Cryo-EM structure of Saccharolobus solfataricus 30S initiation complex bound to Ss-MAP leaderless mRNA

2026-06-24 REL PDBe INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY DATA_COLLECTION em_admin _em_admin.last_update EXPERIMENTAL_SUMMARY em_admin _em_admin.last_update 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 _struct_conn.ptnr1_label_atom_id EXPERIMENTAL_SUMMARY em_admin _em_admin.last_update PDBe PDBe 2024-06-18 2025-01-15 2025-01-15 2026-06-24 Agence Nationale de la Recherche (ANR) France Cryo-EM structure of Saccharolobus solfataricus 30S initiation complex bound to Ss-MAP leaderless mRNA Bourgeois G Coureux PD Mechulam Y Schmitt E 30S, ribosome, Translation, Saccharolobus solfataricus Bourgeois G Coureux PD Lazennec-Schurdevin C Madru C Gaillard T Duchateau M Chamot-Rooke J Bourcier S Mechulam Y Schmitt E Structures of Saccharolobus solfataricus initiation complexes with leaderless mRNAs highlight archaeal features and eukaryotic proximity. Nat Commun UK 16 348 348 2025 39753558 doi:10.1038/s41467-024-55718-5 2041-1723 9fra FULLOVERLAP EMDB EMD-50709 associated EM volume

High-resolution cryo-EM structure of Saccharolobus solfataricus 30S ribosomal subunit bound to mRNA and initiator tRNA High-resolution cryo-EM structure of Saccharolobus solfataricus 30S ribosomal subunit bound to mRNA and initiator tRNA 0 1 2 3 5 6 8 9 10 11 12 13 14 15 16 18 20 21 22 23 25 26 27 28 30 31 32 33 34 Saccharolobus solfataricus P2 rRNA 16S Saccharolobus solfataricus P2 0.48637584399999995 1 AAAUCCGGUUGAUCC(OMU)GCCGGACCCGACCGCUAUCGGGGUGGGGCUAAGCCA(OMU)GGGAGUCGUACGCUCCCGG GCAAGGGAGCGUGGCGGACGGCUGAGUAACACGUGGCUAAC(OMC)UACCCUGAGGAGGGAGAUAACCCCGGGAAACUGG GGAUAAUCUCCCAUAGGCGAGGAGUCCUGGAACGGUUCCUCGCUGAAAGGCUCAUGGGCUAUUCCCCGCUCAUGAGCGCC UCAGGAUGGGGCUGCGGC(OMC)CAUCAGGUAGUUGGGGGGGUAAGGGCCCCCCAAGCCUAUAACGGGUAGGGGCCGUGA GAGCGGGAG(OMC)CCCCAGUUGGGCACUGAGACAAG(OMG)GCCCAGGCCCUACGGGGCGCACCAGGCGCGAAACGUCC CCAAUGCGCGGAAGCGUGAGGGC(OMG)CCACCCCGAGUGCUCCCGUAAGGGAGCUUUUCCCCGCUCUACAAAGGCGGGG GAAUAAGCGGGGGGCAAGUCUGGUGUCAG(OMC)CGCCGCGGUAAU(A2M)CCAGCCCCGCGAGUGGU(OMC)GGGACUC UUACUGGGCCUAAAGCGC(OMC)CGUAGCC(OMG)GCCCGACAAGUCACUCCUUAAAGACCCCGGCUCAACCGGGGGAAU GGGGGUGAUACUGUCGGGCUAGGGGGCGGGAGAGGCCAGCGGUACUCCCGGAGUAGGGGCGAAAUCCUCAGAUCUCGGGA (OMG)GACCACCAGUGGCGAAAGCGGCUGGCUAGAACGCGCC(OMC)GACGGUGAGGGGCGAAAGCCGGGGCAGCAAAAG GGAUUAGAUACCCCUGUAGUCCCGGCUGUAAACAAUGCAGGCUAGGUGUCACAUGGGCUUAGAGCCCAUGUGGUGCCGCA GGGAAGCCGUUAAGCCUGCCGCCUGGGGAGUACGGUCGCAA(OMG)ACUGAAACUUAAAGGAAUUGGCGGGGGAGCACCA CAAGG(OMG)GUGGAACCUGCGGCUCAAUU(OMG)GAG(C4J)CAACGCCUGGAAUCUUACUAGGGGAGACCGCAGGAUG ACGGCCAGGCUAACGACCUUGCCUGACUCGCGGAGAGGAGGUGCAUGGCC(OMG)UCGCCAGCUCGUG(OMU)UGUGAAA UGUCCUGUUAAGUCAGGCAA(OMC)(OMG)AGCGAGACCCCCACCACUAGUUGGUAUCCUGGUCUCCGGGCCGGGACCAC ACUAGUGGGACUGCCGGCGUAAGCCGGAGGAGGGAGGGGGCCACGGCAGGUCAGCAUGCCCCGAAACCCCUGGGCCGCAC GC(OMG)GGUUACAAUGGCAGGGACAGCGGGAUUCCGACCCCGAAAGGGGAAGGUAAUCCCUUAAACCCUGCCGCAGUUG GGAUCGAGGGCUGAAACUCGCCCUCGUGAACGAGGAAUCCCUAGUAACCGCAGAUCAACAAUCUGCGGUGAAUACG (OMU)CCCUGCUCCUUGCACACACCG(OMC)C(5MC)GUCGCUCCACCCGAGUAGGAGAGGGGUGAGGCCCCUUGCCUUU GGGUGGGGGGUCGAGCUUCUCUCCUGCAAGGGGGGAGAAGUCGUA(6MZ)CAAGGUAG(4AC)(4AC)GUAGGGG(MA6) A(4AC)(4AC)UGCGGCUGGAUCACCUCC AE006641.1 Small ribosomal subunit protein eS1 Saccharolobus solfataricus P2 0.023581205 1 LEVO MSAKGGAIKDKWKMKKWYSVITPKAFGEVSLGSTPAYDITQTIGRRVETTLYDLTGDFSQVYVHLYFKIIGNEGDRLITR FVGHELSRDYLRSLIRRKSSKINSIFDVTTKDGYVVRVKGLVLTTYKCHQSQKTAIRKIINETVSKKASELSFDDFTQEV VFGRLANEIFEAAKKIYPLRKAEIEKTKVLKVPENLGKQVESSSVSSG Q9UXD4 Small ribosomal subunit protein uS2 Saccharolobus solfataricus P2 0.02604316 1 LEVO MKVTNLSEKEERGGELTEAEKEELRKSEKGAIIELLVPVDTYLSAGVHIGTHSCTKYMESFVYRVRAEGLYVLDVRKIDE RLRIAAKFLSRYDPQDIIVVASRPYAYRPVQKFAEVVGSRALVGRIIPGTFTNPYLSTYIEPKVLLVSDPRTDTQAIKEA AKVGIPIVAFADTDAKIDYIDLIIPANNKGRKSLALLYWALARQILRERRVIPPDGDLAVPVSEFEMRLVQ P95993 Small zinc finger protein HVO-2753-like zinc-binding pocket domain-containing protein Saccharolobus solfataricus P2 0.007352656 1 LEVO MSVKLSIREEVEPPICSSCGKIIHPREKGVEFYCPNCGEVLIRRDHMCRKQGAEYICPNCGFKGP Q980V0 Small ribosomal subunit protein uS4 Saccharolobus solfataricus P2 0.020784099999999996 1 LEVO MGDPKKSRKKWETPGHPWIKERIGYEQELLGKYGLRNKREIWIAQSIIRKFRHQARSLLALPPAERAVREKQLVGKLLKM GLLKKETATVDDILSLTEQDLLERRLQTIVYKKGLSNTIYQARQLITHGHIAVNGKRVTSPGYIVNVDEENLIDYYVTSS FKSRPPVMSQQEGGEIGVKQA P95987 Small ribosomal subunit protein eS4 Saccharolobus solfataricus P2 0.027564197 1 LEVO MAHITRFEAPWFLMISKKQYKWTVRPNAGPHSIEKSIPLAVVIRDYLKLAGTIREAKHIIFDGKVLVDGKVRKDYKYPVG LMDIVSIPSADLYFRVLPDNVRFMRFSKISADEARYKYVRIINKTTIKEGRIQLNLEDGRNILVDKETAKNFKTLMTLKI ELPSQQILDSFTISERSYAIFVGGRNVGIHGIVKNINLSKFKSRKYSVITLESRDGNTYQTNIMNVMSIGREKSDLRVD Q9UX94 Small ribosomal subunit protein uS5 Saccharolobus solfataricus P2 0.023275062 1 LEVO MAEEVPSLNIEEWKPRTSIGSLVKEGKISSIKELFDRNLPITEPEIVDVLLPKLKYEVVDIKVVQKQTDAGEISRYKVLV IMGNMDGYVSIGTGKAKQLRVAIQKAIRDAKMNIIPVRRGCGSWQCTCGEPHSLPFKVVGKAGSVEVDLLPAPKGTGLVV GSVLKTLLTYAGIKDAWSTTKGETRTTENFVRAGYSALYNTYKFVTLQDWV Q9UX87 Small ribosomal subunit protein eS6 Saccharolobus solfataricus P2 0.023757401999999997 1 LEVO MPDFKIVISDPQSVEPKRIKVKVKASDQVKSITGEKDGKAVPQAKVNEKTKQLLNVDTLLTLEITKQEGDKKVKVKGHFK VDVDNSVPDNEVWISKTMAEKFGAEDFEAFAYRTKTLQISVDQNKATNLVGLKIGDVFEANQLIGLPVKLKITGGSDNSG FPMRFDVIGAAKRKILLSGPPGFYPNENGERRRKTIRGNTISQEIVQINTIIVR Q980A6 Small ribosomal subunit protein uS7 Saccharolobus solfataricus P2 0.022035703 1 LEVO MSLENLQLDIKVFGKWDTKVEIRDPSLKKYISLMPVYLPHTGGRHEHRRFGKAKVPIVERLINQIMRPGRNKGKKHLAYN IVKLAFDIIYLKTGQNPIQVLVRAIENSAPREEVTRIMYGGIVYYVAVDVSPQRRIDLALRHIATGAKDASFNNPKPIEE VLAEEIIAAANNDSKSFAIKRKEEIERIALSSR P35026 Small ribosomal subunit protein uS8 Saccharolobus solfataricus P2 0.015083798 1 LEVO MVFVNPLANALTSIYNNEMRRNKQAIIMPASKLVINVLRVMQKEGYVGEFEYIDDGRWGKITVQLLGRVNKCGPITPRYP LSYRQMIALPDYVRRYLPSKEIGIIIVSTSKGVMSHKEAARLRIGGVALGYVY Q9UX92 Small ribosomal subunit protein eS8 Saccharolobus solfataricus P2 0.014685966 1 LEVO MGFYQGPDNRKITGGLKGKHRDKRKYEIGNPPTFTTLSAEDIRIKDRTLGGNFKVRLKYTTTANVLDPATNTAKKVKILE ILETPANKELARRGIIIRGAKIRTEAGLAVVTSRPGQDGVINAVLLKNESQRS Q980W3 Small ribosomal subunit protein uS9 Saccharolobus solfataricus P2 0.015732471999999997 1 LEVO MSEEQKLVISSARRKTARATCYIYAGKGRVFVNNVPIELIPIEMVRLKIMEPLLLAGNDIRSKIDAKIITYGGGIMGQAD AARMALARALVKFTGSKELEKIYRAYDRTMLAGDPRQTESEKWMRYSARRWRQKSYR P95992 Small ribosomal subunit protein uS10 Saccharolobus solfataricus P2 0.01213344 1 LEVO MPTKARIRLWSTNVENLNYVITQIRGIVEKTGIEMRGPIPLPTSKLEVPIMRLPHGEGRKKWEKWEMRVHKRLIDIAADE RVMRQLMRVRVPEDVYIEIQLI P35027 Small ribosomal subunit protein uS11 Saccharolobus solfataricus P2 0.014065243 1 LEVO MSSRREIRWGIAHIYASQNNTLLTISDLTGAEIISRASGGMVVKADREKSSPYAAMLAANKAASDALEKGIMALHIKVRA PGGYGSKTPGPGAQPAIRALARAGFIIGRIEDVTPIPHDTIRRPGGRRGRRV P95988 Small ribosomal subunit protein uS12 Saccharolobus solfataricus P2 0.016381561 1 LEVO MVKSKSPKGIYAARKLRLKRLKFRRSQRKYKTKILKLKEKYDPLGGAPMARGIVLEKVGIESRQPNSAVRKCVRVQLVRN GRVVTAFVPGDGGVNFIDEHDEVIITGIGGTLGRSMGDLPGVRYKVIMVNGVSLDALYKGKKQKPVR P39573 Small ribosomal subunit protein uS13 Saccharolobus solfataricus P2 0.018662438999999996 1 LEVO MSQQFKYVVRIFGQDVDGTMKLPYALAMVKGIGYNTAKAIIRKLGMDPNARLGELSDAEVKKVESVISDHTIKGLPSWLY NRRKDYESGLDLHLVTSDLIFYVRNDIEREKKSRSWRGVRHSLGLKVRGQRTRTTGRTGMTIGVARKKAAQPQSQQSSSQ QQKSS P95986 Small ribosomal subunit protein uS14 Saccharolobus solfataricus P2 0.006416506999999999 1 LEVO MGKYKPPAERKYGKGVQSCQRCGSKDSVIQKYGIYLCRQCFREVAYELGFRKYW Q97ZQ5 Small ribosomal subunit protein uS15 Saccharolobus solfataricus P2 0.017475532999999998 1 LEVO MNKRRAKGKSHSIRPARAGAPKWVRLTREEVEMLVEELAKRGYTPSMIGIILRDQYGIPLVKQIVGKKVTQILEERGLAP QIPEDLFNLIRKAVNVRRHINEYPRDKTAKKGLEEIESKIRRLTRYYKGIGKLPQEWVYDPAKAELLVAGAS Q980A8 Small ribosomal subunit protein uS17 Saccharolobus solfataricus P2 0.012987173 1 LEVO MVSKGKTVKDPGIPNITIPEKVCEDEDCPYHGSLRVRGITLEGVIVKYRGTKAAVIERQYLYYDSKYKRYERRRSRIHAH VPPCINVREGDKVIIGECRPLSKSISFVVLGKVS Q9UX98 Small ribosomal subunit protein eS17 Saccharolobus solfataricus P2 0.009647069999999999 1 LEVO MGNIYTKDIKRIVKEIYDRYKDEIKDDYNTNKQIVIRYVDVKSKKVRNRIAGYLTRYYKIMKEKETSPAEEKEEISEEI Q980K7 Small ribosomal subunit protein uS19 Saccharolobus solfataricus P2 0.016399315999999997 1 LEVO MSLEIPPEWKNFKYRGKSIDELLNMPMDEFIKLLPSRQRRSLKRGFTDAQRHLLEKVRKYRREGKFNKTIKTHVRNLVIL PELIGLKMAVYNGKEFVEFTVTPEMIGHYLGEYSITTKKVEHGEPGLKATRSSLFLAMKG Q9UXA3 Small ribosomal subunit protein eS19 Saccharolobus solfataricus P2 0.018149432 1 LEVO MSLIMITAEMVPPDLLIKRLAIYLKENVKTVDPPEWALLAKTASFKERVPDNAEDWWYIRAASLLRKLYVNSIIGIEKTR TIYGGRKRRGTRPEKFVKAPGHVNRLIFQQLEKAGLVQKIKNKGRSLSPKGRSLLDKLALEIFKELAENNTSLKVYLE Q980F7 Small ribosomal subunit protein eS24 Saccharolobus solfataricus P2 0.013122203999999998 1 LEVO MESQAKVKISDKAEGIIERDMQNSVIGRREISLKVYHMGSGTPSRKDIIKAIIQALGSQENLVVVRKISTSYGAGISNVK LHIYKSREILEKVEPKYLLDRDAGTKQKKGGSKGGQGAKG Q97ZY6 Small ribosomal subunit protein eS27 Saccharolobus solfataricus P2 0.007396944999999999 1 LEVO MMRKLRVLIPEPKSRFLRVKCPNCGNEQTIFSHATFPVRCLSCGTELVYSMGGKAKIVGEVVRIMG Q97Z80 Small ribosomal subunit protein eS28 Saccharolobus solfataricus P2 0.009393792 1 LEVO MSEKTQQSQGSSIIEEFGFPAEVIQILDRTGVTGEVTQVRVRVLEGRDKGRILTRNVKGPVRVGDILILRETEREARKIT TKR Q980Q5 Small ribosomal subunit protein eS31 Saccharolobus solfataricus P2 0.008703415 1 LEVO MLELNKRKEEAKVAKEQKVKAIVRTYYVIEGNKVKLKNKKCPRCGSIMAHHLKPNERWSCGKCGYTEFIGASKKR Q97ZY7 Small ribosomal subunit protein uS3 Saccharolobus solfataricus P2 0.025862208999999997 1 LEVO MPNIKRYFLEKSIVKVKIDEYLAKQYYNAEYAGVEVLKTPIGTRVIIYAGRPSMIIGRGGRNIKQLAQIFEKVFGLENPQ ITITNVENPELNARVMAFRLAIALEKGYHFRRAAFISMRRIMNAGALGAEIIISGKLTTERARYEKLKEGIVYKSGQQLE KMIDRAIAIAMLKPGIFGVEVVITKPLKIEDKINLKESPSVPQEVSVTNVTFIEESSQKSEEKSEGEKE Q9UXA0 Large ribosomal subunit protein eL8 Saccharolobus solfataricus P2 0.013757939 1 LEVO MSKASYVKFEVPQDLADKVLEAVRKAKESGKIKKGTNETTKAVERGQAKLVIIAEDVQPEEIVAHLPLLCDEKKIPYVYV SSKKALGEACGLQVATASAAILEPGEAKDLVDEIIKRVNEIKGKTSS P55858 aS34 Saccharolobus solfataricus P2 0.008210799999999999 1 LEVO MSIKNRGSNAYGHLGWLTVYCRICNRKLIIGTDILYKCPKCEKKYSAYFCEADKRGLKGKCPYCGTELVPIL Q97ZK4 Small ribosomal subunit protein eS25 Saccharolobus solfataricus P2 0.012372557 1 LEVO MGGASKKPISTMEKRLKKEAEKQQKAEEKKKGPSKTGKEIISRAVTIDEETKKKVLDEIKKESIITPYALATKSGISISV ARKILKELENQNVVKLYSKNRRLEIYIAAS Q97ZZ6 VapB-type antitoxin Saccharolobus solfataricus P2 0.008392802 1 LEVO MEMLKIKLSSGREVEINDDTIAVLNEYVRTQMTLEELSKRLGLSGWEEAYELIKQVPAWVMWSPLPIYKKLA D0KTI0 LSU ribosomal protein S30E (Rps30E) Saccharolobus solfataricus P2 0.006064125 1 LEVO MPSHGSLTKAGKVRSQTPKIQPKEKHKEVPRVRNRKEYEKRVVKARQQAPAR Q97ZH4 mRNA_Map Saccharolobus solfataricus P2 0.005039946 1 (ATP)UGACUGAGGAUGAA tRNA initiator Met Escherichia coli 0.024833903999999997 1 AGCGGGG(4SU)GGAGCAGCCUGG(H2U)AGCUCGUCGGG(OMC)UCAUAACCCGAAGAUCGUCGG(5MU)(PSU)CAAA UCCGGCCCCCGCUACCA CP026027.1 mRNA_Map Saccharolobus solfataricus P2 0.0049599660000000005 1 (A3P)UGACUGAGGAUGAA MAGNESIUM ION 2.4305e-05 58 MG SPERMINE 0.00020234 42 SPM ZINC ION 6.5409e-05 8 ZN water 1.8015e-05 221 HOH singleParticle particle 6.7 ETHANE TFS KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 0.8 2.5 GATAN K3 BIOQUANTUM (6k x 4k) 40.0 1 PHASE FLIPPING AND AMPLITUDE CORRECTION 9FHL 2.8 FSC 0.143 CUT-OFF 62000 ANGULAR RECONSTITUTION MAXIMUM LIKELIHOOD emd_50709.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 438 438 438 0 0 0 438 438 438 365.292 365.292 365.292 90.0 90.0 90.0 X Y Z -0.014759537 0.049936436 0.000069634334 0.0020652376 0.834 0.834 0.834 0.006 AUTHOR ::::EMDATABANK.org::::EMD-50709:::: emd_50709_msk_1.map emd_50709_additional_5.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 438 438 438 0 0 0 438 438 438 365.292 365.292 365.292 90.0 90.0 90.0 X Y Z -0.01503863 0.04967126 -0.00009150374 0.0013944758 0.834 0.834 0.834 AUTHOR ::::EMDATABANK.org::::EMD-50709:::: emd_50709_additional_4.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 438 438 438 0 0 0 438 438 438 365.292 365.292 365.292 90.0 90.0 90.0 X Y Z -0.018278148 0.0564175 0.00006962266 0.0023453094 0.834 0.834 0.834 AUTHOR ::::EMDATABANK.org::::EMD-50709:::: emd_50709_additional_3.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 438 438 438 0 0 0 438 438 438 365.292 365.292 365.292 90.0 90.0 90.0 X Y Z -0.015238424 0.050296318 -0.00005162632 0.0017786027 0.834 0.834 0.834 AUTHOR ::::EMDATABANK.org::::EMD-50709:::: emd_50709_additional_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 438 438 438 0 0 0 438 438 438 365.292 365.292 365.292 90.0 90.0 90.0 X Y Z -0.32386357 1.1684637 0.0016616265 0.022172445 0.834 0.834 0.834 AUTHOR ::::EMDATABANK.org::::EMD-50709:::: emd_50709_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 438 438 438 0 0 0 438 438 438 365.292 365.292 365.292 90.0 90.0 90.0 X Y Z -0.2797942 1.1696184 0.002361022 0.028157413 0.834 0.834 0.834 AUTHOR ::::EMDATABANK.org::::EMD-50709:::: emd_50709_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 438 438 438 0 0 0 438 438 438 365.292 365.292 365.292 90.0 90.0 90.0 X Y Z -0.025234327 0.06192168 0.00006807316 0.0030844451 0.834 0.834 0.834 AUTHOR ::::EMDATABANK.org::::EMD-50709:::: emd_50709_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 438 438 438 0 0 0 438 438 438 365.292 365.292 365.292 90.0 90.0 90.0 X Y Z -0.023066195 0.058061738 0.00007117216 0.0030622534 0.834 0.834 0.834 AUTHOR ::::EMDATABANK.org::::EMD-50709::::