5J8B
Crystal structure of elongation factor 4 (ef-4/lepa) in complex with gdpcp bound to the thermus thermophilus 70s ribosome
PDB DOI: 10.2210/pdb5j8b/pdb
Classification: RIBOSOME Organism(s): Thermus Thermophilus (Strain Hb8 / Atcc 27634 / Dsm 579) , Synthetic Construct
Deposited: 2016-04-07 Deposition Author(s): Gagnon, M.G. , Lin, J. , Steitz, T.A.
Experimental Data Snapshot
Method: X-RAY DIFFRACTION Resolution: 2.6 Å
Crystal structure of elongation factor 4 (ef-4/lepa) in complex with gdpcp bound to the thermus thermophilus 70s ribosome
Gagnon, M.G. , Lin, J. , Steitz, T.A.
Primary Citation of Related Structures: 5J8B
| Nucleic Acids / Hybrid | ||||
|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Sequence |
| 16S Ribosomal RNA | a | 1521 | NA | UUGUUGGAGAGUUUGAUCCUGGCUCAGGGUGAACGCUGGCGGCGUGCCUAAGACAUGCAAGUCGUGCGGGCCGCGGGGUUUUACUCCGUGGUCAGCGGCGGACGGGUGAGUAACGCGUGGGUGACCUACCCGGAAGAGGGGGACAACCCGGGGAAACUCGGGCUAAUCCCCCAUGUGGACCCGCCCCUUGGGGUGUGUCCAAAGGGCUUUGCCCGCUUCCGGAUGGGCCCGCGUCCCAUCAGCUAGUUGGUGGGGUAAUGGCCCACCAAGGCGACGACGGGUAGCCGGUCUGAGAGGAUGGCCGGCCACAGGGGCACUGAGACACGGGCCCCACUCCUACGGGAGGCAGCAGUUAGGAAUCUUCCGCAAUGGGCGCAAGCCUGACGGAGCGACGCCGCUUGGAGGAAGAAGCCCUUCGGGGUGUAAACUCCUGAACCCGGGACGAAACCCCCGACGAGGGGACUGACGGUACCGGGGUAAUAGCGCCGGCCAACUCCGUGCCAGCAGCCGCGGUAAUACGGAGGGCGCGAGCGUUACCCGGAUUCACUGGGCGUAAAGGGCGUGUAGGCGGCCUGGGGCGUCCCAUGUGAAAGACCACGGCUCAACCGUGGGGGAGCGUGGGAUACGCUCAGGCUAGACGGUGGGAGAGGGUGGUGGAAUUCCCGGAGUAGCGGUGAAAUGCGCAGAUACCGGGAGGAACGCCGAUGGCGAAGGCAGCCACCUGGUCCACCCGUGACGCUGAGGCGCGAAAGCGUGGGGAGCAAACCGGAUUAGAUACCCGGGUAGUCCACGCCCUAAACGAUGCGCGCUAGGUCUCUGGGUCUCCUGGGGGCCGAAGCUAACGCGUUAAGCGCGCCGCCUGGGGAGUACGGCCGCAAGGCUGAAACUCAAAGGAAUUGACGGGGGCCCGCACAAGCGGUGGAGCAUGUGGUUUAAUUCGAAGCAACGCGAAGAACCUUACCAGGCCUUGACAUGCUAGGGAACCCGGGUGAAAGCCUGGGGUGCCCCGCGAGGGGAGCCCUAGCACAGGUGCUGCAUGGCCGUCGUCAGCUCGUGCCGUGAGGUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCCCGCCGUUAGUUGCCAGCGGUUCGGCCGGGCACUCUAACGGGACUGCCCGCGAAAGCGGGAGGAAGGAGGGGACGACGUCUGGUCAGCAUGGCCCUUACGGCCUGGGCGACACACGUGCUACAAUGCCCACUACAAAGCGAUGCCACCCGGCAACGGGGAGCUAAUCGCAAAAAGGUGGGCCCAGUUCGGAUUGGGGUCUGCAACCCGACCCCAUGAAGCCGGAAUCGCUAGUAAUCGCGGAUCAGCCAUGCCGCGGUGAAUACGUUCCCGGGCCUUGUACACACCGCCCGUCACGCCAUGGGAGCGGGCUCUACCCGAAGUCGCCGGGAGCCUACGGGCAGGCGCCGAGGGUAGGGCCCGUGACUGGGGCGAAGUCGUAACAAGGUAGCUGUACCGGAAGGUGCGGCUGGAUCACCUCCUUUCU |
| mRNA | v | 24 | NA | GGCAAGGAGGUAAAAAUGUUCUAA |
| A-site tRNA | w | 76 | NA | GCCCGGAUAGCUCAGUCGGUAGAGCAGGGGAUUGAAAAUCCCCGUGUCCUUGGUUCGAUUCCGAGUCCGGGCACCA |
| P-site tRNA | x | 77 | NA | CGCGGGGUGGAGCAGCCUGGUAGCUCGUCGGGCUCAUAACCCGAAGGUCGUCGGUUCAAAUCCGGCCCCCGCAACCA |
| E-site tRNA | y | 76 | NA | GCCCGGAUAGCUCAGUCGGUAGAGCAGGGGAUUGAAAAUCCCCGUGUCCUUGGUUCGAUUCCGAGUCCGGGCACCA |
| Proteins | ||||
|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Sequence |
| 30S ribosomal protein S11 | K | 129 | Thermus Thermophilus (Strain Hb8 / Atcc 27634 / Dsm 579) , Synthetic Construct | MAKKPSKKKVKRQVASGRAYIHASYNNTIVTITDPDGNPITWSSGGVIGYKGSRKGTPYAAQLAALDAAKKAMAYGMQSVDVIVRGTGAGREQAIRALQASGLQVKSIVDDTPVPHNGCRPKKKFRKAS |
| 30S ribosomal protein S14 type Z | N | 61 | Thermus Thermophilus (Strain Hb8 / Atcc 27634 / Dsm 579) , Synthetic Construct | MARKALIEKAKRTPKFKVRAYTRCVRCGRARSVYRFFGLCRICLRELAHKGQLPGVRKASW |
| 30S ribosomal protein S15 | O | 89 | Thermus Thermophilus (Strain Hb8 / Atcc 27634 / Dsm 579) , Synthetic Construct | MPITKEEKQKVIQEFARFPGDTGSTEVQVALLTLRINRLSEHLKVHKKDHHSHRGLLMMVGQRRRLLRYLQREDPERYRALIEKLGIRG |
| 30S ribosomal protein S16 | P | 88 | Thermus Thermophilus (Strain Hb8 / Atcc 27634 / Dsm 579) , Synthetic Construct | MVKIRLARFGSKHNPHYRIVVTDARRKRDGKYIEKIGYYDPRKTTPDWLKVDVERARYWLSVGAQPTDTARRLLRQAGVFRQEAREGA |
| 30S ribosomal protein S17 | Q | 105 | Thermus Thermophilus (Strain Hb8 / Atcc 27634 / Dsm 579) , Synthetic Construct | MPKKVLTGVVVSDKMQKTVTVLVERQFPHPLYGKVIKRSKKYLAHDPEEKYKLGDVVEIIESRPISKRKRFRVLRLVESGRMDLVEKYLIRRQNYESLSKRGGKA |
| 30S ribosomal protein S18 | R | 88 | Thermus Thermophilus (Strain Hb8 / Atcc 27634 / Dsm 579) , Synthetic Construct | MSTKNAKPKKEAQRRPSRKAKVKATLGEFDLRDYRNVEVLKRFLSETGKILPRRRTGLSAKEQRILAKTIKRARILGLLPFTEKLVRK |
| 30S ribosomal protein S19 | S | 93 | Thermus Thermophilus (Strain Hb8 / Atcc 27634 / Dsm 579) , Synthetic Construct | MPRSLKKGVFVDDHLLEKVLELNAKGEKRLIKTWSRRSTIVPEMVGHTIAVYNGKQHVPVYITENMVGHKLGEFAPTRTYRGHGKEAKATKKK |
| 30S ribosomal protein S20 | T | 106 | Thermus Thermophilus (Strain Hb8 / Atcc 27634 / Dsm 579) , Synthetic Construct | MAQKKPKRNLSALKRHRQSLKRRLRNKAKKSAIKTLSKKAIQLAQEGKAEEALKIMRKAESLIDKAAKGSTLHKNAAARRKSRLMRKVRQLLEAAGAPLIGGGLSA |
| 30S ribosomal protein Thx | U | 27 | Thermus Thermophilus (Strain Hb8 / Atcc 27634 / Dsm 579) , Synthetic Construct | MGKGDRRTRRGKIWRGTYGKYRPRKKK |
| 30S ribosomal protein S2 | B | 256 | Thermus Thermophilus (Strain Hb8 / Atcc 27634 / Dsm 579) , Synthetic Construct | MPVEITVKELLEAGVHFGHERKRWNPKFARYIYAERNGIHIIDLQKTMEELERTFRFIEDLAMRGGTILFVGTKKQAQDIVRMEAERAGMPYVNQRWLGGMLTNFKTISQRVHRLEELEALFASPEIEERPKKEQVRLKHELERLQKYLSGFRLLKRLPDAIFVVDPTKEAIAVREARKLFIPVIALADTDSDPDLVDYIIPGNDDAIRSIQLILSRAVDLIIQARGGVVEPSPSYALVQEAEATETPEGESEVEA |
| GDPCP fused to the N-terminus of the ribosomal protein L9,Elongation factor 4 | Z | 679 | Thermus Thermophilus (Strain Hb8 / Atcc 27634 / Dsm 579) , Synthetic Construct | MKVILLEPLENLGDVGQVVDVKPGYARNYLLPRGLAVLATESNLKALEARIRAQAKRLAERKAEAERLKEILENLSRIRNFSIIAHVDHGKSTLADRILELTHAVSDREMREQFLDSLELERERGITIKASAVRVTYRAKDGEEYVFHLIDTPGHVDFTYEVSRALAAVEGVLLVVDASQGVEAETLAKFYMALEHGHVIIPVINKIDLPNARPLEVALEVEEVLGLPADEAIFASGKTGEGVEEILEAIVQRIPPPKGDPEAPLKALIFDSVYDAYQGVIPYLRLFEGRVRPGDRIRIYSTGKEFTVDKVGVFTPQGLVATEALEAGEVGWLVAAIRDIHDVQVGDTITLADRPTPSPYPGFRPAKPVVFAGLYPVDSGDYGKLRDALEKLKLNDAALTFEPESSTALGFGFRCGFLGLLHAEIVQERLEREFGLSLIATAPSVVYKVRLKSGEEVEVHNPADLPDPTRIEEILEPYVKLTIFTPEEYVGSLMQLLQEKRGRLVNMNYLPGAQKRVELVYEAPFAEILYDFHDRLKSVSRGYASMDYEQAGYRPGDLVKVNVLVHGEVVDALTFIAHREKAYTMARAIVDKLAEVIPRQLFEVPIQAAIGGKIIARATVKALRKDVLAKCYGGDVTRKKKLLEKQKEGKKRLKAIGKVEVPQEAFLAVLSAGRDEPKG |
| 50S ribosomal protein L27 | 0 | 85 | Thermus Thermophilus (Strain Hb8 / Atcc 27634 / Dsm 579) , Synthetic Construct | MAHKKGLGSTRNGRDSQAKRLGVKRYEGQVVRAGNILVRQRGTRFKPGKNVGMGRDFTLFALVDGVVEFQDRGRLGRYVHVRPLA |
| 50S ribosomal protein L28 | 1 | 98 | Thermus Thermophilus (Strain Hb8 / Atcc 27634 / Dsm 579) , Synthetic Construct | MSKVCEISGKRPIVANSIQRRGKAKREGGVGKKTTGISKRRQYPNLQKVRVRVAGQEITFRVAASHIPKVYELVERAKGLKLEGLSPKEIKKELLKLL |
| 50S ribosomal protein L29 | 2 | 72 | Thermus Thermophilus (Strain Hb8 / Atcc 27634 / Dsm 579) , Synthetic Construct | MKLSEVRKQLEEARKLSPVELEKLVREKKRELMELRFQASIGQLSQNHKIRDLKRQIARLLTVLNEKRRQNA |
| 50S ribosomal protein L30 | 3 | 60 | Thermus Thermophilus (Strain Hb8 / Atcc 27634 / Dsm 579) , Synthetic Construct | MPRLKVKLVKSPIGYPKDQKAALKALGLRRLQQERVLEDTPAIRGNVEKVAHLVRVEVVE |
| 50S ribosomal protein L31 | 4 | 71 | Thermus Thermophilus (Strain Hb8 / Atcc 27634 / Dsm 579) , Synthetic Construct | MKEGIHPKLVPARIICGCGNVIETYSTKPEIYVEVCSKCHPFYTGQQRFVDTEGRVERFQRRYGDSYRKGR |
| 50S ribosomal protein L32 | 5 | 60 | Thermus Thermophilus (Strain Hb8 / Atcc 27634 / Dsm 579) , Synthetic Construct | MAKHPVPKKKTSKARRDARRSHHALTPPTLVPCPECKAMKPPHTVCPECGYYAGRKVLEV |
| 30S ribosomal protein S3 | C | 239 | Thermus Thermophilus (Strain Hb8 / Atcc 27634 / Dsm 579) , Synthetic Construct | MGNKIHPIGFRLGITRDWESRWYAGKKQYRHLLLEDQRIRGLLEKELYSAGLARVDIERAADNVAVTVHVAKPGVVIGRGGERIRVLREELAKLTGKNVALNVQEVQNPNLSAPLVAQRVAEQIERRFAVRRAIKQAVQRVMESGAKGAKVIVSGRIGGAEQARTEWAAQGRVPLHTLRANIDYGFALARTTYGVLGVKAYIFLGEVIGGQKPKARPELPKAEERPRRRRPAVRVKKEE |
| 50S ribosomal protein L33 | 6 | 54 | Thermus Thermophilus (Strain Hb8 / Atcc 27634 / Dsm 579) , Synthetic Construct | MASEVRIKLLLECTECKRRNYATEKNKRNTPNKLELRKYCPWCRKHTVHREVKI |
| 50S ribosomal protein L34 | 7 | 49 | Thermus Thermophilus (Strain Hb8 / Atcc 27634 / Dsm 579) , Synthetic Construct | MKRTWQPNRRKRAKTHGFRARMRTPGGRKVLKRRRQKGRWRLTPAVRKR |
| 50S ribosomal protein L35 | 8 | 65 | Thermus Thermophilus (Strain Hb8 / Atcc 27634 / Dsm 579) , Synthetic Construct | MPKMKTHKGAKKRVKITASGKVVAMKTGKRHLNWQKSGKEIRQKGRKFVLAKPEAERIKLLLPYE |
| 50S ribosomal protein L36 | 9 | 37 | Thermus Thermophilus (Strain Hb8 / Atcc 27634 / Dsm 579) , Synthetic Construct | MKVRASVKRICDKCKVIRRHGRVYVICENPKHKQRQG |
| 50S ribosomal protein L2 | D | 276 | Thermus Thermophilus (Strain Hb8 / Atcc 27634 / Dsm 579) , Synthetic Construct | MAVKKFKPYTPSRRFMTVADFSEITKTEPEKSLVKPLKKTGGRNNQGRITVRFRGGGHKRLYRIIDFKRWDKVGIPAKVAAIEYDPNRSARIALLHYVDGEKRYIIAPDGLQVGQQVVAGPDAPIQVGNALPLRFIPVGTVVHAVELEPKKGAKLARAAGTSAQIQGREGDYVILRLPSGELRKVHGECYATVGAVGNADHKNIVLGKAGRSRWLGRRPHVRGAAMNPVDHPHGGGEGRAPRGRPPASPWGWQTKGLKTRKRRKPSSRFIIARRKK |
| 50S ribosomal protein L3 | E | 206 | Thermus Thermophilus (Strain Hb8 / Atcc 27634 / Dsm 579) , Synthetic Construct | MKGILGVKVGMTRIFRDDRAVPVTVILAGPCPVVQRRTPEKDGYTAVQLGFLPQNPKRVNRPLKGHFAKAGVEPVRILREIRDFNPEGDTVTVEIFKPGERVDVTGTSKGRGFAGVMKRWNFAGGPDSHGAHKIHRHPGSIGNRKTPGRVYKGKKMAGHYGAERVTVMNLEVVDVIPEENLLLVKGAVPGPNGGLVIVRETKKAAK |
| 50S ribosomal protein L4 | F | 210 | Thermus Thermophilus (Strain Hb8 / Atcc 27634 / Dsm 579) , Synthetic Construct | MKEVAVYQIPVLSPSGRRELAADLPAEINPHLLWEVVRWQLAKRRRGTASTKTRGEVAYSGRKIWPQKHTGRARHGDIGAPIFVGGGVVFGPKPRDYSYTLPKKVRKKGLAMAVADRAREGKLLLVEAFAGVNGKTKEFLAWAKEAGLDGSESVLLVTGNELVRRAARNLPWVVTLAPEGLNVYDIVRTERLVMDLDAWEVFQNRIGGEA |
| 50S ribosomal protein L5 | G | 182 | Thermus Thermophilus (Strain Hb8 / Atcc 27634 / Dsm 579) , Synthetic Construct | MPLDVALKRKYYEEVRPELIRRFGYQNVWEVPRLEKVVINQGLGEAKEDARILEKAAQELALITGQKPAVTRAKKSISNFKLRKGMPIGLRVTLRRDRMWIFLEKLLNVALPRIRDFRGLNPNSFDGRGNYNLGLREQLIFPEITYDMVDALRGMDIAVVTTAETDEEARALLELLGFPFRK |
| 50S ribosomal protein L6 | H | 180 | Thermus Thermophilus (Strain Hb8 / Atcc 27634 / Dsm 579) , Synthetic Construct | MSRIGRLPIPVPKGVSVEVAPGRVKVKGPKGELEVPVSPEMRVVVEEGVVRVERPSDERRHKSLHGLTRTLIANAVKGVSEGYSKELLIKGIGYRARLVGRALELTVGFSHPVVVEPPEGITFEVPEPTRVRVSGIDKQKVGQVAANIRAIRKPSAYHEKGIYYAGEPVRLKPGKAGAKK |
| 30S ribosomal protein S9 | I | 128 | Thermus Thermophilus (Strain Hb8 / Atcc 27634 / Dsm 579) , Synthetic Construct | MEQYYGTGRRKEAVARVFLRPGNGKVTVNGQDFNEYFQGLVRAVAALEPLRAVDALGHFDAYITVRGGGKSGQIDAIKLGIARALVQYNPDYRAKLKPLGFLTRDARVVERKKYGKHKARRAPQYSKR |
| 50S ribosomal protein L10 | J | 173 | Thermus Thermophilus (Strain Hb8 / Atcc 27634 / Dsm 579) , Synthetic Construct | MPNKRNVELLATLKENLERAQGSFFLVNYQGLPAKETHALRQALKQNGARLFVAKNTLIRLALKELGLPELDGLQGPSAVVFYEDPVAAAKTLVQFAKSNPKGIPQVKSGLLQGQILTAKDVEALAELPTMDELRAELVGVLQAPMAELVGVLGGVARELVGILEAYAEKKAA |
| 30S ribosomal protein S12 | L | 132 | Thermus Thermophilus (Strain Hb8 / Atcc 27634 / Dsm 579) , Synthetic Construct | MPTINQLVRKGREKVRKKSKVPALKGAPFRRGVCTVVRTVTPKKPNSALRKVAKVRLTSGYEVTAYIPGEGHNLQEHSVVLIRGGRVKDLPGVRYHIVRGVYDAAGVKDRKKSRSKYGTKKPKEAAKTAAKK |
| 30S ribosomal protein S13 | M | 126 | Thermus Thermophilus (Strain Hb8 / Atcc 27634 / Dsm 579) , Synthetic Construct | MARIAGVEIPRNKRVDVALTYIYGIGKARAKEALEKTGINPATRVKDLTEAEVVRLREYVENTWKLEGELRAEVAANIKRLMDIGCYRGLRHRRGLPVRGQRTRTNARTRKGPRKTVAGKKKAPRK |
Experimental Data
Method: X-RAY DIFFRACTION
Deposited Date: 2016-04-07 Deposition Author(s): Gagnon, M.G. , Lin, J. , Steitz, T.A.