Cryo-EM structure of the Arabidopsis thaliana 40S ribosomal subunit

2026-08-19 REL PDBe INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY DATABASE_REFERENCES citation citation_author em_admin _citation.country _citation.journal_abbrev _citation.journal_id_ASTM _citation.journal_id_CSD _citation.journal_id_ISSN _citation.pdbx_database_id_DOI _citation.pdbx_database_id_PubMed _citation.title _citation.year _em_admin.last_update EXPERIMENTAL_SUMMARY citation citation_author em_admin _citation.country _citation.journal_abbrev _citation.journal_id_ASTM _citation.journal_id_CSD _citation.journal_id_ISSN _citation.pdbx_database_id_DOI _citation.pdbx_database_id_PubMed _citation.title _citation.year _em_admin.last_update DATABASE_REFERENCES citation em_admin _citation.journal_volume _citation.page_first _citation.title _em_admin.last_update EXPERIMENTAL_SUMMARY citation em_admin _citation.journal_volume _citation.page_first _citation.title _em_admin.last_update PDBe PDBe 2025-08-14 2026-06-10 2026-06-10 2026-08-19 National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) 1R01GM132649[PVO1] United States Academy of Finland 338836 and 314672 Finland Cryo-EM structure of the Arabidopsis thaliana 40S ribosomal subunit Karki S Lu X Paatero AO Ruonala R Tranter D Guryanov S Rehan S Hellmann E Haakonsson A Butcher SJ Huiskonen JT Kajander T Helariutta Y Paavilainen VO Arabidopsis, Ribosome, CryoEM Karki S Lu X Paatero AO Ruonala R Tranter D Guryanov S Rehan S Hellmann E Haakonsson A Butcher SJ Huiskonen JT Kajander T Helariutta Y Paavilainen VO Cryo-EM structure of the Arabidopsis thaliana ribosome in translating and non-translating states. Structure UK 34 1195 2026 42361795 doi:10.1016/j.str.2026.06.001 0969-2126 2005 STRUE6 9sdp FULLOVERLAP EMDB EMD-54789 associated EM volume

60S LSU Arabidopsis (root) ribosome complex 60S LSU Arabidopsis (root) ribosome complex 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 Arabidopsis 4.3 18S RNA Arabidopsis thaliana 0.5819656879999999 1 UACCUGGUUGAUCCUGCCAGUAGUCAU(A2M)UGCUUGUCU(OMC)AAAGAUUAAGCCAUGCAUGUGUAAGUAUGAACGA AUUCAGACUGUGAAACUGCGAAUGGCUCAUUAAAUCAGUUAUAGUUUGUU(OMU)GAUGGUAACUACUACU(OMC)GGAU AACCGUAGUAAUUCUAGAGCUAAUACGUGCAACAAACCCCGACUUAUGGAAGGGACGCAUUUAUUAGAUAAAAGGUCGAC GCGGGCUCUGGCUUGCUCU(OMG)AUGAUUCAUGAUAACUCGACGGAUCGCAUGGCCUCUGUGCUGGCGACGCAUCAUUC AAAUUUCUGCCCUAUCAACUUUCGAUGGUAGGAUAGUGGCCUACCAUGGUGGUAACGGGUGACGGAGAAUUAGGGUUCGA UUCCGGAGA(OMG)GGAGCCUGAGAAACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGCAAAUUACCCAAUCCUGACA CGGGGAGGU(A2M)GUGA(OMC)AAUAAAUAACAAUACCGGGCUCUUUCGAGUCUGGUAAUUGGAAUGAGUACAAUCUAA AUCCCUUAACGAGGAUCCAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUA(UY1)AU UUAAGUUG(OMU)UGCAGUU(A2M)AAAAGCUCGUAGUUGAACCUUGGGAUGGGUCGGCCGGUCCGCCUUUGGUGUGCAU UGGUCGGCUUGUCCCUUCGGUCGGCGAUACGCUCCUGGUCUUAAUUGGCCGGGUCGUGCCUCCGGCGCUGUUACUUUGAA GAAAUUAGAGUGCUCAAAGCAAGCCUACGCUCUGGAUACAUUAGCAUGGGAUAACAUCAUAGGAUUUCGAUCCUAUUGUG UUGGCUUCGGGAUCGGAGUAAUGAUUAACAGGGACAGUCGGGGGCAUUCGUAUUUCAUAGUCAGAGGUGAAAUUCUUGGA UUUAUGAAAGACGAACAACUGCGAAAGCAUUUGCCAAGGAUGUUUUCAUUAAUCAAGA(A2M)CGAAAGUUGGGGGCUCG AAGACGAUCAGAUACCG(OMU)CCUAGUCUCAACCAUAAACGAUGCCGACCAGGGAUCAGCGGAUGUUGCUUAUAGGACU CCGCUGGCACCUUAUGAGAAAUCAAAGUUUUUGGGUUCCGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGA CGGAAGGGCACCACCAGGAGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGGAAACUUACCAGGUCCAGACAUAGUAA GGAUUGACAGACUGAGAGCUCUUUCUUGAUUCUAUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGCGAUUUGUCU GGUUAAUUCCGUUAACGAACGAGACCUCAGCCUGCUAACUAGCUACGUGGAGGCAUCCCUUCACGGCCGGCUUCUUAGAG GGACUAUGGCCGUUUAGGCCAAGGAAGUUUGAGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUUCUGGGCCGCACGCGC GCUACACUGAUGUAUUCAACGAGUUCACACCUUGCCGACAGGCCCGGGUAAUCUUUGAAAUUUCAUCGUGAUGGGGAUAG AUCAUUGCAAUUGUUGGUCUUCAACGAGGAAUUCCUAGUAAGCGCGAGUCAUCAGCUCGCGUUGACUACGUCCCUGCCCU UUGUACACACCG(OMC)CCGUCGCUCCUACCGAUUGAAUGAUCCGGUGAAGUGUUCGGAUCGCGGCGACGUGGGUGGUUC GCCGCCCGCGACGUCGCGAGAAGUCCACUAAACCUUAUCAUUUAGAGGA(A2M)GGAGAAGUCGUAACAAGGUUUC (4AC)GUAGGUG(MA6)(MA6)CCUGCGGAAGGAUCAUUG X16077.1 Small ribosomal subunit protein uS2y Arabidopsis thaliana 0.030682752 1 LEVO MAANGVATAGRQVSEKEADIQMMLSADVHLGTKNCNYQMERYVFKRRDDGIYIINLGKTWDKLQMAARVIVAIENPKDII VQSARPYGQRAVLKFAQYTGVNAIAGRHTPGTFTNQMQTSFSEPRLLILTDPRTDHQPIKEGALGNIPTIAFCDTDSPMG FVDIGIPANNKGKHSIGCLFWLLARMVLQMRGTILAAQKWDVMVDLFFYREPEEAKQEGDEEAEVQADYGMVGGDQWTTA QISDAAWSGEVEQPISAAPAVGVTVAAGWEAASVPAAGWE Q8H173 Small ribosomal subunit protein eS1z Arabidopsis thaliana 0.029906732 1 LEVO MAVGKNKRISKGRKGGKKKAVDPFSKKDWYDVKAPSIFTHRNVGKTLVSRTQGTKIASEGLKHRVFEVSLADLQGDEDNA YRKIRLRAEDVQGRNVLCQFWGMDFTTDKLRSLVKKWQTLIEAHVDVKTTDSYTLRLFCIAFTKRRANQVKRTCYAQSSQ IRQIRRKMRDIMVREASSCDLKDLVAKFIPEAIGREIEKATQGIYPLQNVFIRKVKILKAPKFDLGKLMDVHGDYSAEDV GVKVDRPADEMAVEEPTEIIGA Q9CAV0 Small ribosomal subunit protein uS5w Arabidopsis thaliana 0.030169190999999998 1 LEVO MAERGVERGGDRGDFGRGFGGRGGGRGGPRGRGRRAGRAPEEEKWVPVTKLGRLVKEGKITKIEQIYLHSLPVKEYQIID LLVGPSLKDEVMKIMPVQKQTRAGQRTRFKAFIVVGDSNGHVGLGVKCSKEVATAIRGAIILAKLSVVPIRRGYWGNKIG KPHTVPCKVTGKCGSVTVRMVPAPRGSGIVAARVPKKVLQFAGIDDVFTSSRGSTKTLGNFVKATFDCLQKTYGFLTPEF WKETRFSKSPYQEHTDFLLIPPGVKISEVVVDKSVE Q9SCM3 Small ribosomal subunit protein eS4z Arabidopsis thaliana 0.029862006 1 LEVO MARGLKKHLKRLNAPKHWMLDKLGGAFAPKPSSGPHKSRECLPLVLIIRNRLKYALTYREVISILMQRHIQVDGKVRTDK TYPAGFMDVVSIPKTNENFRLLYDTKGRFRLHSIKDEEAKFKLCKVRSIQFGQKGIPYLNTYDGRTIRYPDPLIKPNDTI KLDLEENKIVEFIKFDVGNVVMVTGGRNRGRVGVIKNREKHKGSFETIHIQDSTGHEFATRLGNVYTIGKGTKPWVSLPK GKGIKLTIIEEARKRLSAQQA Q93VH9 Small ribosomal subunit protein eS6y Arabidopsis thaliana 0.028228201 1 LEVO MKFNVANPTTGCQKKLEIDDDQKLRAFFDKRLSQEVSGDALGEEFKGYVFKIMGGCDKQGFPMKQGVLTPGRVRLLLHRG TPCFRGHGRRTGERRRKSVRGCIVSPDLSVLNLVIVKKGVSDLPGLTDTEKPRMRGPKRASKIRKLFNLGKEDDVRKYVN TYRRTFTNKKGKKVSKAPKIQRLVTPLTLQRKRARIADKKKRIAKANSDAADYQKLLASRLKEQRDRRSESLAKKRSRLS SAPAKPVAA P51430 Small ribosomal subunit protein eS7z Arabidopsis thaliana 0.021964521 1 LEVO MFSAQHKIHKEKGVELSELDEQVAQAFFDLENTNQELKSELKDLYVNSAVQVDISGGRKAIVVNVPYRLRKAYRKIHVRL VRELEKKFSGKDVILIATRRIVRPPKKGSAAKRPRNRTLTSVHEAILDDVVLPAEIVGKRTRYRLDGTKIMKVFLDPKER NNTEYKVEAFSAVYKKLTGKDVVFEFPITEA Q9C514 Small ribosomal subunit protein eS8z Arabidopsis thaliana 0.025047752 1 LEVO MGISRDSIHKRRATGGKQKQWRKKRKYEMGRQPANTKLSSNKTVRRIRVRGGNVKWRALRLDTGNYSWGSEATTRKTRVL DVVYNASNNELVRTKTLVKSAIVQVDAAPFKQWYLSHYGVELGRKKKSASSTKKDGEEGEEAAVAAPEEVKKSNHLLRKI ASRQEGRSLDSHIEDQFASGRLLACISSRPGQCGRADGYILEGKELEFYMKKIQKKKGKGAA Q93VG5 Small ribosomal subunit protein uS4y Arabidopsis thaliana 0.023207768 1 LEVO MVNVRFYRNYGKTFKKPRRPYEKERLDAELKLVGEYGLRCKRELWRVQYTLSRIRNAARELLTLDEKNPRRIFEGEALLR RMNRYGLLDETQNKLDYVLALTVENFLERRLQTIVFKSGMAKSIHHARVLIRQRHIRVGRQLVNIPSFMVRVESQKHVDF SLTSPFGGGRPGRVKRRNERAGAKKASGGDGDEDDEE Q9FLF0 Small ribosomal subunit protein uS17z Arabidopsis thaliana 0.017996197 1 LEVO MAEQTEKAFLKQPKVFLSSKKSGKGKRPGKGGNRFWKNIGLGFKTPREAIDGAYVDKKCPFTGTVSIRGRILAGTCHSAK MQRTIIVRRDYLHFVKKYQRYEKRHSNIPAHVSPCFRVKEGDHIIIGQCRPLSKTVRFNVLKVIPAGSSSSFGKKAFTGM P16181 Small ribosomal subunit protein uS15y Arabidopsis thaliana 0.017123188999999997 1 LEVO MGRMHSRGKGISASALPYKRSSPSWLKTTSQDVDESICKFAKKGLTPSQIGVILRDSHGIPQVKSVTGSKILRILKAHGL APEIPEDLYHLIKKAVAIRKHLERNRKDKDSKFRLILVESRIHRLARYYKKTKKLPPVWKYESTTASTLVA P59224 Small ribosomal subunit protein uS11x Arabidopsis thaliana 0.016268776 1 LEVO MSKRKTKEPKVENVTLGPAVREGEQVFGVVHVFASFNDTFIHVTDLSGRETLVRITGGMKVKADRDESSPYAAMLAAQDV AQRCKELGITAIHVKLRATGGNKTKTPGPGAQSALRALARSGMKIGRIEDVTPIPTDSTRRKGGRRGRRL P42036 Small ribosomal subunit protein eS21z Arabidopsis thaliana 0.009086206 1 LEVO MENDAGQVTELYIPRKCSATNRMITSKDHASVQLNIGHLDANGLYTGQFTTFALCGFVRAQGDADSGVDRLWQKKKVEAK QQ Q9M337 Small ribosomal subunit protein uS8z/uS8w Arabidopsis thaliana 0.014829390999999999 1 LEVO MVRISVLNDALKSMYNAEKRGKRQVMIRPSSKVIIKFLIVMQKHGYIGEFEYVDDHRSGKIVVELNGRLNKCGVISPRFD VGVKEIEGWTARLLPSRQFGYIVLTTSAGIMDHEEARRKNVGGKVLGFFY P42798 Small ribosomal subunit protein uS12y Arabidopsis thaliana 0.015770618 1 LEVO MGKTRGMGAGRKLKRLRINQRWADKQYKKSHLGNEWKKPFAGSSHAKGIVLEKIGIEAKQPNSAIRKCARVQLIKNGKKI AAFVPNDGCLNYIEENDEVLIAGFGRKGHAVGDIPGVRFKVVKVSGVSLLALFKEKKEKPRS P49201 Small ribosomal subunit protein eS24z Arabidopsis thaliana 0.015412304 1 LEVO MAEKAVTIRTRKFMTNRLLSRKQFVIDVLHPGRANVSKAELKEKLARMYEVKDPNAIFVFKFRTHFGGGKSSGFGLIYDT VESAKKFEPKYRLIRNGLDTKIEKSRKQIKERKNRAKKIRGVKKTKAGDAKKK Q9SS17 Small ribosomal subunit protein eS26x Arabidopsis thaliana 0.014662092 1 LEVO MTFKRRNGGRNKHNRGHVKPIRCSNCGKCCPKDKAIKRFIVRNIVEQAAIRDVQEASVYEGYTLPKLYAKTQYCVSCAIH SHVVRVRSRTNRRVRTPPPRFARRKEDTPKPAQPGQAPRPAGGAPAAPRA Q9LYK9 Small ribosomal subunit protein eS27y Arabidopsis thaliana 0.009614209999999998 1 LEVO MVLQNDIDLLNPPAELEKRKHKLKRLVQSPNSFFMDVKCQGCFNITTVFSHSQTVVVCGNCQTILCQPTGGKAKLTEGCS FRRKGD Q9M2F1 Small ribosomal subunit protein eS30z/eS30y/eS30x Arabidopsis thaliana 0.006910187999999999 1 LEVO MGKVHGSLARAGKVRGQTPKVAKQDKKKKPRGRAHKRLQHNRRFVTAVVGFGKKRGPNSSEK P49689 Small ribosomal subunit protein eS32 eS32z/eS32y/eS32x/eS32w/eS32v Arabidopsis thaliana 0.0034454369999999995 1 LEVO MRAKWKKKRMRRLKRKRRKMRQRSK P62120 POTASSIUM ION 3.9098e-05 3 K MAGNESIUM ION 2.4305e-05 14 MG ZINC ION 6.5409e-05 1 ZN singleParticle tissue 7.4

50 mM Hepes, pH 7.4, 5 mM MgAc, 100 mM KAc, pH 7.5, 1 mM DTT, Complete protease inhibitor

ETHANE TFS KRIOS OTHER OTHER FIELD EMISSION GUN 300 2.7 0.6 1.2 105000.0 GATAN K3 (6k x 4k) 24.512 1 NONE 3.3 FSC 0.143 CUT-OFF cryoSPARC 115070 OTHER OTHER emd_54789.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 450 450 450 0 0 0 450 450 450 378.0 378.0 378.0 90.0 90.0 90.0 X Y Z -0.11574677 0.31933743 0.0029591837 0.016527385 0.84 0.84 0.84 0.06 AUTHOR ::::EMDATABANK.org::::EMD-54789:::: emd_54789_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 450 450 450 0 0 0 450 450 450 378.0 378.0 378.0 90.0 90.0 90.0 X Y Z -0.97170305 1.0845525 0.001274714 0.11684012 0.84 0.84 0.84 AUTHOR ::::EMDATABANK.org::::EMD-54789:::: emd_54789_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 450 450 450 0 0 0 450 450 450 378.0 378.0 378.0 90.0 90.0 90.0 X Y Z -1.0248959 0.9946418 0.0012877552 0.116887145 0.84 0.84 0.84 AUTHOR ::::EMDATABANK.org::::EMD-54789::::