Structure of the 30S Pre-Initiation Complex 1 (30S IC-1) Stalled by GE81112

2025-10-01 REL PDBe INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY EXPERIMENTAL_SUMMARY em_admin _em_admin.last_update DERIVED_CALCULATIONS em_imaging_optics em_software pdbx_validate_polymer_linkage struct_conn _em_imaging_optics.energyfilter_name _em_software.name AUTHOR_SUPPORTING_EVIDENCE pdbx_audit_support _pdbx_audit_support.funding_organization DERIVED_CALCULATIONS pdbx_validate_close_contact pdbx_validate_polymer_linkage struct_conn DERIVED_CALCULATIONS pdbx_validate_close_contact struct_conn OTHER atom_sites cell _atom_sites.fract_transf_matrix[1][1] _atom_sites.fract_transf_matrix[2][2] _atom_sites.fract_transf_matrix[3][3] _cell.Z_PDB OTHER symmetry _symmetry.Int_Tables_number _symmetry.space_group_name_H-M REFINEMENT_DESCRIPTION chem_comp_atom chem_comp_bond database_2 em_3d_fitting_list pdbx_initial_refinement_model struct_conn _database_2.pdbx_DOI _database_2.pdbx_database_accession _em_3d_fitting_list.accession_code _em_3d_fitting_list.initial_refinement_model_id _em_3d_fitting_list.source_name _em_3d_fitting_list.type _struct_conn.pdbx_dist_value _struct_conn.pdbx_leaving_atom_flag _struct_conn.ptnr1_label_atom_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_entry_details pdbx_modification_feature pdbx_validate_close_contact struct_conn _em_admin.last_update PDBe PDBe 2016-11-14 2017-01-11 2017-01-11 2025-10-01 European Union QLRT- 2001-00892 Italy Marie Curie Actions; COFUND Spain Marie Curie Action Career Integration Grant PCIG14-GA-2013-632072 Spain Spanish Ministry of Economy and Competitiveness CTQ2014-55907-R Spain Structure of the 30S Pre-Initiation Complex 1 (30S IC-1) Stalled by GE81112 Lopez-Alonso JP Fabbretti A Ribosome, Initiation of Translation Lopez-Alonso JP Fabbretti A Kaminishi T Iturrioz I Brandi L Gil-Carton D Gualerzi CO Fucini P Connell SR Structure of a 30S pre-initiation complex stalled by GE81112 reveals structural parallels in bacterial and eukaryotic protein synthesis initiation pathways. Nucleic Acids Res. UK 45 2179 2187 2017 27986852 doi:10.1093/nar/gkw1251 1362-4962 0389 NARHAD 5me0 FULLOVERLAP EMDB EMD-3494 associated EM volume

Structure of a 30S Pre-Initiation Complex 1 (30S IC-1) Stalled by GE81112

30S Pre-Initiation Complex Stalled by GE81112 30S Pre-Initiation Complex Stalled by GE81112 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 26 Escherichia coli 16S ribosomal RNA Escherichia coli K-12 0.497404969

Taken from PDB entry 4YBB

1 AAAUUGAAGAGUUUGAUCAUGGCUCAGAUUGAACGCUGGCGGCAGGCCUAACACAUGCAAGUCGAACGGUAACAGGAAGA AGCUUGCUUCUUUGCUGACGAGUGGCGGACGGGUGAGUAAUGUCUGGGAAACUGCCUGAUGGAGGGGGAUAACUACUGGA AACGGUAGCUAAUACCGCAUAACGUCGCAAGACCAAAGAGGGGGACCUUCGGGCCUCUUGCCAUCGGAUGUGCCCAGAUG GGAUUAGCUAGUAGGUGGGGUAACGGCUCACCUAGGCGACGAUCCCUAGCUGGUCUGAGAGGAUGACCAGCCACACUGGA ACUGAGACACGGUCCAGACUCCUACGGGAGGCAGCAGUGGGGAAUAUUGCACAAUGGGCGCAAGCCUGAUGCAGCCAUGC CGCGUGUAUGAAGAAGGCCUUCGGGUUGUAAAGUACUUUCAGCGGGGAGGAAGGGAGUAAAGUUAAUACCUUUGCUCAUU GACGUUACCCGCAGAAGAAGCACCGGCUAACUCCG(PSU)GCCAGCAGCC(G7M)CGGUAAUACGGAGGGUGCAAGCGUU AAUCGGAAUUACUGGGCGUAAAGCGCACGCAGGCGGUUUGUUAAGUCAGAUGUGAAAUCCCCGGGCUCAACCUGGGAACU GCAUCUGAUACUGGCAAGCUUGAGUCUCGUAGAGGGGGGUAGAAUUCCAGGUGUAGCGGUGAAAUGCGUAGAGAUCUGGA GGAAUACCGGUGGCGAAGGCGGCCCCCUGGACGAAGACUGACGCUCAGGUGCGAAAGCGUGGGGAGCAAACAGGAUUAGA UACCCUGGUAGUCCACGCCGUAAACGAUGUCGACUUGGAGGUUGUGCCCUUGAGGCGUGGCUUCCGGAGCUAACGCGUUA AGUCGACCGCCUGGGGAGUACGGCCGCAAGGUUAAAACUCAAAUGAAUUGACGGGGGCCCGCACAAGCGGUGGAGCAUGU GGUUUAAUUCGAU(2MG)(5MC)AACGCGAAGAACCUUACCUGGUCUUGACAUCCACGGAAGUUUUCAGAGAUGAGAAUG UGCCUUCGGGAACCGUGAGACAGGUGCUGCAUGGCUGUCGUCAGCUCGUGUUGUGAAAUGUUGGGUUAAGUCCCGCAACG AGCGCAACCCUUAUCCUUUGUUGCCAGCGGUCCGGCCGGGAACUCAAAGGAGACUGCCAGUGAUAAACUGGAGGAAGGUG GGGAUGACGUCAAGUCAUCAUG(2MG)CCCUUACGACCAGGGCUACACACGUGCUACAAUGGCGCAUACAAAGAGAAGCG ACCUCGCGAGAGCAAGCGGACCUCAUAAAGUGCGUCGUAGUCCGGAUUGGAGUCUGCAACUCGACUCCAUGAAGUCGGAA UCGCUAGUAAUCGUGGAUCAGAAUGCCACGGUGAAUACGUUCCCGGGCCUUGUACACACCG(4OC)CCGU(5MC)ACACC AUGGGAGUGGGUUGCAAAAGAAGUAGGUAGCUUAACCUUCGGGAGGGCGCUUACCACUUUGUGAUUCAUGACUGGGGUGA AGUCG(UR3)AACAAGGUAACCGUAGG(2MG)G(MA6)(MA6)CCUGCGGUUGGAUCA CP011320.1 30S ribosomal protein S2 Escherichia coli K-12 0.026781669999999997

Taken from PDB entry 4YBB

1 LEVO MATVSMRDMLKAGVHFGHQTRYWNPKMKPFIFGARNKVHIINLEKTVPMFNEALAELNKIASRKGKILFVGTKRAASEAV KDAALSCDQFFVNHRWLGGMLTNWKTVRQSIKRLKDLETQSQDGTFDKLTKKEALMRTRELEKLENSLGGIKDMGGLPDA LFVIDADHEHIAIKEANNLGIPVFAIVDTNSDPDGVDFVIPGNDDAIRAVTLYLGAVAATVREGRSQDLASQAEESFVEA E P0A7V0 30S ribosomal protein S3 Escherichia coli K-12 0.026031316

Taken from PDB entry 4YBB

1 LEVO MGQKVHPNGIRLGIVKPWNSTWFANTKEFADNLDSDFKVRQYLTKELAKASVSRIVIERPAKSIRVTIHTARPGIVIGKK GEDVEKLRKVVADIAGVPAQINIAEVRKPELDAKLVADSITSQLERRVMFRRAMKRAVQNAMRLGAKGIKVEVSGRLGGA EIARTEWYREGRVPLHTLRADIDYNTSEAHTTYGVIGVKVWIFKGEILGGMAAVEQPEKPAAQPKKQQRKGRK P0A7V3 30S ribosomal protein S4 Escherichia coli K-12 0.023514199

Taken from PDB entry 4YBB

1 LEVO MARYLGPKLKLSRREGTDLFLKSGVRAIDTKCKIEQAPGQHGARKPRLSDYGVQLREKQKVRRIYGVLERQFRNYYKEAA RLKGNTGENLLALLEGRLDNVVYRMGFGATRAEARQLVSHKAIMVNGRVVNIASYQVSPNDVVSIREKAKKQSRVKAALE LAEQREKPTWLEVDAGKMEGTFKRKPERSDLSADINEHLIVELYSK P0A7V8 30S ribosomal protein S5 Escherichia coli K-12 0.017629398

Taken from PDB entry 4YBB

1 LEVO MAHIEKQAGELQEKLIAVNRVSKTVKGGRIFSFTALTVVGDGNGRVGFGYGKAREVPAAIQKAMEKARRNMINVALNNGT LQHPVKGVHTGSRVFMQPASEGTGIIAGGAMRAVLEVAGVHNVLAKAYGSTNPINVVRATIDGLENMNSPEMVAAKRGKS VEEILGK P0A7W1 30S ribosomal protein S6 Escherichia coli K-12 0.015211058

Taken from PDB entry 4YBB

1 LEVO MRHYEIVFMVHPDQSEQVPGMIERYTAAITGAEGKIHRLEDWGRRQLAYPINKLHKAHYVLMNVEAPQEVIDELETTFRF NDAVIRSMVMRTKHAVTEASPMVKAKDERRERRDDFANETADDAEAGDSEE P02358 30S ribosomal protein S7 Escherichia coli K-12 0.017637444999999998

Taken from PDB entry 4YBB

1 LEVO MPRRRVIGQRKILPDPKFGSELLAKFVNILMVDGKKSTAESIVYSALETLAQRSGKSELEAFEVALENVRPTVEVKSRRV GGSTYQVPVEVRPVRRNALAMRWIVEAARKRGDKSMALRLANELSDAAENKGTAVKKREDVHRMAEANKAFAHYRW P02359 30S ribosomal protein S8 Escherichia coli K-12 0.014146557

Taken from PDB entry 4YBB

1 LEVO MSMQDPIADMLTRIRNGQAANKAAVTMPSSKLKVAIANVLKEEGFIEDFKVEGDTKPELELTLKYFQGKAVVESIQRVSR PGLRIYKRKDELPKVMAGLGIAVVSTSKGVMTDRAARQAGLGGEIICYVA P0A7W7 30S ribosomal protein S9 Escherichia coli K-12 0.01488627

Taken from PDB entry 4YBB

1 LEVO MAENQYYGTGRRKSSAARVFIKPGNGKIVINQRSLEQYFGRETARMVVRQPLELVDMVEKLDLYITVKGGGISGQAGAIR HGITRALMEYDESLRSELRKAGFVTRDARQVERKKVGLRKARRRPQFSKR P0A7X3 30S ribosomal protein S10 Escherichia coli K-12 0.011755597

Taken from PDB entry 4YBB

1 LEVO MQNQRIRIRLKAFDHRLIDQATAEIVETAKRTGAQVRGPIPLPTRKERFTVLISPHVNKDARDQYEIRTHLRLVDIVEPT EKTVDALMRLDLAAGVDVQISLG P0A7R5 30S ribosomal protein S11 Escherichia coli K-12 0.013870974999999999

Taken from PDB entry 4YBB

1 LEVO MAKAPIRARKRVRKQVSDGVAHIHASFNNTIVTITDRQGNALGWATAGGSGFRGSRKSTPFAAQVAAERCADAVKEYGIK NLEVMVKGPGPGRESTIRALNAAGFRITNITDVTPIPHNGCRPPKKRRV P0A7R9 30S ribosomal protein S12 Escherichia coli K-12 0.013683052999999999

Taken from PDB entry 4YBB

1 LEVO ATVNQLVRKPRARKVAKSNVPALEACPQKRGVCTRVYTTTPKKPNSALRKVCRVRLTNGFEVTSYIGGEGHNLQEHSVIL IRGGRVK(D2T)LPGVRYHTVRGALDCSGVKDRKQARSKYGVKRPKA P0A7S3 30S ribosomal protein S13 Escherichia coli K-12 0.013128467

Taken from PDB entry 4YBB

1 LEVO MARIAGINIPDHKHAVIALTSIYGVGKTRSKAILAAAGIAEDVKISELSEGQIDTLRDEVAKFVVEGDLRREISMSIKRL MDLGCYRGLRHRRGLPVRGQRTKTNARTRKGPRKPIKK P0A7S9 30S ribosomal protein S14 Escherichia coli K-12 0.011606559999999998

Taken from PDB entry 4YBB

1 LEVO MAKQSMKAREVKRVALADKYFAKRAELKAIISDVNASDEDRWNAVLKLQTLPRDSSPSRQRNRCRQTGRPHGFLRKFGLS RIKVREAAMRGEIPGLKKASW P0AG59 30S ribosomal protein S15 Escherichia coli K-12 0.010290816

Taken from PDB entry 4YBB

1 LEVO MSLSTEATAKIVSEFGRDANDTGSTEVQVALLTAQINHLQGHFAEHKKDHHSRRGLLRMVSQRRKLLDYLKRKDVARYTQ LIERLGLRR P0ADZ4 30S ribosomal protein S16 Escherichia coli K-12 0.011464126

Taken from PDB entry 4YBB

1 LEVO MTPDSVPRWGPVVLFTQEDVMVTIRLARHGAKKRPFYQVVVADSRNARNGRFIERVGFFNPIASEKEEGTRLDLDRIAHW VGQGATISDRVAALIKEVNKAA A0A0U4BH30 30S ribosomal protein S17 Escherichia coli K-12 0.009724491

Taken from PDB entry 4YBB

1 LEVO MTDKIRTLQGRVVSDKMEKSIVVAIERFVKHPIYGKFIKRTTKLHVHDENNECGIGDVVEIRECRPLSKTKSWTLVRVVE KAVL P0AG63 30S ribosomal protein S18 Escherichia coli K-12 0.009005471999999999

Taken from PDB entry 4YBB

1 LEVO MARYFRRRKFCRFTAEGVQEIDYKDIATLKNYITESGKIVPSRITGTRAKYQRQLARAIKRARYLSLLPYTDRHQ P0A7T7 30S ribosomal protein S19 Escherichia coli K-12 0.010455355

Taken from PDB entry 4YBB

1 LEVO MPRSLKKGPFIDLHLLKKVEKAVESGDKKPLRTWSRRSTIFPNMIGLTIAVHNGRQHVPVFVTDEMVGHKLGEFAPTRTY RGHAADKKAKKK P0A7U3 30S ribosomal protein S20 Escherichia coli K-12 0.009708464

Taken from PDB entry 4YBB

1 LEVO MANIKSAKKRAIQSEKARKHNASRRSMMRTFIKKVYAAIEAGDKAAAQKAFNEMQPIVDRQAAKGLIHKNKAARHKANLT AQINKLA P0A7U7 30S ribosomal protein S21 Escherichia coli K-12 0.008524039

Taken from PDB entry 4YBB

1 LEVO MPVIKVRENEPFDVALRRFKRSCEKAGVLAEVRRREFYEKPTTERKRAKASAVKRHAKKLARENARRTRLY P68679 Translation initiation factor IF-1 Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) HB8 / ATCC 27634 / DSM 579 0.008247664

Taken from PDB entry 1HR0

1 Escherichia coli LEVO MAKEKDTIRTEGVVTEALPNATFRVKLDSGPEILAYISGKMRMHYIRILPGDRVVVEITPYDPTRGRIVYRK Q5SHR1 Translation initiation factor IF-2 Escherichia coli K-12 0.097498164

Taken from PDB entry 3JCN

1 Escherichia coli LEVO MTDVTIKTLAAERQTSVERLVQQFADAGIRKSADDSVSAQEKQTLIDHLNQKNSGPDKLTLQRKTRSTLNIPGTGGKSKS VQIEVRKKRTFVKRDPQEAERLAAEEQAQREAEEQARREAEESAKREAQQKAEREAAEQAKREAAEQAKREAAEKDKVSN QQDDMTKNAQAEKARREQEAAELKRKAEEEARRKLEEEARRVAEEARRMAEENKWTDNAEPTEDSSDYHVTTSQHARQAE DESDREVEGGRGRGRNAKAARPKKGNKHAESKADREEARAAVRGGKGGKRKGSSLQQGFQKPAQAVNRDVVIGETITVGE LANKMAVKGSQVIKAMMKLGAMATINQVIDQETAQLVAEEMGHKVILRRENELEEAVMSDRDTGAAAEPRAPVVTIMGHV DHGKTSLLDYIRSTKVASGEAGGITQHIGAYHVETENGMITFLDTPGHAAFTSMRARGAQATDIVVLVVAADDGVMPQTI EAIQHAKAAQVPVVVAVNKIDKPEADPDRVKNELSQYGILPEEWGGESQFVHVSAKAGTGIDELLDAILLQAEVLELKAV RKGMASGAVIESFLDKGRGPVATVLVREGTLHKGDIVLCGFEYGRVRAMRNELGQEVLEAGPSIPVEILGLSGVPAAGDE VTVVRDEKKAREVALYRQGKFREVKLARQQKSKLENMFANMTEGEVHEVNIVLKADVQGSVEAISDSLLKLSTDEVKVKI IGSGVGGITETDATLAAASNAILVGFNVRADASARKVIEAESLDLRYYSVIYNLIDEVKAAMSGMLSPELKQQIIGLAEV RDVFKSPKFGAIAGCMVTEGVVKRHNPIRVLRDNVVIYEGELESLRRFKDDVNEVRNGMECGIGVKNYNDVRTGDVIEVF EIIEIQRTIA P0A705 Translation initiation factor IF-3 Geobacillus stearothermophilus 0.019717984

Taken from PDB entry 1TIF

1 Escherichia coli LEVO SKDFIINEQIRAREVRLIDQNGDQLGIKSKQEALEIAARRNLDLVLVAPNAKPPVCRIMDYGKFRFEQQKKEKEARKKQK VINVKEVRLSPTIEEHDFNTKLRNARKFLEKGDKVKATIRFKGRAITHKEIGQRVLDRLSEACADIAVVETAPKMDGRNM FLVLAPKNDNK P03000 Translation initiation factor IF-3 Escherichia coli K-12 0.016667476999999997

Taken from PDB entry 2IFE

1 Escherichia coli LEVO MSLREALEKAEEAGVDLVEISPNAEPPVCRIMDYGKFLYEKSKSSKEQKKKQKVIQVKEIKFRPGTDEGDYQVKLRSLIR FLEEGDKAKITLRFRGREMAHQQIGMEVLNRVKDDLQELAVVESFPTKIEGRQMIMVLAPKKKQ P0A707 fMet-tRNA Escherichia coli K-12 0.024818892999999998

Taken from PDB entry 3JCN

1 CGCGGGG(4SU)GGAGCAGCCUGG(H2U)AGCUCGUCGGGCUCAUAACCCGAAGAUCGUCGG(5MU)(PSU)CAAAUCCG GCCCCCGCAACCA CP009789.1 N-FORMYLMETHIONINE 0.000177221 1 FME singleParticle particle 7.7 10.0 TrisHCl Tris 7.0 MgCl2 Magnesium chloride 60.0 CH3CO2NH4 Ammonium acetate Quantifoil R2/1 COPPER 200 GLOW DISCHARGE 50 AIR 0.02 ETHANE 95 277 FEI VITROBOT MARK II JEOL 2200FSC FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 200 2.0 50000.0 74183.0 GATAN LIQUID NITROGEN NITROGEN In-column Omega Filter GATAN ULTRASCAN 4000 (4k x 4k) 4096 4096 1 261 0.3 17.0 1 174142 CTFFIND 4 PHASE FLIPPING AND AMPLITUDE CORRECTION

Previous empty 30S volume obtained in our lab.

1 C1 13.5 FSC 0.143 CUT-OFF RELION 1.4 23112 PROJECTION MATCHING RELION 1.4 PROJECTION MATCHING RELION 1.4 3 RELION 1.4 emd_3494.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 180 180 180 0 0 0 180 180 180 363.6 363.6 363.6 90.0 90.0 90.0 X Y Z -0.083444044 0.34673113 0.005679719 0.031103546 2.02 2.02 2.02 0.0747 AUTHOR ::::EMDATABANK.org::::EMD-3494:::: 4YBB PDB experimental model 3JCN v PDB experimental model 3JCN b PDB experimental model 1HR0 W PDB experimental model 2IFE A 90-180 PDB experimental model 1TIF A 3-78 PDB experimental model RIGID BODY FIT

The fitting of the model to the EM volume was performed through rigid body fitting. The head and the body of the 30S were treated as independent bodies. Due to the low resolution of the volume, the conformation of the linking bases was not minimized. In addition, some of the clashes of the model are produced by flexible loops or protein side chains that were not refined.

emd_3494_msk_1.map emd_3494_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 180 180 180 0 0 0 180 180 180 363.6 363.6 363.6 90.0 90.0 90.0 X Y Z -0.024030857 0.13683358 0.0017756877 0.014872072 2.02 2.02 2.02 AUTHOR ::::EMDATABANK.org::::D_1200001520:::: emd_3494_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 180 180 180 0 0 0 180 180 180 363.6 363.6 363.6 90.0 90.0 90.0 X Y Z -0.026231483 0.13625544 0.0017406734 0.014891765 2.02 2.02 2.02 AUTHOR ::::EMDATABANK.org::::D_1200001520::::