Structure of bacterial 30S-IF1-IF3-mRNA-tRNA translation pre-initiation complex(state-2B)

2025-10-01 REL PDBe INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY EXPERIMENTAL_SUMMARY database_2 em_admin _database_2.pdbx_DOI _database_2.pdbx_database_accession _em_admin.last_update EXPERIMENTAL_SUMMARY em_admin _em_admin.last_update STRUCTURE_SUMMARY chem_comp_atom chem_comp_bond database_2 em_admin pdbx_entry_details pdbx_modification_feature struct_conn _database_2.pdbx_DOI _database_2.pdbx_database_accession _em_admin.last_update _struct_conn.conn_type_id _struct_conn.id _struct_conn.pdbx_dist_value _struct_conn.pdbx_leaving_atom_flag _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id STRUCTURE_SUMMARY em_admin pdbx_modification_feature pdbx_validate_close_contact struct_conn _em_admin.last_update PDBe PDBe 2016-08-01 2016-08-17 2016-10-05 2025-10-01 Structure of bacterial 30S-IF1-IF3-mRNA-tRNA translation pre-initiation complex(state-2B) Hussain T Llacer JL ribosome, translation, initiation factors, 30S, IF1, IF3, tRNAi, PIC, Thermus thermophilus 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 5lmr unknown EMDB EMD-4077 associated EM volume

30S-IF1-IF3-mRNA-tRNA pre-initiation complex (state-2B) 30S-IF1-IF3-mRNA-tRNA pre-initiation complex (state-2B) 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 25 0.8497 16S rRNA 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 AP008226.1 30S ribosomal protein S2 Thermus thermophilus HB8 0.029317703 1 LEVO MPVEITVKELLEAGVHFGHERKRWNPKFARYIYAERNGIHIIDLQKTMEELERTFRFIEDLAMRGGTILFVGTKKQAQDI VRMEAERAGMPYVNQRWLGGMLTNFKTISQRVHRLEELEALFASPEIEERPKKEQVRLKHELERLQKYLSGFRLLKRLPD AIFVVDPTKEAIAVREARKLFIPVIALADTDSDPDLVDYIIPGNDDAIRSIQLILSRAVDLIIQARGGVVEPSPSYALVQ EAEATETPEGESEVEA P80371 30S ribosomal protein S3 Thermus thermophilus HB8 0.026751076 1 LEVO MGNKIHPIGFRLGITRDWESRWYAGKKQYRHLLLEDQRIRGLLEKELYSAGLARVDIERAADNVAVTVHVAKPGVVIGRG GERIRVLREELAKLTGKNVALNVQEVQNPNLSAPLVAQRVAEQIERRFAVRRAIKQAVQRVMESGAKGAKVIVSGRIGGA EQARTEWAAQGRVPLHTLRANIDYGFALARTTYGVLGVKAYIFLGEVIGGQKPKARPELPKAEERPRRRRPAVRVKKEE P80372 30S ribosomal protein S4 Thermus thermophilus HB8 0.024373447 1 LEVO MGRYIGPVCRLCRREGVKLYLKGERCYSPKCAMERRPYPPGQHGQKRARRPSDYAVRLREKQKLRRIYGISERQFRNLFE EASKKKGVTGSVFLGLLESRLDNVVYRLGFAVSRRQARQLVRHGHITVNGRRVDLPSYRVRPGDEIAVAEKSRNLELIRQ NLEAMKGRKVGPWLSLDVEGMKGKFLRLPDREDLALPVNEQLVIEFYSR P80373 30S ribosomal protein S5 Thermus thermophilus HB8 0.017583416 1 LEVO MPETDFEEKMILIRRTARMQAGGRRFRFGALVVVGDRQGRVGLGFGKAPEVPLAVQKAGYYARRNMVEVPLQNGTIPHEI EVEFGASKIVLKPAAPGTGVIAGAVPRAILELAGVTDILTKELGSRNPINIAYATMEALRQLRTKADVERLRKGEAHAQA QG Q5SHQ5 30S ribosomal protein S6 Thermus thermophilus HB8 0.011988753 1 LEVO MRRYEVNIVLNPNLDQSQLALEKEIIQRALENYGARVEKVEELGLRRLAYPIAKDPQGYFLWYQVEMPEDRVNDLARELR IRDNVRRVMVVKSQEPFLANA Q5SLP8 30S ribosomal protein S7 Thermus thermophilus HB8 0.018050973 1 LEVO MARRRRAEVRQLQPDLVYGDVLVTAFINKIMRDGKKNLAARIFYDACKIIQEKTGQEPLKVFKQAVENVKPRMEVRSRRV GGANYQVPMEVSPRRQQSLALRWLVQAANQRPERRAAVRIAHELMDAAEGKGGAVKKKEDVERMAEANRAYAHYRW P17291 30S ribosomal protein S8 Thermus thermophilus HB8 0.01586857 1 LEVO MLTDPIADMLTRIRNATRVYKESTDVPASRFKEEILRILAREGFIKGYERVDVDGKPYLRVYLKYGPRRQGPDPRPEQVI HHIRRISKPGRRVYVGVKEIPRVRRGLGIAILSTSKGVLTDREARKLGVGGELICEVW Q5SHQ2 30S ribosomal protein S9 Thermus thermophilus HB8 0.014410613999999999 1 LEVO MEQYYGTGRRKEAVARVFLRPGNGKVTVNGQDFNEYFQGLVRAVAALEPLRAVDALGHFDAYITVRGGGKSGQIDAIKLG IARALVQYNPDYRAKLKPLGFLTRDARVVERKKYGKHKARRAPQYSKR P80374 30S ribosomal protein S10 Thermus thermophilus HB8 0.011954968 1 LEVO MPKIRIKLRGFDHKTLDASAQKIVEAARRSGAQVSGPIPLPTRVRRFTVIRGPFKHKDSREHFELRTHNRLVDIINPNRK TIEQLMTLDLPTGVEIEIKTVGGGR Q5SHN7 30S ribosomal protein S11 Thermus thermophilus HB8 0.013737868 1 LEVO MAKKPSKKKVKRQVASGRAYIHASYNNTIVTITDPDGNPITWSSGGVIGYKGSRKGTPYAAQLAALDAAKKAMAYGMQSV DVIVRGTGAGREQAIRALQASGLQVKSIVDDTPVPHNGCRPKKKFRKAS P80376 30S ribosomal protein S12 Thermus thermophilus HB8 0.014637384 1 LEVO MPTINQLVRKGREKVRKKSKVPALKGAPFRRGVCTVVRTVTPKKPNSALRKVAKVRLTSGYEVTAYIPGEGHNLQEHSVV LIRGGRVKDLPGVRYHIVRGVYDAAGVKDRKKSRSKYGTKKPKEAAKTAAKK Q5SHN3 30S ribosomal protein S13 Thermus thermophilus HB8 0.014338861 1 LEVO MARIAGVEIPRNKRVDVALTYIYGIGKARAKEALEKTGINPATRVKDLTEAEVVRLREYVENTWKLEGELRAEVAANIKR LMDIGCYRGLRHRRGLPVRGQRTRTNARTRKGPRKTVAGKKKAPRK P80377 30S ribosomal protein S14 type Z Thermus thermophilus HB8 0.007158725 1 LEVO MARKALIEKAKRTPKFKVRAYTRCVRCGRARSVYRFFGLCRICLRELAHKGQLPGVRKASW Q5SHQ1 30S ribosomal protein S15 Thermus thermophilus HB8 0.010578406999999998 1 LEVO MPITKEEKQKVIQEFARFPGDTGSTEVQVALLTLRINRLSEHLKVHKKDHHSHRGLLMMVGQRRRLLRYLQREDPERYRA LIEKLGIRG Q5SJ76 30S ribosomal protein S16 Thermus thermophilus HB8 0.010409983 1 LEVO MVKIRLARFGSKHNPHYRIVVTDARRKRDGKYIEKIGYYDPRKTTPDWLKVDVERARYWLSVGAQPTDTARRLLRQAGVF RQEAREGA Q5SJH3 30S ribosomal protein S17 Thermus thermophilus HB8 0.012325655 1 LEVO MPKKVLTGVVVSDKMQKTVTVLVERQFPHPLYGKVIKRSKKYLAHDPEEKYKLGDVVEIIESRPISKRKRFRVLRLVESG RMDLVEKYLIRRQNYESLSKRGGKA Q5SHP7 30S ribosomal protein S18 Thermus thermophilus HB8 0.010258299 1 LEVO MSTKNAKPKKEAQRRPSRKAKVKATLGEFDLRDYRNVEVLKRFLSETGKILPRRRTGLSAKEQRILAKTIKRARILGLLP FTEKLVRK Q5SLQ0 30S ribosomal protein S19 Thermus thermophilus HB8 0.010605464 1 LEVO MPRSLKKGVFVDDHLLEKVLELNAKGEKRLIKTWSRRSTIVPEMVGHTIAVYNGKQHVPVYITENMVGHKLGEFAPTRTY RGHGKEAKATKKK Q5SHP2 30S ribosomal protein S20 Thermus thermophilus HB8 0.011736143 1 LEVO MAQKKPKRNLSALKRHRQSLKRRLRNKAKKSAIKTLSKKAIQLAQEGKAEEALKIMRKAESLIDKAAKGSTLHKNAAARR KSRLMRKVRQLLEAAGAPLIGGGLSA P80380 30S ribosomal protein Thx Thermus thermophilus HB8 0.00335003 1 LEVO MGKGDRRTRRGKIWRGTYGKYRPRKKK Q5SIH3 Translation initiation factor IF-1 Thermus thermophilus HB8 0.008247664 1 Escherichia coli BL21(DE3) LEVO MAKEKDTIRTEGVVTEALPNATFRVKLDSGPEILAYISGKMRMHYIRILPGDRVVVEITPYDPTRGRIVYRK Q5SHR1 Translation initiation factor IF-3 Thermus thermophilus HB8 0.019904377 1 Escherichia coli BL21(DE3) LEVO MKEYLTNERIRAKQVRVVGPDGKQLGIMDTREALRLAQEMDLDLVLVGPNADPPVARIMDYSKWRYEQQMAEKEARKKAK RTEVKSIKFRVKIDEHDYQTKLGHIKRFLQEGHKVKVTIMFRGREVAHPELGERILNRVTEDLKDLAVVEMKPEMLGRDM NMLLAPVKVSA Q5SKU2 mRNA Thermus thermophilus HB8 0.013466019 1 GCUCUUUUAACAAUUUAUCAGGCAAGGAGGUAAAAAUGUUCA tRNAi Thermus thermophilus HB8 0.024861937999999997 1 CGCGGGG(4SU)GGAGCAGCCUGGUAGCUCGUCGGG(OMC)UCAUAACCCGAAG(G7M)UCGUCGG(5MU)(PSU)CAAA UCCGGCCCCCGCAACCA ZINC ION 6.5409e-05 2 ZN MAGNESIUM ION 2.4305e-05 2 MG 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 20 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 78000.0 104478.0 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 PHASE FLIPPING AND AMPLITUDE CORRECTION 1HR0 FOURIER SPACE 4.45 FSC 0.143 CUT-OFF RELION 1.4 17176 PROJECTION MATCHING RELION 1.4 ANGULAR RECONSTITUTION RELION 1.4 RELION 1.4 emd_4077.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 -0.12851952 0.4375484 0.00017137593 0.022150738 1.34 1.34 1.34 0.075 AUTHOR ::::EMDATABANK.org::::D_1200000980:::: OTHER FSC RECIPROCAL emd_4077_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 -0.038821995 0.11390632 0.00008653689 0.008278763 1.34 1.34 1.34 AUTHOR ::::EMDATABANK.org::::D_1200000980:::: emd_4077_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 -0.037609283 0.12319351 0.00008070199 0.008301642 1.34 1.34 1.34 AUTHOR ::::EMDATABANK.org::::D_1200000980::::