IC2 head of cryo-EM structure of a full archaeal ribosomal translation initiation complex devoid of aIF1 in P. abyssi

2025-12-24 REL PDBe INITIAL_RELEASE REPOSITORY 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 EXPERIMENTAL_SUMMARY em_admin _em_admin.last_update DATA_COLLECTION chem_comp chem_comp_atom chem_comp_bond em_admin _chem_comp.mon_nstd_flag _chem_comp_atom.atom_id _chem_comp_bond.atom_id_2 _em_admin.last_update PDBe PDBe 2019-09-20 2020-02-19 2020-02-19 2025-12-24 French National Research Agency ANR-17-CE11-0037 France IC2 head of cryo-EM structure of a full archaeal ribosomal translation initiation complex devoid of aIF1 in P. abyssi Coureux P-D Mechulam Y Schmitt E Translation initiation, cryo-EM, ribosome, tRNA, evolution, archaea, rRNA modifications Coureux PD Lazennec-Schurdevin C Bourcier S Mechulam Y Schmitt E Cryo-EM study of an archaeal 30S initiation complex gives insights into evolution of translation initiation. Commun Biol UK 3 58 58 2020 32029867 doi:10.1038/s42003-020-0780-0 2399-3642 6swe FULLOVERLAP EMDB EMD-10324 associated EM volume

Archaeal translation initiation complex devoid of aIF1 - IC2 head Archaeal translation initiation complex devoid of aIF1 - IC2 head 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 1.05 30S 1 1 2 3 4 5 6 7 8 9 10 11 12 13 Pyrococcus abyssi (strain GE5 / Orsay) initiator Met-tRNA fMet from E. coli (A1U72 variant) 1 14 Escherichia coli translation initiation factor 1A 1 15 Pyrococcus abyssi (strain GE5 / Orsay) 16S ribosomal RNA Pyrococcus abyssi GE5 0.152069453 1 GUAAGGCGGGGGAGCACUACAAGGGGUGGAGCGUGCGGUUUAAUUGGAU(B8H)(5MC)AACGCCGGGAACCUCAC (4AC)GGGGGCGACGGCAGGAUGAAGGCCAGGCUGAAGGUCUUGCCGGACGCGCCGAGAGGAGGUGCAUGGCCGC(4AC) GUCAGCUCGGCGUCCACUUAAGUGUGGUAACGAGCGAGACCCGCGCCCCCAGUUGCCAGUCCCUCCCGCUCGGGAGGGAG GCACUCUGGGGGGACUGCCGGCGAUAAGC(4AC)GGAGGAAGGGGCGGGCGACGGUAGGUCAGUAUGCCC(4AC)GAAAC CCC(4AC)GGGCUACA(5MC)GCGCGCUACAAUGGGCGGGACAAUGGGUGC(4AC)GACCC(4AC)GAAAGGGGGAGGUA AUCCCCUAAACCCGCCCUCAGUUCGGAUCGCGGGCUGCAACUCGCCCGCGUGAAGCUGGAAUCCCUAGUACCCGCGCGUC AUCAUCGCGCGGCGAAUACGUCCCUGCUCCUU 30S ribosomal protein S7 Pyrococcus abyssi (strain GE5 / Orsay) GE5 / Orsay 0.024662818 1 LEVO MAKPLSERFFIPHEIKVMGRWSTEDVEVRDPSLKPYINLEPRLLPHTHGRHAKKHFGKANVHIVERLINKIMRSGGSHYK VAGHFMRREHRSLNSKKVKAYEVVKEAFKIIEKRTGKNPIQVLVWAIENAAPREDTTSVMFGGIRYHVAVDISPMRRLDV ALRNIALGASAKCYRTKMSFAEALAEEIILAANKDPKSYAYSKKLEIERIAESSR Q9V109 30S ribosomal protein S9 Pyrococcus abyssi (strain GE5 / Orsay) GE5 / Orsay 0.015293867 1 LEVO MRIIQTTGKRKTAIARAVIREGKGRVRINGKPVELVEPEIARFTILEPLILAGEEIWNSVDIDVKVQGGGFMGQAEAARI AIARALVEWTGDMNLKEKFIKYDRTMLVGDPRRTEPHKPNRSTKGPRAKRQKSYR Q9V195 30S ribosomal protein S10 Pyrococcus abyssi (strain GE5 / Orsay) GE5 / Orsay 0.011795769 1 LEVO MQKARIKLASTNVRSLEEVANQIKQIAERTGVRMSGPIPLPTKRIRIVTRKSPDGEGSATFDRWELRIHKRLIDIEADER AMRQIMRIRVPEDVTIEIELIS Q9V0V6 30S ribosomal protein S13 Pyrococcus abyssi (strain GE5 / Orsay) GE5 / Orsay 0.016992912 1 LEVO MADFRHIVRVAGVDLDGNKQLRWALTAIKGVGINFATMVCRVAGLDPFMKAGYLTDEQVKKIEEILQDPVAHGIPRWAVN RPKDYETGRDLHLITAKLDMAIREDIMRLRRIRAYRGIRHELGLPVRGQRTRSNFRRGQTVGVSRKKK Q9V1A0 30S ribosomal protein S14 type Z Pyrococcus abyssi (strain GE5 / Orsay) GE5 / Orsay 0.006644064 1 LEVO MAKADYNKRKPRKFGKGARRCIRCGQYGPIIRIHGLMLCRHCFREVAPKLGFRKYE P62012 30S ribosomal protein S17e Pyrococcus abyssi (strain GE5 / Orsay) GE5 / Orsay 0.008059528 1 LEVO MGKIRQGFIKRVARELFNKYPNEFTRDFEHNKKKVEELTNVTSKKIRNRIAGYITKLVRMKEEGKIL Q9V0G0 30S ribosomal protein S19 Pyrococcus abyssi (strain GE5 / Orsay) GE5 / Orsay 0.015307318999999998 1 LEVO MARKEFRYRGYTLEQLMNMSLEELAKLLPARQRRSLKRGLTPEQKKLLRKIRLAKKGKYNKPIRTHCRDMIVLPEMVGLT IYVHNGKEFVPVEIKPEMIGHYLGEFAPTRKRVQHGAPGIGATRSSMFVAVK Q9V1T9 30S ribosomal protein S19e Pyrococcus abyssi (strain GE5 / Orsay) GE5 / Orsay 0.01742225 1 LEVO MATVYDVPGDLLVERVAQRLKEIPEIKPPEWAPFVKTGRHKERLPEQEDWWYYRVASILRRVYLDGPVGIERLRTYYGGR KNRGHAPERFYKAGGSIIRKALQQLEAAGFVEKVPGKGRVITPKGRSFLDKIATELKKELEEIIPELKKY Q9V0G8 30S ribosomal protein S28e Pyrococcus abyssi (strain GE5 / Orsay) GE5 / Orsay 0.008102305 1 LEVO MAEDEGYPAEVIEIIGRTGTTGDVTQVKVRILEGRDKGRVIRRNVRGPVRVGDILILRETEREAREIKSRR P61029 30S ribosomal protein S27ae Pyrococcus abyssi (strain GE5 / Orsay) GE5 / Orsay 0.005992167999999999 1 LEVO MGQKWKLYIVKDGKVIRKNKFCPRCGPGVFMADHGDRWACGRCGYTEWKKK P61238 30S ribosomal protein S3 Pyrococcus abyssi (strain GE5 / Orsay) GE5 / Orsay 0.023472309 1 LEVO MAIERYFIREAVKEMLIDEFLEKELRRAGYGGLDIKKTPLGTKVIIFAANPGYVIGRGGRRIRELTRILERQFGLENPQI DVQEIKNPYLNAKVQAVRIAQALERGIHFRRAAYAAMRAIMSNGARGVEIRISGKLTGERAKSVRFYQGYLAKVGNPAET LVSKGYAQALLKLGVIGVKVAIMPPDARLPDEIEIIEKPVEEEVSSNEAE Q9V1U1 50S ribosomal protein L7Ae Pyrococcus abyssi (strain GE5 / Orsay) GE5 / Orsay 0.013442678 1 LEVO MAKPSYVKFEVPKELAEKALQAVEIARDTGKIRKGTNETTKAVERGQAKLVIIAEDVDPEEIVAHLPPLCEEKEIPYIYV PSKKELGAAAGIEVAAASVAIIEPGKARDLVEEIAMKVRELMK P62008 initiator Met-tRNA fMet from E. coli (A1U72 variant) Escherichia coli 0.005761509 1 GUCGGG(OMC)UCAUAACCCGA Translation initiation factor 1A Pyrococcus abyssi (strain GE5 / Orsay) GE5 / Orsay 0.013078264999999999 1 Escherichia coli LEVO MPKKERKVEGDEVIRVPLPEGNQLFGVVEQALGAGWMDVRCEDGKIRRCRIPGKLRRRVWIRVGDLVIVQPWPVQSDKRG DIVYRYTQTQVDWLLRKGKITQEFLTGGSLLVE Q9V138 MAGNESIUM ION 2.4305e-05 8 MG ZINC ION 6.5409e-05 1 ZN water 1.8015e-05 18 HOH singleParticle particle 6.7 ETHANE FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 GATAN K2 SUMMIT (4k x 4k) 2.0 1 PHASE FLIPPING AND AMPLITUDE CORRECTION 3.1 FSC 0.143 CUT-OFF 142000 MAXIMUM LIKELIHOOD MAXIMUM LIKELIHOOD emd_10324.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 348 348 348 0 0 0 348 348 348 379.32 379.32 379.32 90.0 90.0 90.0 X Y Z -0.02097708 0.05286314 -0.00027031792 0.0014324628 1.09 1.09 1.09 0.004 AUTHOR ::::EMDATABANK.org::::EMD-10324:::: IC2 head map emd_10324_msk_1.map emd_10324_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 348 348 348 0 0 0 348 348 348 379.32 379.32 379.32 90.0 90.0 90.0 X Y Z -0.25633243 0.3700689 0.00017248433 0.0066541536 1.09 1.09 1.09 AUTHOR ::::EMDATABANK.org::::EMD-10324:::: IC2 head postprocessed map emd_10324_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 348 348 348 0 0 0 348 348 348 379.32 379.32 379.32 90.0 90.0 90.0 X Y Z -0.02560777 0.056974757 -0.00022127593 0.0017401234 1.09 1.09 1.09 AUTHOR ::::EMDATABANK.org::::EMD-10324:::: IC2 head half2 map emd_10324_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 348 348 348 0 0 0 348 348 348 379.32 379.32 379.32 90.0 90.0 90.0 X Y Z -0.023290161 0.05850072 -0.00022147845 0.001830804 1.09 1.09 1.09 AUTHOR ::::EMDATABANK.org::::EMD-10324:::: IC2 head half1 map