 12203 / Ncimb 8253 / Ath 2.4.1.) MFAIVKTGGKQYRVEPGLKLRVEKLDAEPGATVELPVLLLGGEKTVVGTPVVEGASVVAEVLGHGRGKKILVSKFKAKVQYRRKKGHRQPYTELLIKEIRG
50S ribosomal protein L22 W 112 Sphingobium Sp. (Strain Nbrc 103272 / Syk-6) , Haementeria Ghilianii , Rhodobacter Sphaeroides (Strain Atcc 17023 / Dsm 158 / Jcm 6121 / Nbrc 12203 / Ncimb 8253 / Ath 2.4.1.) MEAKAIARYVRISPRKVRLVVDLIRGKSLEEARNILRYTNKRGAYFVAKVLESAAANAVNNHDMLEDRLYVKAAYVDEGPALKRVLPRARGRADIIKKRTSHITVILGEKHG
30S ribosomal protein S2 B 231 Sphingobium Sp. (Strain Nbrc 103272 / Syk-6) , Haementeria Ghilianii , Rhodobacter Sphaeroides (Strain Atcc 17023 / Dsm 158 / Jcm 6121 / Nbrc 12203 / Ncimb 8253 / Ath 2.4.1.) VKELLEAGVHFGHERKRWNPKFARYIYAERNGIHIIDLQKTMEELERTFRFIEDLAMRGGTILFVGTKKQAQDIVRMEAERAGMPYVNQRWLGGMLTNFKTISQRVHRLEELEALFASPEIEERPKKEQVRLKHELERLQKYLSGFRLLKRLPDAIFVVDPTKEAIAVREARKLFIPVIALADTDSDPDLVDYIIPGNDDAIRSIQLILSRAVDLIIQARGGVVEPSPSYA
50S ribosomal protein L27 0 77 Sphingobium Sp. (Strain Nbrc 103272 / Syk-6) , Haementeria Ghilianii , Rhodobacter Sphaeroides (Strain Atcc 17023 / Dsm 158 / Jcm 6121 / Nbrc 12203 / Ncimb 8253 / Ath 2.4.1.) GSTRNGRDSQAKRLGVKRYEGQVVRAGNILVRQRGTRFKPGKNVGMGRDFTLFALVDGVVEFQDRGRLGRYVHVRPL
50S ribosomal protein L28 1 97 Sphingobium Sp. (Strain Nbrc 103272 / Syk-6) , Haementeria Ghilianii , Rhodobacter Sphaeroides (Strain Atcc 17023 / Dsm 158 / Jcm 6121 / Nbrc 12203 / Ncimb 8253 / Ath 2.4.1.) SKVCEISGKRPIVANSIQRRGKAKREGGVGKKTTGISKRRQYPNLQKVRVRVAGQEITFRVAASHIPKVYELVERAKGLKLEGLSPKEIKKELLKLL
50S ribosomal protein L29 2 70 Sphingobium Sp. (Strain Nbrc 103272 / Syk-6) , Haementeria Ghilianii , Rhodobacter Sphaeroides (Strain Atcc 17023 / Dsm 158 / Jcm 6121 / Nbrc 12203 / Ncimb 8253 / Ath 2.4.1.) MKLSEVRKQLEEARKLSPVELEKLVREKKRELMELRFQASIGQLSQNHKIRDLKRQIARLLTVLNEKRRQ
50S ribosomal protein L30 3 59 Sphingobium Sp. (Strain Nbrc 103272 / Syk-6) , Haementeria Ghilianii , Rhodobacter Sphaeroides (Strain Atcc 17023 / Dsm 158 / Jcm 6121 / Nbrc 12203 / Ncimb 8253 / Ath 2.4.1.) PRLKVKLVKSPIGYPKDQKAALKALGLRRLQQERVLEDTPAIRGNVEKVAHLVRVEVVE
50S ribosomal protein L31 4 69 Sphingobium Sp. (Strain Nbrc 103272 / Syk-6) , Haementeria Ghilianii , Rhodobacter Sphaeroides (Strain Atcc 17023 / Dsm 158 / Jcm 6121 / Nbrc 12203 / Ncimb 8253 / Ath 2.4.1.) MKEGIHPKLVPARIICGCGNVIETYSTKPEIYVEVCSKCHPFYTGQQRFVDTEGRVERFQRRYGDSYRK
50S ribosomal protein L32 5 59 Sphingobium Sp. (Strain Nbrc 103272 / Syk-6) , Haementeria Ghilianii , Rhodobacter Sphaeroides (Strain Atcc 17023 / Dsm 158 / Jcm 6121 / Nbrc 12203 / Ncimb 8253 / Ath 2.4.1.) AKHPVPKKKTSKARRDARRSHHALTPPTLVPCPECKAMKPPHTVCPECGYYAGRKVLEV
50S ribosomal protein L33 6 53 Sphingobium Sp. (Strain Nbrc 103272 / Syk-6) , Haementeria Ghilianii , Rhodobacter Sphaeroides (Strain Atcc 17023 / Dsm 158 / Jcm 6121 / Nbrc 12203 / Ncimb 8253 / Ath 2.4.1.) ASEVRIKLLLECTECKRRNYATEKNKRNTPNKLELRKYCPWCRKHTVHREVKI
50S ribosomal protein L34 7 48 Sphingobium Sp. (Strain Nbrc 103272 / Syk-6) , Haementeria Ghilianii , Rhodobacter Sphaeroides (Strain Atcc 17023 / Dsm 158 / Jcm 6121 / Nbrc 12203 / Ncimb 8253 / Ath 2.4.1.) MKRTWQPNRRKRAKTHGFRARMRTPGGRKVLKRRRQKGRWRLTPAVRK
30S ribosomal protein S4 D 208 Sphingobium Sp. (Strain Nbrc 103272 / Syk-6) , Haementeria Ghilianii , Rhodobacter Sphaeroides (Strain Atcc 17023 / Dsm 158 / Jcm 6121 / Nbrc 12203 / Ncimb 8253 / Ath 2.4.1.) GRYIGPVCRLCRREGVKLYLKGERCYSPKCAMERRPYPPGQHGQKRARRPSDYAVRLREKQKLRRIYGISERQFRNLFEEASKKKGVTGSVFLGLLESRLDNVVYRLGFAVSRRQARQLVRHGHITVNGRRVDLPSYRVRPGDEIAVAEKSRNLELIRQNLEAMKGRKVGPWLSLDVEGMKGKFLRLPDREDLALPVNEQLVIEFYSR
50S ribosomal protein L35 8 64 Sphingobium Sp. (Strain Nbrc 103272 / Syk-6) , Haementeria Ghilianii , Rhodobacter Sphaeroides (Strain Atcc 17023 / Dsm 158 / Jcm 6121 / Nbrc 12203 / Ncimb 8253 / Ath 2.4.1.) PKMKTHKGAKKRVKITASGKVVAMKTGKRHLNWQKSGKEIRQKGRKFVLAKPEAERIKLLLPYE
50S ribosomal protein L36 9 37 Sphingobium Sp. (Strain Nbrc 103272 / Syk-6) , Haementeria Ghilianii , Rhodobacter Sphaeroides (Strain Atcc 17023 / Dsm 158 / Jcm 6121 / Nbrc 12203 / Ncimb 8253 / Ath 2.4.1.) MKVRASVKRICDKCKVIRRHGRVYVICENPKHKQRQG
50S ribosomal protein L1 C 226 Sphingobium Sp. (Strain Nbrc 103272 / Syk-6) , Haementeria Ghilianii , Rhodobacter Sphaeroides (Strain Atcc 17023 / Dsm 158 / Jcm 6121 / Nbrc 12203 / Ncimb 8253 / Ath 2.4.1.) KHGKRYRALLEKVDPNKVYTIDEAARLVKELATAKFDETVEVHAKLGIDPRRSDQNVRGTVSLPHGLGKQVRVLAIAKGEKIKEAEEAGADYVGGEEIIQKILDGWMDFDAVVATPDVGAVGSKLGRILGPRGLLPNPKAGTVGFNIGEIIREIKAGRIEFRNDKTGAIHAPVGKASFPPEKLADNIRAFIRALEAHKPEGAKGTFLRSVYVTTTMGPSVRINPHS
50S ribosomal protein L3 E 204 Sphingobium Sp. (Strain Nbrc 103272 / Syk-6) , Haementeria Ghilianii , Rhodobacter Sphaeroides (Strain Atcc 17023 / Dsm 158 / Jcm 6121 / Nbrc 12203 / Ncimb 8253 / Ath 2.4.1.) MKGILGVKVGMTRIFRDDRAVPVTVILAGPCPVVQRRTPEKDGYTAVQLGFLPQNPKRVNRPLKGHFAKAGVEPVRILREIRDFNPEGDTVTVEIFKPGERVDVTGTSKGRGFAGVMKRWNFAGGPDSHGAHKIHRHPGSIGNRKTPGRVYKGKKMAGHYGAERVTVMNLEVVDVIPEENLLLVKGAVPGPNGGLVIVRETKKA
50S ribosomal protein L4 F 203 Sphingobium Sp. (Strain Nbrc 103272 / Syk-6) , Haementeria Ghilianii , Rhodobacter Sphaeroides (Strain Atcc 17023 / Dsm 158 / Jcm 6121 / Nbrc 12203 / Ncimb 8253 / Ath 2.4.1.) VYQIPVLSPSGRRELAADLPAEINPHLLWEVVRWQLAKRRRGTASTKTRGEVAYSGRKIWPQKHTGRARHGDIGAPIFVGGGVVFGPKPRDYSYTLPKKVRKKGLAMAVADRAREGKLLLVEAFAGVNGKTKEFLAWAKEAGLDGSESVLLVTGNELVRRAARNLPWVVTLAPEGLNVYDIVRTERLVMDLDAWEVFQNRIGG
50S ribosomal protein L5 G 181 Sphingobium Sp. (Strain Nbrc 103272 / Syk-6) , Haementeria Ghilianii , Rhodobacter Sphaeroides (Strain Atcc 17023 / Dsm 158 / Jcm 6121 / Nbrc 12203 / Ncimb 8253 / Ath 2.4.1.) PLDVALKRKYYEEVRPELIRRFGYQNVWEVPRLEKVVINQGLGEAKEDARILEKAAQELALITGQKPAVTRAKKSISNFKLRKGMPIGLRVTLRRDRMWIFLEKLLNVALPRIRDFRGLNPNSFDGRGNYNLGLREQLIFPEITYDMVDALRGMDIAVVTTAETDEEARALLELLGFPFRK
50S ribosomal protein L6 H 173 Sphingobium Sp. (Strain Nbrc 103272 / Syk-6) , Haementeria Ghilianii , Rhodobacter Sphaeroides (Strain Atcc 17023 / Dsm 158 / Jcm 6121 / Nbrc 12203 / Ncimb 8253 / Ath 2.4.1.) RIGRLPIPVPKGVSVEVAPGRVKVKGPKGELEVPVSPEMRVVVEEGVVRVERPSDERRHKSLHGLTRTLIANAVKGVSEGYSKELLIKGIGYRARLVGRALELTVGFSHPVVVEPPEGITFEVPEPTRVRVSGIDKQKVGQVAANIRAIRKPSAYHEKGIYYAGEPVRLKPGK
50S ribosomal protein L9 I 146 Sphingobium Sp. (Strain Nbrc 103272 / Syk-6) , Haementeria Ghilianii , Rhodobacter Sphaeroides (Strain Atcc 17023 / Dsm 158 / Jcm 6121 / Nbrc 12203 / Ncimb 8253 / Ath 2.4.1.) MKVILLEPLENLGDVGQVVDVKPGYARNYLLPRGLAVLATESNLKALEARIRAQAKRLAERKAEAERLKEILENLTLTIPVRAGETKIYGSVTAKDIAEALSRQHGVTIDPKRLALEKPIKELGEYVLTYKPHPEVPIQLKVSVVA
30S ribosomal protein S10 J 96 Sphingobium Sp. (Strain Nbrc 103272 / Syk-6) , Haementeria Ghilianii , Rhodobacter Sphaeroides (Strain Atcc 17023 / Dsm 158 / Jcm 6121 / Nbrc 12203 / Ncimb 8253 / Ath 2.4.1.) RIKLRGFDHKTLDASAQKIVEAARRSGAQVSGPIPLPTRVRRFTVIRGPFKHKDSREHFELRTHNRLVDIINPNRKTIEQLMTLDLPTGVEIEIKT
30S ribosomal protein S11 K 114 Sphingobium Sp. (Strain Nbrc 103272 / Syk-6) , Haementeria Ghilianii , Rhodobacter Sphaeroides (Strain Atcc 17023 / Dsm 158 / Jcm 6121 / Nbrc 12203 / Ncimb 8253 / Ath 2.4.1.) QVASGRAYIHASYNNTIVTITDPDGNPITWSSGGVIGYKGSRKGTPYAAQLAALDAAKKAMAYGMQSVDVIVRGTGAGREQAIRALQASGLQVKSIVDDTPVPHNGCRPKKKFR
30S ribosomal protein S12 L 122 Sphingobium Sp. (Strain Nbrc 103272 / Syk-6) , Haementeria Ghilianii , Rhodobacter Sphaeroides (Strain Atcc 17023 / Dsm 158 / Jcm 6121 / Nbrc 12203 / Ncimb 8253 / Ath 2.4.1.) PTINQLVRKGREKVRKKSKVPALKGAPFRRGVCTVVRTVTPKKPNSALRKVAKVRLTSGYEVTAYIPGEGHNLQEHSVVLIRGGRVKXLPGVRYHIVRGVYDAAGVKDRKKSRSKYGTKKPK
30S ribosomal protein S13 M 114 Sphingobium Sp. (Strain Nbrc 103272 / Syk-6) , Haementeria Ghilianii , Rhodobacter Sphaeroides (Strain Atcc 17023 / Dsm 158 / Jcm 6121 / Nbrc 12203 / Ncimb 8253 / Ath 2.4.1.) RIAGVEIPRNKRVDVALTYIYGIGKARAKEALEKTGINPATRVKDLTEAEVVRLREYVENTWKLEGELRAEVAANIKRLMDIGCYRGLRHRRGLPVRGQRTRTNARTRKGPRKT
50S ribosomal protein L13 N 140 Sphingobium Sp. (Strain Nbrc 103272 / Syk-6) , Haementeria Ghilianii , Rhodobacter Sphaeroides (Strain Atcc 17023 / Dsm 158 / Jcm 6121 / Nbrc 12203 / Ncimb 8253 / Ath 2.4.1.) MKTYVPKQVEPRWVLIDAEGKTLGRLATKIATLLRGKHRPDWTPNVAMGDFVVVVNADKIRVTGKKLEQKIYTRYSGYPGGLKKIPLEKMLATHPERVLEHAVKGMLPKGPLGRRLFKRLKVYAGPDHPHQAQRPEKLEV
Experimental Data

Method: ELECTRON MICROSCOPY

Deposited Date: 2017-02-07
Deposition Author(s): Dunham, C.M. , Hong, S. , Skiniotis, G. , Zhang, Y.