2026-06-24 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_software _em_admin.last_update _em_software.name EXPERIMENTAL_SUMMARY em_admin _em_admin.last_update STRUCTURE_SUMMARY em_admin em_software pdbx_entry_details _em_admin.last_update _em_software.name _pdbx_entry_details.has_protein_modification DERIVED_CALCULATIONS atom_site chem_comp chem_comp_atom chem_comp_bond em_admin pdbx_struct_conn_angle struct_conn _atom_site.auth_atom_id _atom_site.label_atom_id _chem_comp.mon_nstd_flag _chem_comp_atom.atom_id _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _em_admin.last_update _pdbx_struct_conn_angle.ptnr1_label_atom_id _pdbx_struct_conn_angle.ptnr3_label_atom_id _struct_conn.ptnr1_label_atom_id PDBe PDBe 2022-04-06 2022-06-29 2022-06-29 2026-06-24 Agence Nationale de la Recherche (ANR) France Kazan R Bourgeois G Mechulam Y Coureux PD Schmitt E Initiation complex, translation initiation, small ribosomal subunit, aIF5b, TRANSLATION Kazan R Bourgeois G Lazennec-Schurdevin C Larquet E Mechulam Y Coureux PD Schmitt E Nucleic Acids Res. UK 50 6532 6548 2022 35694843 doi:10.1093/nar/gkac490 1362-4962 0389 NARHAD 7zhg FULLOVERLAP EMDB EMD-14731 associated EM volume

Cryo-EM structure of an archaeal aIF5B bound to the ssu translation initiation complex

High resolution 30S ribosomal subunit with a fragment of mRNA and tRNA High resolution 30S ribosomal subunit with a fragment of mRNA and tRNA 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 27 28 29 30 31 High resolution 30S ribosomal subunit with a fragment of mRNA 1 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 27 28 29 30 Pyrococcus abyssi GE5 Met-tRNAiMet 1 31 Pyrococcus abyssi GE5 rRNA 16S Pyrococcus abyssi GE5 0.487993062 1 AUUC(4AC)GG(OMU)UGAUCCUGCCGGAGGCCACUGCUAUGGGGGUC(4AC)GACUAAGCCA(OMU)GCGAGUCAAGGG GGCGUCCCUUCUGGGACGCCACCGGCGGACGGCUCAGUAACACGUCGGUAAC(OMC)UACCCUCGGGAGGGGGAUAACCC CGGGAAACUGGGGCUAAUCCCCCAUAGGCCUGGGGUACUGGAAGGUCCCCAGGCCGAAAGGGAGCCGUAAGGCUCCGCCC GAGGAUGGGCCGGCGGC(LHH)GAUUAGGUAGUUGGUGGGGUAACGGCCCACCAAGC(4AC)GAAGAUCGGUACGGGC (4AC)GUGAGAGCGGGAGCC(4AC)GGAGAUGGACACUGAGACACGGGUCCAGGCCCUACGGGGCGCAGCAGGCGCGA (A2M)ACCUC(4AC)GCAAUGCGGGAAAC(4AC)GCGACGGGGGGACCCCCAGUGCCGUGCCUCUGGCACGGCUUUUCCG GAGUGUAAAAAGCUCCGGGAAUAAGG(OMG)CUG(OMG)GCAAGGC(4AC)GGUGGCAGCCGCCGCGGUAAUACCGGCGG CC(4AC)GAGUGGU(OMG)GCCACUAUUAUUGGG(5MC)CUAAAGCGGC(4AC)GUAGCCGGGCCCGUAAGUCCCUGGCG AAAUCCCACGGCUCAAC(4AC)GUGGGGCUCGCUGGGGAUACUGCGGGCCUUGGGAC(4AC)GGGAGAGGC(4AC)GGGG GUACCCCCGGGGUAGG(OMG)GUGAAAUCCUAUAAUCCCGGGG(OMG)GACCGCCAGUGG(5MC)GAAGGCGCC(4AC)G GCUGGAACGGGUC(4AC)GACGGUGAGGGC(4AC)GAAGGCCAGGGGAGCGAAC(4AC)GGAUUAGAUACCCGGGUAGUC (OMC)(OMU)GGCUGUAAAGGA(OMU)GCGGGCUAGGUGUCGGGCGAGCUUCGAGCUCGCCCGGUGC(4AC)G(OMU)AG GGAAGC(4AC)GUUAAG(OMC)C(4AC)GC(4AC)GCCUGGGGAGUACGGC(4AC)GCAA(OMG)G(5MC)UGAAACUUA AAGGAAUUGGCGGGGGAGCACUACAAGG(OMG)GUGGAGCGUGCGGUUUAAUU(OMG)GAU(B8H)CAACGCCGGGAACC UCAC(4AC)GGGGGCGACGGCAGGAUGAAGGCCAGGCUGAAGGUCUUGCCGGACGCGCCGAGAGGAGGUGCAUGGC (5MC)GC(4AC)GUCAGCU(OMC)GUA(OMC)(LHH)GUGAGGCGUCCACUUAAGUGUGGUAAC(OMG)AGCGAGACCCG CGCCCCCAGUUGCCAGUCCCUCCCGCUCGGGAGGGAGGCACUCUGGGGGGACUGCCGGCGAUAAGC(4AC)GGAGGAAGG GGCGGGCGACGGUAGGUCAG(OMU)AUGCCC(4AC)GAAACCCCCGGGCUACA(5MC)GCGCGCUACAAUGGGCGGGACA AUGGGUGC(4AC)GACCC(4AC)GAAAGGGGGAGGUAAUCCCCUAAACCCGCCCUCAGUUCGGAUCGCGGGCUGCAACUC GCCCGCGUGAAGCUGGAAUCCCUAGUACCCGCGCGUCAUCAUCGCGCGGCGAAUACGUCCCUGCUCCUUGCACACAC (5MC)G(OMC)CCG(OMU)CACUCCACCCGAGCGGGGCCUAGGUGAGGCCCGAUCUCCUUCGGGAGGUCGGGUCGAGCCU AGGCUCCGUGAGGGGGGAGAAGUCG(UR3)A(6MZ)CAAGGUAGC(4AC)GUAGGGG(MA6)(MA6)CCUACGG(5MC)U (5MC)GAUCAC(5MC)UCCU AJ248283.1 30S ribosomal protein S3Ae Pyrococcus abyssi GE5 GE5 / Orsay 0.022888067999999998 1 LEVO MAAKRRVSAAKDKWKLKQWYVIYAPDFFGGVEVGLTPADDPEKVLNRVVEVTLKDITGDFLKGHVKLYFQVYDVKGQNAY TKFKGMKLARSYIRSLVRRRTTRIDGIFNITTKDGYKLRVMAMVIAARRIQTSQERAIRKIMQEIIYKKAEELNFKDFVL EAVNGKIAAEIAKEAKKIYPLKKAEIRKIKVLGEPEVAA Q9V2K7 30S ribosomal protein S2 Pyrococcus abyssi GE5 GE5 / Orsay 0.023026865 1 LEVO MADEYLVPLDQYLAAGVHIGTQQKTKDMKKFIYRVRQDGLYVLDVRKTDERLKVAGKFLARFDPQSILAVSVRLYGQKPV KKFGEVTGARAIPGRFLPGTMTNPAVKNFFEPDVIIITDPRADHQAMKEAIEIGIPIVALVDTENLLSYVDLAIPTNNKG RKALALIYWILAREILYNRGEISSREEFKIPVEEFEMKIVRR Q9V191 Zn-ribbon RNA-binding protein involved in translation Pyrococcus abyssi GE5 GE5 / Orsay 0.007163395 1 LEVO MAENVELKFEIPVCTSCGREITPREHATHFVCPNCGEAIIWRCETCRLLAKPYKCPKCGWEGP G8ZFK7 30S ribosomal protein S4 Pyrococcus abyssi GE5 GE5 / Orsay 0.02138191 1 LEVO MGDPKRQRKKYETPPHPWIKERLDRERVLMDKYELKNKKELWKHETQLKNFRRRARRLLAARGKQAEIEREQLLARLKRL GLLPEDAVLDDVLSLTIEDILERRLQTIVYKKGLARTMRQARQLIVHGHIEVNGQIIRSPSYLVLKEEEDTITYARTSPF ANPQHPERMMIEKAKQGGEA P61992 30S ribosomal protein S4e Pyrococcus abyssi GE5 GE5 / Orsay 0.028246118999999997 1 LEVO MARKGPKRHLKRLAAPTSWYIERKAYKWAVRPRPGPHNMRTSIPLLYIVRDYLGYAKTAREARKILNEGKFLVDGRVRKD YKFPVGIMDVVSIPETGEHYRVLPNRIGKLILHPISEEEANIKPLRIRNKRMVKGAKIQLNFHDGTNHLIPLSEKDNYFT SYTVLMKVPEREILEVLPFEKGAYVFVTQGKNVARKGRIVEIKKFPMGWPDVVTIEDEEGELFDTLKEYAFVVGRDKPRI SLP Q9V1U8 30S ribosomal protein S5 Pyrococcus abyssi GE5 GE5 / Orsay 0.026523903999999997 1 LEVO MSQEWKEYAKRVLDEWQPKTKLGMLVKEGQITDIHEIFRKGYQIKEPEIIDVLLPEVNARENQEILDIALTVRMTDSGRR VRFRVLAAVGNRDGYVGLGIGHGREVGIAIRKAINYAKLNIIEIKRGCGSWECRCRRPHSVPFTVEGKEGSVRVKLIPGP RGLGLVIGDVGKKILRLAGIQDVWSQTLGETRTTVNFAKAVFNALYNTNKVVVTPEMIERYGIVVGRAMPASFTLE Q9V1V5 30S ribosomal protein S6e Pyrococcus abyssi GE5 GE5 / Orsay 0.014029460999999998 1 LEVO MATFKLVISDPKTGIAKQIEITGPEAEKLIGKRIGDQIPVKELGINLNELFGKEFPEDVKMEIRGGTDKDGFPMRPDIHG PRRVRILLSKGPGFRPKEKGERRKKTVRGNTISPEIVQVNVKLVY Q9UYS3 30S ribosomal protein S7 Pyrococcus abyssi GE5 GE5 / Orsay 0.024662818 1 LEVO MAKPLSERFFIPHEIKVMGRWSTEDVEVRDPSLKPYINLEPRLLPHTHGRHAKKHFGKANVHIVERLINKIMRSGGSHYK VAGHFMRREHRSLNSKKVKAYEVVKEAFKIIEKRTGKNPIQVLVWAIENAAPREDTTSVMFGGIRYHVAVDISPMRRLDV ALRNIALGASAKCYRTKMSFAEALAEEIILAANKDPKSYAYSKKLEIERIAESSR Q9V109 30S ribosomal protein S8 Pyrococcus abyssi GE5 GE5 / Orsay 0.014772246 1 LEVO MTLLDPLANALSHITNSERVGKREVYIKPASKLIGEVLRVMQKYGYIGEFEFIDDGRAGVYRVQLLGKINKAGAIKPRFP VKARDYERWEKRFLPAFEFGILIVSTSQGVMSHKEAREKGIGGRLIAYVY Q9V1V0 30S ribosomal protein S8e Pyrococcus abyssi GE5 GE5 / Orsay 0.014293733 1 LEVO MAIWQGRSLRKPSGGRIVLARKKRKRELGREPSNTRVAEQDKRKIIRTYGGNKKVRLTAAAYANVFDKSGKGRKVRIIRV IENPANRQFARRNIITKGAIIETEIGKAKVTSRPGQDGVVNAILLEE Q9UZL4 30S ribosomal protein S9 Pyrococcus abyssi GE5 GE5 / Orsay 0.015293867 1 LEVO MRIIQTTGKRKTAIARAVIREGKGRVRINGKPVELVEPEIARFTILEPLILAGEEIWNSVDIDVKVQGGGFMGQAEAARI AIARALVEWTGDMNLKEKFIKYDRTMLVGDPRRTEPHKPNRSTKGPRAKRQKSYR Q9V195 30S ribosomal protein S10 Pyrococcus abyssi GE5 GE5 / Orsay 0.011795769 1 LEVO MQKARIKLASTNVRSLEEVANQIKQIAERTGVRMSGPIPLPTKRIRIVTRKSPDGEGSATFDRWELRIHKRLIDIEADER AMRQIMRIRVPEDVTIEIELIS Q9V0V6 30S ribosomal protein S11 Pyrococcus abyssi GE5 GE5 / Orsay 0.01477295 1 LEVO MSEEQVNIKKKEKWGIAHIYSSYNNTIIHITDITGAETISRWSGGMVVKADRDEPSPYAAMLAARRAAEEALEKGIVGVH IRVRAPGGSKSKTPGPGAQAAIRALARAGLKIGRVEDVTPIPHDGTRPKGGRRGRRV P62010 30S ribosomal protein S12 Pyrococcus abyssi GE5 GE5 / Orsay 0.016477620999999998 1 LEVO MPGKKAPNGEFAGRKLKLKRKKFRWSDIRYKRRVLRLKEKSDPLEGAPQARGIVLEKIAVEAKQPNSGMRKAVRVQLIKN GKVVTAFCPGDGAIKFIDEHDEVIIEGIGGPKGGSMGDIPGIRYKVVKVNRVSLKELVKGRKEKPRR P61994 30S ribosomal protein S13 Pyrococcus abyssi GE5 GE5 / Orsay 0.016992912 1 LEVO MADFRHIVRVAGVDLDGNKQLRWALTAIKGVGINFATMVCRVAGLDPFMKAGYLTDEQVKKIEEILQDPVAHGIPRWAVN RPKDYETGRDLHLITAKLDMAIREDIMRLRRIRAYRGIRHELGLPVRGQRTRSNFRRGQTVGVSRKKK Q9V1A0 30S ribosomal protein S14 type Z Pyrococcus abyssi GE5 GE5 / Orsay 0.006644064 1 LEVO MAKADYNKRKPRKFGKGARRCIRCGQYGPIIRIHGLMLCRHCFREVAPKLGFRKYE P62012 30S ribosomal protein S15 Pyrococcus abyssi GE5 GE5 / Orsay 0.018697143 1 LEVO MARMHARKRGKSGSKRPPRTAPPIWLEYTVEDIENLVVKLRKEGYSTAMIGTILRDQYGIPTVKLFRDPDNPNRKLTITR ILEKHGLAPEIPEDLMFLIKRAVNLRKHLEQHPKDLHSMRGLQLIESKIRRLVKYYKRKGKLPKDWRYDPEQAKLLVR Q9V2K9 30S ribosomal protein S17 Pyrococcus abyssi GE5 GE5 / Orsay 0.013364603999999999 1 LEVO MVRDIGLRIQPPAEKCDDPKCPWHGHLKIHGRVFEGIVVSDKPRKTVTVERQYYHYLKKYERYELRRSRIHAHNPPCINA KVGDRVLIAETRPLSKTKHFVVVAVLERAEERR Q9V1U5 30S ribosomal protein S17e Pyrococcus abyssi GE5 GE5 / Orsay 0.008059528 1 LEVO MGKIRQGFIKRVARELFNKYPNEFTRDFEHNKKKVEELTNVTSKKIRNRIAGYITKLVRMKEEGKIL Q9V0G0 30S ribosomal protein S19 Pyrococcus abyssi GE5 GE5 / Orsay 0.015307318999999998 1 LEVO MARKEFRYRGYTLEQLMNMSLEELAKLLPARQRRSLKRGLTPEQKKLLRKIRLAKKGKYNKPIRTHCRDMIVLPEMVGLT IYVHNGKEFVPVEIKPEMIGHYLGEFAPTRKRVQHGAPGIGATRSSMFVAVK Q9V1T9 30S ribosomal protein S19e Pyrococcus abyssi GE5 GE5 / Orsay 0.01742225 1 LEVO MATVYDVPGDLLVERVAQRLKEIPEIKPPEWAPFVKTGRHKERLPEQEDWWYYRVASILRRVYLDGPVGIERLRTYYGGR KNRGHAPERFYKAGGSIIRKALQQLEAAGFVEKVPGKGRVITPKGRSFLDKIATELKKELEEIIPELKKY Q9V0G8 30S ribosomal protein S24e Pyrococcus abyssi GE5 GE5 / Orsay 0.011798637 1 LEVO MEIKITEVKENKLIGRKEIYFEIYHPGEPTPSRKDVKGKLVAMLDLNPETTVIQYIRSYFGSYKSKGYAKYYYDKDRMLY IEPEYILIRDGIIEKKEGE Q9UY20 30S ribosomal protein S27e Pyrococcus abyssi GE5 GE5 / Orsay 0.007186609 1 LEVO MALPRNVIPMPRSRFLRVKCIDCGNEQIVFSHPATRVRCNVCGATLVEPTGGKGIIRAKILEVLE Q9UXZ3 30S ribosomal protein S28e Pyrococcus abyssi GE5 GE5 / Orsay 0.008102305 1 LEVO MAEDEGYPAEVIEIIGRTGTTGDVTQVKVRILEGRDKGRVIRRNVRGPVRVGDILILRETEREAREIKSRR P61029 30S ribosomal protein S27ae Pyrococcus abyssi GE5 GE5 / Orsay 0.005992167999999999 1 LEVO MGQKWKLYIVKDGKVIRKNKFCPRCGPGVFMADHGDRWACGRCGYTEWKKK P61238 30S ribosomal protein S3 Pyrococcus abyssi GE5 GE5 / Orsay 0.023472309 1 LEVO MAIERYFIREAVKEMLIDEFLEKELRRAGYGGLDIKKTPLGTKVIIFAANPGYVIGRGGRRIRELTRILERQFGLENPQI DVQEIKNPYLNAKVQAVRIAQALERGIHFRRAAYAAMRAIMSNGARGVEIRISGKLTGERAKSVRFYQGYLAKVGNPAET LVSKGYAQALLKLGVIGVKVAIMPPDARLPDEIEIIEKPVEEEVSSNEAE Q9V1U1 50S ribosomal protein L41e Pyrococcus abyssi GE5 ATCC 43587 / DSM 3638 / JCM 8422 / Vc1 0.004910237 1 LEVO MKRRPRKWKKKGRMRWKWIKKRIRRLKRQRKKERGL Q8U232 50S ribosomal protein L7Ae Pyrococcus abyssi GE5 GE5 / Orsay 0.013442678 1 LEVO MAKPSYVKFEVPKELAEKALQAVEIARDTGKIRKGTNETTKAVERGQAKLVIIAEDVDPEEIVAHLPPLCEEKEIPYIYV PSKKELGAAAGIEVAAASVAIIEPGKARDLVEEIAMKVRELMK P62008 mRNA Pyrococcus abyssi GE5 0.005509302 1 UGGAGGUGAUUUAAAUG Met-tRNAiMet Pyrococcus abyssi GE5 0.024833903999999997 1 AGCGGGG(4SU)GGAGCAGCCUGG(H2U)AGCUCGUCGGG(OMC)UCAUAACCCGAAGAUCGUCGG(5MU)(PSU)CAAA UCCGGCCCCCGCUACCA CP026027.1 MAGNESIUM ION 2.4305e-05 90 MG ZINC ION 6.5409e-05 6 ZN water 1.8015e-05 2083 HOH singleParticle particle 6.7 Quantifoil R2/1 COPPER CARBON CONTINUOUS 2.0 ETHANE TFS KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 0.8 2.5 FEI TITAN KRIOS AUTOGRID HOLDER GATAN K3 BIOQUANTUM (6k x 4k) 39.0 1 2000000 PHASE FLIPPING AND AMPLITUDE CORRECTION 6SWC 2.25 FSC 0.143 CUT-OFF 1000000 ANGULAR RECONSTITUTION MAXIMUM LIKELIHOOD AB INITIO MODEL REAL emd_14731_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 432 432 432 0 0 0 432 432 432 371.52002 371.52002 371.52002 90.0 90.0 90.0 X Y Z -0.01305583 0.08088628 0.00024944352 0.002848076 0.8600001 0.8600001 0.8600001 AUTHOR ::::EMDATABANK.org::::EMD-14731:::: emd_14731_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 432 432 432 0 0 0 432 432 432 371.52002 371.52002 371.52002 90.0 90.0 90.0 X Y Z -0.0141767 0.0862847 0.00024852733 0.0029828534 0.8600001 0.8600001 0.8600001 AUTHOR ::::EMDATABANK.org::::EMD-14731:::: emd_14731_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 432 432 432 0 0 0 432 432 432 371.52002 371.52002 371.52002 90.0 90.0 90.0 X Y Z -0.014423148 0.08597753 0.00025036346 0.0029823913 0.8600001 0.8600001 0.8600001 AUTHOR ::::EMDATABANK.org::::EMD-14731::::