Structure of bacterial 30S-IF1-IF3-mRNA translation pre-initiation complex (state-1A)

2019-10-02 REL PDBe PDBe PDBe 2016-08-01 2016-08-24 2016-10-05 2019-10-02 Medical Research Council (United Kingdom) MC_U105184332 United Kingdom HHMI United States Wellcome Trust WT096570 United Kingdom Structure of bacterial 30S-IF1-IF3-mRNA translation pre-initiation complex (state-1A) Hussain T Llacer JL Wimberly BT Ramakrishnan V Hussain T Llacer JL Wimberly BT Kieft JS Ramakrishnan V Large-Scale Movements of IF3 and tRNA during Bacterial Translation Initiation. Cell 167 133 144.e13 2016 27662086 doi:10.1016/j.cell.2016.08.074 1097-4172 EMD-4073 associated EM volume

5lmn unknown 30S-IF1-IF3-mRNA pre-initiation complex (state-1A) 30S-IF1-IF3-mRNA pre-initiation complex (state-1A) 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 0.8261 16S ribosomal RNA Thermus thermophilus HB8 0.493958281 1 UUUGUUGGAGAGUUUGAUCCUGGCUCAGGGUGAACGCUGGCGGCGUGCCUAAGACAUGCAAGUCGUGCGGGCCGCGGGGU UUUACUCCGUGGUCAGCGGCGGACGGGUGAGUAACGCGUGGGUGACCUACCCGGAAGAGGGGGACAACCCGGGGAAACUC GGGCUAAUCCCCCAUGUGGACCCGCCCCUUGGGGUGUGUCCAAAGGGCUUUGCCCGCUUCCGGAUGGGCCCGCGUCCCAU CAGCUAGUUGGUGGGGUAAUGGCCCACCAAGGCGACGACGGGUAGCCGGUCUGAGAGGAUGGCCGGCCACAGGGGCACUG AGACACGGGCCCCACUCCUACGGGAGGCAGCAGUUAGGAAUCUUCCGCAAUGGGCGCAAGCCUGACGGAGCGACGCCGCU UGGAGGAAGAAGCCCUUCGGGGUGUAAACUCCUGAACCCGGGACGAAACCCCCGACGAGGGGACUGACGGUACCGGGGUA AUAGCGCCGGCCAACUCCGUGCCAGCAGCCGCGGUAAUACGGAGGGCGCGAGCGUUACCCGGAUUCACUGGGCGUAAAGG GCGUGUAGGCGGCCUGGGGCGUCCCAUGUGAAAGACCACGGCUCAACCGUGGGGGAGCGUGGGAUACGCUCAGGCUAGAC GGUGGGAGAGGGUGGUGGAAUUCCCGGAGUAGCGGUGAAAUGCGCAGAUACCGGGAGGAACGCCGAUGGCGAAGGCAGCC ACCUGGUCCACCCGUGACGCUGAGGCGCGAAAGCGUGGGGAGCAAACCGGAUUAGAUACCCGGGUAGUCCACGCCCUAAA CGAUGCGCGCUAGGUCUCUGGGUCUCCUGGGGGCCGAAGCUAACGCGUUAAGCGCGCCGCCUGGGGAGUACGGCCGCAAG GCUGAAACUCAAAGGAAUUGACGGGGGCCCGCACAAGCGGUGGAGCAUGUGGUUUAAUUCGAAGCAACGCGAAGAACCUU ACCAGGCCUUGACAUGCUAGGGAACCCGGGUGAAAGCCUGGGGUGCCCCGCGAGGGGAGCCCUAGCACAGGUGCUGCAUG GCCGUCGUCAGCUCGUGCCGUGAGGUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCCCGCCGUUAGUUGCCAGCGGUUC GGCCGGGCACUCUAACGGGACUGCCCGCGAAAGCGGGAGGAAGGAGGGGACGACGUCUGGUCAGCAUGGCCCUUACGGCC UGGGCGACACACGUGCUACAAUGCCCACUACAAAGCGAUGCCACCCGGCAACGGGGAGCUAAUCGCAAAAAGGUGGGCCC AGUUCGGAUUGGGGUCUGCAACCCGACCCCAUGAAGCCGGAAUCGCUAGUAAUCGCGGAUCAGCCAUGCCGCGGUGAAUA CGUUCCCGGGCCUUGUACACACCGCCCGUCACGCCAUGGGAGCGGGCUCUACCCGAAGUCGCCGGGAGCCUACGGGCAGG CGCCGAGGGUAGGGCCCGUGACUGGGGCGAAGUCGUAACAAGGUAGCUGUACCGGAAGGUGCGGCUGGAUCACCUCCUUU CU 30S ribosomal protein S2 Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) HB8 / ATCC 27634 / DSM 579 0.029317703 1 LEVO MPVEITVKELLEAGVHFGHERKRWNPKFARYIYAERNGIHIIDLQKTMEELERTFRFIEDLAMRGGTILFVGTKKQAQDI VRMEAERAGMPYVNQRWLGGMLTNFKTISQRVHRLEELEALFASPEIEERPKKEQVRLKHELERLQKYLSGFRLLKRLPD AIFVVDPTKEAIAVREARKLFIPVIALADTDSDPDLVDYIIPGNDDAIRSIQLILSRAVDLIIQARGGVVEPSPSYALVQ EAEATETPEGESEVEA 30S ribosomal protein S3 Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) HB8 / ATCC 27634 / DSM 579 0.026751076 1 LEVO MGNKIHPIGFRLGITRDWESRWYAGKKQYRHLLLEDQRIRGLLEKELYSAGLARVDIERAADNVAVTVHVAKPGVVIGRG GERIRVLREELAKLTGKNVALNVQEVQNPNLSAPLVAQRVAEQIERRFAVRRAIKQAVQRVMESGAKGAKVIVSGRIGGA EQARTEWAAQGRVPLHTLRANIDYGFALARTTYGVLGVKAYIFLGEVIGGQKPKARPELPKAEERPRRRRPAVRVKKEE 30S ribosomal protein S4 Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) HB8 / ATCC 27634 / DSM 579 0.024373447 1 LEVO MGRYIGPVCRLCRREGVKLYLKGERCYSPKCAMERRPYPPGQHGQKRARRPSDYAVRLREKQKLRRIYGISERQFRNLFE EASKKKGVTGSVFLGLLESRLDNVVYRLGFAVSRRQARQLVRHGHITVNGRRVDLPSYRVRPGDEIAVAEKSRNLELIRQ NLEAMKGRKVGPWLSLDVEGMKGKFLRLPDREDLALPVNEQLVIEFYSR 30S ribosomal protein S5 Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) HB8 / ATCC 27634 / DSM 579 0.017583416

Uniprot code Q5SHQ5

1 LEVO MPETDFEEKMILIRRTARMQAGGRRFRFGALVVVGDRQGRVGLGFGKAPEVPLAVQKAGYYARRNMVEVPLQNGTIPHEI EVEFGASKIVLKPAAPGTGVIAGAVPRAILELAGVTDILTKELGSRNPINIAYATMEALRQLRTKADVERLRKGEAHAQA QG 30S ribosomal protein S6 Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) HB8 / ATCC 27634 / DSM 579 0.011988753

Uniprot code Q5SLP8

1 LEVO MRRYEVNIVLNPNLDQSQLALEKEIIQRALENYGARVEKVEELGLRRLAYPIAKDPQGYFLWYQVEMPEDRVNDLARELR IRDNVRRVMVVKSQEPFLANA 30S ribosomal protein S7 Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) HB8 / ATCC 27634 / DSM 579 0.018050973

Uniprot code P17291

1 LEVO MARRRRAEVRQLQPDLVYGDVLVTAFINKIMRDGKKNLAARIFYDACKIIQEKTGQEPLKVFKQAVENVKPRMEVRSRRV GGANYQVPMEVSPRRQQSLALRWLVQAANQRPERRAAVRIAHELMDAAEGKGGAVKKKEDVERMAEANRAYAHYRW 30S ribosomal protein S8 Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) HB8 / ATCC 27634 / DSM 579 0.01586857

Uniprot code Q5SHQ2

1 LEVO MLTDPIADMLTRIRNATRVYKESTDVPASRFKEEILRILAREGFIKGYERVDVDGKPYLRVYLKYGPRRQGPDPRPEQVI HHIRRISKPGRRVYVGVKEIPRVRRGLGIAILSTSKGVLTDREARKLGVGGELICEVW 30S ribosomal protein S9 Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) HB8 / ATCC 27634 / DSM 579 0.014410614

Uniprot code P80374

1 LEVO MEQYYGTGRRKEAVARVFLRPGNGKVTVNGQDFNEYFQGLVRAVAALEPLRAVDALGHFDAYITVRGGGKSGQIDAIKLG IARALVQYNPDYRAKLKPLGFLTRDARVVERKKYGKHKARRAPQYSKR 30S ribosomal protein S10 Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) HB8 / ATCC 27634 / DSM 579 0.011954968

Uniprot code Q5SHN7

1 LEVO MPKIRIKLRGFDHKTLDASAQKIVEAARRSGAQVSGPIPLPTRVRRFTVIRGPFKHKDSREHFELRTHNRLVDIINPNRK TIEQLMTLDLPTGVEIEIKTVGGGR 30S ribosomal protein S11 Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) HB8 / ATCC 27634 / DSM 579 0.013737868

Uniprot code P80376

1 LEVO MAKKPSKKKVKRQVASGRAYIHASYNNTIVTITDPDGNPITWSSGGVIGYKGSRKGTPYAAQLAALDAAKKAMAYGMQSV DVIVRGTGAGREQAIRALQASGLQVKSIVDDTPVPHNGCRPKKKFRKAS 30S ribosomal protein S12 Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) HB8 / ATCC 27634 / DSM 579 0.014637384

Uniprot code Q5SHN3

1 LEVO MPTINQLVRKGREKVRKKSKVPALKGAPFRRGVCTVVRTVTPKKPNSALRKVAKVRLTSGYEVTAYIPGEGHNLQEHSVV LIRGGRVKDLPGVRYHIVRGVYDAAGVKDRKKSRSKYGTKKPKEAAKTAAKK 30S ribosomal protein S13 Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) HB8 / ATCC 27634 / DSM 579 0.014338861

P80377

1 LEVO MARIAGVEIPRNKRVDVALTYIYGIGKARAKEALEKTGINPATRVKDLTEAEVVRLREYVENTWKLEGELRAEVAANIKR LMDIGCYRGLRHRRGLPVRGQRTRTNARTRKGPRKTVAGKKKAPRK 30S ribosomal protein S14 type Z Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) HB8 / ATCC 27634 / DSM 579 0.007158725

Q5SHQ1

1 LEVO MARKALIEKAKRTPKFKVRAYTRCVRCGRARSVYRFFGLCRICLRELAHKGQLPGVRKASW 30S ribosomal protein S15 Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) HB8 / ATCC 27634 / DSM 579 0.010578407

Q5SJ76

1 LEVO MPITKEEKQKVIQEFARFPGDTGSTEVQVALLTLRINRLSEHLKVHKKDHHSHRGLLMMVGQRRRLLRYLQREDPERYRA LIEKLGIRG 30S ribosomal protein S16 Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) HB8 / ATCC 27634 / DSM 579 0.010409983

Q5SJH3

1 LEVO MVKIRLARFGSKHNPHYRIVVTDARRKRDGKYIEKIGYYDPRKTTPDWLKVDVERARYWLSVGAQPTDTARRLLRQAGVF RQEAREGA 30S ribosomal protein S17 Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) HB8 / ATCC 27634 / DSM 579 0.012325655

Q5SHP7

1 LEVO MPKKVLTGVVVSDKMQKTVTVLVERQFPHPLYGKVIKRSKKYLAHDPEEKYKLGDVVEIIESRPISKRKRFRVLRLVESG RMDLVEKYLIRRQNYESLSKRGGKA 30S ribosomal protein S18 Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) HB8 / ATCC 27634 / DSM 579 0.010258299

Q5SLQ0

1 LEVO MSTKNAKPKKEAQRRPSRKAKVKATLGEFDLRDYRNVEVLKRFLSETGKILPRRRTGLSAKEQRILAKTIKRARILGLLP FTEKLVRK 30S ribosomal protein S19 Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) HB8 / ATCC 27634 / DSM 579 0.010605464

Q5SHP2

1 LEVO MPRSLKKGVFVDDHLLEKVLELNAKGEKRLIKTWSRRSTIVPEMVGHTIAVYNGKQHVPVYITENMVGHKLGEFAPTRTY RGHGKEAKATKKK 30S ribosomal protein S20 Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) HB8 / ATCC 27634 / DSM 579 0.011736143

P80380

1 LEVO MAQKKPKRNLSALKRHRQSLKRRLRNKAKKSAIKTLSKKAIQLAQEGKAEEALKIMRKAESLIDKAAKGSTLHKNAAARR KSRLMRKVRQLLEAAGAPLIGGGLSA 30S ribosomal protein Thx Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) HB8 / ATCC 27634 / DSM 579 0.00335003

Q5SIH3

1 LEVO MGKGDRRTRRGKIWRGTYGKYRPRKKK Translation initiation factor IF-1 Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) HB8 / ATCC 27634 / DSM 579 0.008247664

Q5SHR1

1 Escherichia coli BL21(DE3) LEVO MAKEKDTIRTEGVVTEALPNATFRVKLDSGPEILAYISGKMRMHYIRILPGDRVVVEITPYDPTRGRIVYRK Translation initiation factor IF-3 Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) HB8 / ATCC 27634 / DSM 579 0.019904377

Q5SKU2

1 Escherichia coli BL21(DE3) LEVO MKEYLTNERIRAKQVRVVGPDGKQLGIMDTREALRLAQEMDLDLVLVGPNADPPVARIMDYSKWRYEQQMAEKEARKKAK RTEVKSIKFRVKIDEHDYQTKLGHIKRFLQEGHKVKVTIMFRGREVAHPELGERILNRVTEDLKDLAVVEMKPEMLGRDM NMLLAPVKVSA mRNA Thermus thermophilus 0.013466019 1 GCUCUUUUAACAAUUUAUCAGGCAAGGAGGUAAAAAUGUUCA MAGNESIUM ION 2.4305e-05 127 MG ZINC ION 6.5409e-05 2 ZN singleParticle particle 0.08 7.5 5.0 Hepes-K 10.0 Magnessium acetate 50.0 Potassium chloride 10.0 Ammonium chloride 6.0 Beta mercaptoethanol Quantifoil COPPER 400 CARBON HOLEY GLOW DISCHARGE ETHANE 100 277 FEI VITROBOT MARK I

FEI POLARA 300 FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 50.0 2.0 1.5 3.5 78000. 104478. NITROGEN 90.0 100.0 OTHER 5 4400 1.1 30.0

Recorded in a FEI Falcon III direct electron detector. Images were collected in movie-mode at 32 frames per second

FEI Falcon III

666610 CTFFIND 3 1HR0 FOURIER SPACE 3.55 FSC 0.143 CUT-OFF RELION 1.4 86892 PROJECTION MATCHING RELION 1.4 ANGULAR RECONSTITUTION RELION 1.4 RELION 1.4 emd_4073.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 260 260 260 0 0 0 260 260 260 348.4 348.4 348.4 90.0 90.0 90.0 X Y Z -0.36352223 0.9275878 -0.000101041 0.029434646 1.34 1.34 1.34 0.09 AUTHOR ::::EMDATABANK.org::::D_1200000872:::: For optimal visualization of IF3 N-terminal domain, gauss-filter de map by 1.1 and display it at 0.05 contour OTHER FSC RECIPROCAL 89.700000000000003 emd_4073_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 260 260 260 0 0 0 260 260 260 348.4 348.4 348.4 90.0 90.0 90.0 X Y Z -0.022839686 0.13576588 -0.000050698174 0.007164411 1.34 1.34 1.34 AUTHOR ::::EMDATABANK.org::::D_1200000872:::: emd_4073_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 260 260 260 0 0 0 260 260 260 348.4 348.4 348.4 90.0 90.0 90.0 X Y Z -0.021175213 0.13593064 -0.000049685277 0.0071436865 1.34 1.34 1.34 AUTHOR ::::EMDATABANK.org::::D_1200000872::::