2025-06-11 REL RCSB RCSB RCSB 2025-03-11 2025-06-11 2025-06-11 2025-06-11 Howard Hughes Medical Institute (HHMI) United States Gen R Seattle Structural Genomics Center for Infectious Disease (SSGCID) Veesler D SARS-CoV-2, RIBOSOME, Seattle Structural Genomics Center for Infectious Disease, SSGCID Gen R Addetia A Asarnow D Park YJ Quispe J Chan MC Brown JT Lee J Campbell MG Lapointe CP Veesler D Cell Rep US 44 115696 115696 2025 40359110 doi:10.1016/j.celrep.2025.115696 2211-1247 9npz FULLOVERLAP SARS-CoV-2 nsp1-Rhinolophus lepidus ribosome complex, consensus map SARS-CoV-2 nsp1-Rhinolophus lepidus ribosome complex, consensus map 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 Rhinolophus lepidus 40S ribosomal subunit 1 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 19 20 21 22 23 24 Rhinolophus lepidus SARS-CoV-2 nsp1 1 17 Severe acute respiratory syndrome coronavirus 2 Eukaryotic translation initiation factor 1 1 18 Homo sapiens 40S ribosomal protein uS5, RPS2 Rhinolophus lepidus 0.031257351999999995 1 LEVO MADDAGAAGGAGAPGGPGLGGRGGFRGGFGSGVRGRGRGRGRGRGRGRGARGGKAEDKEWIPVTKLGRLVKDMKIKSLEE IYLFSLPIKESEIIDFFLGASLKDEVLKIMPVQKQTRAGQRTRFKAFVAIGDYNGHVGLGVKCSKEVATAIRGAIILAKL SIVPVRRGYWGNKIGKPHTVPCKVTGRCGSVLVRLIPAPRGTGIVSAPVPKKLLMMAGIDDCYTSARGCTATLGNFAKAT FDAISKTYSYLTPDLWKETVFTKSPYQEFTDHLVKTHTRVSVQRTQAPAVATT 40S ribosomal protein eS4 X isoform, RPS4 Rhinolophus lepidus 0.029640846 1 LEVO MARGPKKHLKRVAAPKHWMLDKLTGVFAPRPSTGPHKLRECLPLIIFLRNRLKYALTGDEVKKICMQRFIKIDGKVRTDV TYPAGFMDVISIDKTGENFRLIYDTKGRFAVHRITPEEAKYKLCKVRKIFVGTKGIPHLVTHDARTIRYPDPLIKVNDTI QIDLETGKITDFIKFDTGNLCMVTGGANLGRIGVITNRERHPGSFDVVHVKDANGNSFATRLSNIFVIGKGNKPWISLPR GKGIRLTIAEERDKRLAAKQSSG 40S ribosomal protein eS6, RPS6 Rhinolophus lepidus 0.028751905999999997 1 LEVO MKLNISFPATGCQKLIEVDDERKLRTFYEKRMATEVAADALGEEWKGYVVRISGGNDKQGFPMKQGVLTHGRVRLLLSKG HSCYRPRRTGERKRKSVRGCIVDANLSVLNLVIVKKGEKDIPGLTDTTVPRRLGPKRASRIRKLFNLSKEDDVRQYVVRK PLNKEGKKPRTKAPKIQRLVTPRVLQHKRRRIALKKQRTKKNKEEAAEYAKLLAKRMKEAKEKRQEQIAKRRRLSSLRAS TSKSESSQK 40S ribosomal protein eS8, RPS8 Rhinolophus lepidus 0.024249358999999998 1 LEVO MGISRDNWHKRRKTGGKRKPYHKKRKYELGRPAANTKIGPRRIHTVRVRGGNKKYRALRLDVGNFSWGSECCTRKTRIID VVYNASNNELVRTKTLVKNCIVLVDSTPYRQWYESHYALPLGRKKGAKLTPEEEEILNKKRSKKIQKKYDERKKNAKISS LLEEQFQQGKLLACIASRPGQCGRADGYVLEGKELEFYLRKIKARKGK 40S ribosomal protein uS4, RPS9 Rhinolophus lepidus 0.022641563999999996 1 LEVO MPVARSWVCRKTYVTPRRPFEKSRLDQELKLIGEYGLRNKREVWRVKFTLAKIRKAARELLTLDEKDPRRLFEGNALLRR LVRIGVLDEGKMKLDYILGLKIEDFLERRLQTQVFKLGLAKSIHHARVLIRQRHIRVRKQVVNIPSFIVRLDSQKHIDFS LRSPYGGGRPGRVKRKNAKKGQGGAGAGDDEEED 40S ribosomal protein uS15, RPS13 Rhinolophus lepidus 0.017259389 1 LEVO MGRMHAPGKGLSQSALPYRRSVPTWLKLTSDDVKEQIYKLAKKGLTPSQIGVILRDSHGVAQVRFVTGNKILRILKSKGL APDLPEDLYHLIKKAVAVRKHLERNRKDKDAKFRLILIESRIHRLARYYKTKRVLPPNWKYESSTASALVA 40S ribosomal protein uS11, RPS14 Rhinolophus lepidus 0.016302772 1 LEVO MAPRKGKEKKEEQVISLGPQVAEGENVFGVCHIFASFNDTFVHVTDLSGKETICRVTGGMKVKADRDESSPYAAMLAAQD VAQRCKELGITALHIKLRATGGNRTKTPGPGAQSALRALARSGMKIGRIEDVTPIPS(IAS)STRRKGGRRGRRL 40S ribosomal protein uS8, RPS15a Rhinolophus lepidus 0.014865554999999999 1 LEVO MVRMNVLADALKSINNAEKRGKRQVLIRPCSKVIVRFLTVMMKHGYIGEFEIIDDHRAGKIVVNLTGRLNKCGVISPRFD VQLKDLEKWQNNLLPSRQFGFIVLTTSAGIMDHEEARRKHTGGKILGFFF 40S ribosomal protein eS17, RPS17 Rhinolophus lepidus 0.015552119 1 LEVO MGRVRTKTVKKAARVIIEKYYTRLGNDFHTNKRVCEEIAIIPSKKLRNKIAGYVTHLMKRIQRGPVRGISIKLQEEERER RDNYVPEVSALDQEIIEVDPDTKEMLKLLDFGSLSNLQVTQPTVGMNFKTPRGAV 40S ribosomal protein eS21, RPS21 Rhinolophus lepidus 0.009150427 1 LEVO (ACE)MQNDAGEFVDLYVPRKCSASNRIIGAKDHASIQMNVAEVDKVTGRFNGQFKTYAICGAIRRMGESDDSILRLAKA DGIVSKNF 40S ribosomal protein uS12, RPS23 Rhinolophus lepidus 0.015860666 1 LEVO MGKCRGLRTARKLRSHRRDQKWHDKQYKKAHLGTALKANPFGGASHAKGIVLEKVGVEAKQ(HY3)NSAIRKCVRVQLIK NGKKITAFVPNDGCLNFIEENDEVLVAGFGRKGHAVGDIPGVRFKVVKVANVSLLALYKGKKERPRS 40S ribosomal protein eS24, RPS24 Rhinolophus lepidus 0.015094925999999998 1 LEVO MNDTVTIRTRKFMTNRLLQRKQMVIDVLHPGKATVPKTEIREKLAKMYKTTPDVIFVFGFRTHFGGGKTTGFGMIYDSLD YAKKNEPKHRLARHGLYEKKKTSRKQRKERKNRMKKVRGTAKATVGAGKK 40S ribosomal protein eS26, RPS26 Rhinolophus lepidus 0.013047531999999999 1 LEVO MTKKRRNNGRAKKGRGHVQPIRCTNCARCVPKDKAIKKFVIRNIVEAAAVRDISEASVFDAYVLPKLYVKLHYCVSCAIH SKVVRNRSREARKDRTPPPRFRPAGAAPRPPPKPM 40S ribosomal protein eS27, RPS27 Rhinolophus lepidus 0.009480186 1 LEVO MPLAKDLLHPSPEEEKRKHKKKRLVQSPNSYFMDVKCPGCYKITTVFSHAQTVVLCVGCSTVLCQPTGGKARLTEGCSFR RKQH 40S ribosomal protein eS32, L41 Rhinolophus lepidus 0.003473451 1 LEVO MRAKWRKKRMRRLKRKRRKMRQRSK 40S ribosomal protein uS2, RPSA Rhinolophus lepidus 0.03275077 1 LEVO (ACE)SGALDVLQMKEEDVLKFLAAGTHLGGTNLDFQMEQYIYKRKSDGIYIINLKRTWEKLLLAARAIVAIENPADVSV ISSRNTGQRAVLKFAAATGATPIAGRFTPGTFTNQIQAAFREPRLLVVTDPRADHQPLTEASYVNLPTIALCNTDSPLRY VDIAIPCNNKGAHSVGLMWWMLAREVLRMRGTISREHAWEVMPDLYFYRDPEEIEKEEQAAAEKAVTKEEFQGEWTAPAP EFTAAQPEVADWSEGVQVPAVPIQQFPTEDWSAQPATEDWSAAPTAQATEWVGTTTEWS Host translation inhibitor nsp1 Severe acute respiratory syndrome coronavirus 2 0.019859324 1 Escherichia coli LEVO MESLVPGFNEKTHVQLSLPVLQVRDVLVRGFGDSVEEVLSEARQHLKDGTCGLVEVEKGVLPQLEQPYVFIKRSDARTAP HGHVMVELVAELEGIQYGRSGETLGVLVPHVGEIPVAYRKVLLRKNGNKGAGGHSYGADLKSFDLGDELDTDPYEDFQEN WNTKHSSGVTRELMRELNGG P0DTD1 Eukaryotic translation initiation factor 1 Homo sapiens 0.012752498 1 Escherichia coli LEVO MSAIQNLHSFDPFADASKGDDLLPAGTEDYIHIRIQQRNGRKTLTTVQGIADDYDKKKLVKAFKKKFACNGTVIEHPEYG EVIQLQGDQRKNICQFLVEIGLAKDDQLKVHGF P41567 40S ribosomal protein eS7, RPS7 Rhinolophus lepidus 0.022168914 1 LEVO MFSSSAKIVKPNGEKPDEFESGISQALLELEMNSDLKAQLRELNITAAKEIEVGGGRKAIIIFVPVPQLKSFQKIQVRLV RELEKKFSGKHVVFIAQRRILPKPTRKSRTKNKQKRPRSRTLTAVHDAILEDLVFPSEIVGKRIRVKLDGSRLIKVHLDK AQQNNVEHKVETFSGVYKKLTGKDVNFEFPEFQL 40S ribosomal protein uS17, RPS11 Rhinolophus lepidus 0.018468826 1 LEVO MADIQTERAYQKQPTIFQNKKRVLLGETGKEKLPRYYKNIGLGFKTPKEAIEGTYIDKKCPFTGNVSIRGRILSGVVTKM KMQRTIVIRRDYLHYIRKYNRFEKRHKNMSVHLSPCFRDVQIGDIVTVGECRPLSKTVRFNVLKVTKAAGTKKQFQKF 40S ribosomal protein eS30, RPS30 Rhinolophus lepidus 0.006857185 1 LEVO MGKVHGSLARAGKVRGQTPKVAKQEKKKKKTGRAKRRMQYNRRFVNVVPTFGKKKGPNANS 40S ribosomal protein eS1, RPS3a Rhinolophus lepidus 0.030002061 1 LEVO MAVGKNKRLTKGGKKGAKKKVVDPFSKKDWYDVKAPAMFNIRNIGKTLVTRTQGTKIASDGLKGRVFEVSLADLQNDEVA FRKFKLITEDVQGKNCLTNFHGMDLTRDKMCSMVKKWQTMIEAHVDVKTTDGYLLRLFCVGFTKKRNNQIRKTSYAQHQQ VRQIRKKMMEIMTREVQTNDLKEVVNKLIPDSIGKDIEKACQSIYPLHDVFVRKVKMLKKPKFELGKLMELHGEGSSSGK ATGDETGAKVERADGYEPPVQESV 18S ribosomal RNA Rhinolophus lepidus 0.44771275 1 UACCUGGUUGAUCCUGCCAGUAGCAU(A2M)UGCUUG(PSU)C(PSU)CAAAGAUUAAGCCAUGCAUGUCUAAGUACGCA CGGCUGGUACAGUGAAACUGCGAA(PSU)GGCUC(A2M)UUAAA(PSU)CAG(PSU)UAUGGU(OMU)CC(PSU)U (OMU)GGUCGCUCGCUCCUCUCCUACUUGGAUAACUGUGGUA(A2M)UUCUAG(A2M)GCUAA(OMU)A(OMC)AUGCCG ACGGGCGCUGACCCCCCUCGCGGGGGGGAUGCGUGCA(PSU)UUAUCAGAUCAAAACCAACCCGGUCAGCCUCCCCUCGG CCCCGGCCGGGGGGCGGGCGCCGGCGGCUUUGGUGACUCUAGAUAACCUCGGGCCGAUCGCACGCCCCCCGUGGCGGCGA CGACCCAUUCGAACGUC(OMU)GCCCUAUCAACUUUCGAUGGUAGUCGCCGUGCCUACCAUGGUGACCACGGG(PSU)GA CGGGGAAUCAGGGUUCGAU(OMU)CCGGAGA(OMG)GGAGCCUGAGAAACGGCUACCACAU(OMC)CAAGG(A2M)AGGC AGCAGGCGCGC(A2M)AAUUACCCACUCCCGACCCGGGGA(OMG)GU(A2M)GUGA(OMC)GAAAAAUAACAAUACAGGA CUCUUUCGAGGCCCUGUAAUUGGAAUGAGUCCACU(PSU)UAA(A2M)UCCUUUAACGAGG(A2M)UCCAUUGGAG (OMG)GCAAGUC(PSU)GGUGCCAGCAGCCGCGG(OMU)AAUUCCAGCUCCAAUA(OMG)CGUA(PSU)A(PSU)UAAAG UUGCUGCAGUU(A2M)AAAAGCUCGUAG(PSU)U(OMG)GA(PSU)CUUGGGAGCGGGCGGGCGGUCCGCCGCGAGGCGA GCCACCGCCCGUCCCCGCCCCUUGCCUCUCGGCGCCCCCUCGAUGCUCUUAGCUGAGUGUCCCGCGGGGCCCGAAG (OMC)G(OMU)UUACUUUGAAAAAA(PSU)(PSU)AGAGUG(PSU)UCAAAGCAGGCCCGAGCCGCCUGGAUACCGCAGC UAGGAA(PSU)AA(PSU)GGAAUAGGACCGCGGUUCUAUUUUGUUGGUUUUCGGAACUGAGGCCAUGAUUAAGAGGGACG GCCGGGGGCAUUCGUAUUGCGCCGCUAGAGGUGAAAU(PSU)CUUGGACCGGCGCAAGACGGACCAGAGCGAAAGCAUU (PSU)GCCAAGAAUGUUUUCAUUAAUCAAGA(A2M)CGAAAGUCGGAGG(PSU)(PSU)CGAAGACGA(PSU)CAGAUAC CGUCGUAGUUCCGACCA(PSU)AAACGAUGCCGACUGGCGAUGCGGCGGCGUUAUUCCCAUGACCCGCCGGGCAGC (PSU)UCCGGGAAACCAAAGUCUUUGGGUUCCGGGGGGAGUA(PSU)GG(PSU)UGCAAAGCUGAAACUUAAAGGAAUUG ACGGA(PSU)GUACACACCG(OMC)CCGUCGCUACUACCGAUUGGAUGGUUUAGUGAGGCCCUCGGAUCGGCCCCGCCGG GGUCGGCCCACGGCCCUGGCGGAGCGCUGAGAAGACGGUCGAACU(OMU)GACUAUCUAGAGGAAGUAAAAGUCGUA (6MZ)CAAGGUUUC(4AC)GUAGGUG(MA6)(MA6)CCUGCGGAAGGAUCAUUA 40S ribosomal protein uS3, RPS3 Rhinolophus lepidus 0.026715344 1 LEVO MAVQISKKRKFVADGIFKAELNEFLTRELAEDGYSGVEVRVTPTRTEIIILATRTQNVLGEKGRRIRELTAVVQKRFGFP EGSVELYAEKVATRGLCAIAQAESLRYKLLGGLAVRRACYGVLRFIMESGAKGCEVVVSGKLRGQRAKSMKFVDGLMIHS GDPVNYYVDTAVRHVLLRQGVLGIKVKIMLPWDPSGKIGPKKPLPDHVSIVEPKDEILPTTPISEQKGGKPEPPAMPQPV PTA MAGNESIUM ION 2.4305e-05 57 MG POTASSIUM ION 3.9098e-05 13 K ZINC ION 6.5409e-05 1 ZN water 1.8015e-05 1640 HOH singleParticle particle 7.4 ETHANE TFS KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 0.6 1.6 GATAN K3 (6k x 4k) 30.7 1 NONE

Ab initio

2.1 FSC 0.143 CUT-OFF 1205667 PROJECTION MATCHING PROJECTION MATCHING emd_49637_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 512 512 512 0 0 0 512 512 512 424.448 424.448 424.448 90.0 90.0 90.0 X Y Z -0.40801284 0.9403187 0.0003220329 0.018182104 0.829 0.829 0.829 AUTHOR ::::EMDATABANK.org::::EMD-49637:::: emd_49637_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 512 512 512 0 0 0 512 512 512 424.448 424.448 424.448 90.0 90.0 90.0 X Y Z -0.08146074 0.35351124 0.00039234993 0.011374289 0.829 0.829 0.829 AUTHOR ::::EMDATABANK.org::::EMD-49637:::: emd_49637_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 512 512 512 0 0 0 512 512 512 424.448 424.448 424.448 90.0 90.0 90.0 X Y Z -0.0816156 0.3368499 0.00039055644 0.011388902 0.829 0.829 0.829 AUTHOR ::::EMDATABANK.org::::EMD-49637::::