2024-05-01 REL PDBe PDBe PDBe 2020-07-06 2020-07-29 2020-07-29 2024-05-01 German Research Foundation (DFG) SFB/TRR-174 Germany German Research Foundation (DFG) BE1814/15-1 Germany German Research Foundation (DFG) BE1814/1-1 Germany SARS-CoV-2 Nsp1 bound to a pre-40S-like ribosome complex - state 2 Thoms M Buschauer R Translational Inhibition, SARS-CoV-2, Immune Evasion, Human Ribosome, VIRAL PROTEIN Thoms M Buschauer R Ameismeier M Koepke L Denk T Hirschenberger M Kratzat H Hayn M Mackens-Kiani T Cheng J Straub JH Sturzel CM Frohlich T Berninghausen O Becker T Kirchhoff F Sparrer KMJ Beckmann R Structural basis for translational shutdown and immune evasion by the Nsp1 protein of SARS-CoV-2. Science US 369 1249 1255 2020 32680882 doi:10.1126/science.abc8665 1095-9203 0038 SCIEAS EMD-11276 other EM volume 6zn5 FULLOVERLAP SARS-CoV-2 Nsp1 bound to a human pre-40S-like ribosome complex SARS-CoV-2 Nsp1 bound to a human pre-40S-like ribosome complex 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 32 33 34 35 36 human pre-40S-like ribosome complex 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 31 32 33 34 36 Homo sapiens SARS-CoV-2 Nsp1 1 35 Severe acute respiratory syndrome coronavirus 2 40S ribosomal protein SA Homo sapiens 0.023102564 1 LEVO SGALDVLQMKEEDVLKFLAAGTHLGGTNLDFQMEQYIYKRKSDGIYIINLKRTWEKLLLAARAIVAIENPADVSVISSRN TGQRAVLKFAAATGATPIAGRFTPGTFTNQIQAAFREPRLLVVTDPRADHQPLTEASYVNLPTIALCNTDSPLRYVDIAI PCNNKGAHSVGLMWWMLAREVLRMRGTISREHPWEVMPDLYFYRDP P08865 40S ribosomal protein S3a Homo sapiens 0.024759145 1 LEVO VVDPFSKKDWYDVKAPAMFNIRNIGKTLVTRTQGTKIASDGLKGRVFEVSLADLQNDEVAFRKFKLITEDVQGKNCLTNF HGMDLTRDKMCSMVKKWQTMIEAHVDVKTTDGYLLRLFCVGFTKKRNNQIRKTSYAQHQQVRQIRKKMMEIMTREVQTND LKEVVNKLIPDSIGKDIEKACQSIYPLHDVFVRKVKMLKKPKFELGKLMELHG P61247 40S ribosomal protein S2 Homo sapiens 0.024091453 1 LEVO EWMPVTKLGRLVKDMKIKSLEEIYLFSLPIKESEIIDFFLGASLKDEVLKIMPVQKQTRAGQRTRFKAFVAIGDYNGHVG LGVKCSKEVATAIRGAIILAKLSIVPVRRGYWGNKIGKPHTVPCKVTGRCGSVLVRLIPAPRGTGIVSAPVPKKLLMMAG IDDCYTSARGCTATLGNFAKATFDAISKTYSYLTPDLWKETVFTKSPYQEFTDHLVKT P15880 40S ribosomal protein S4, X isoform Homo sapiens 0.029523673999999996 1 LEVO ARGPKKHLKRVAAPKHWMLDKLTGVFAPRPSTGPHKLRECLPLIIFLRNRLKYALTGDEVKKICMQRFIKIDGKVRTDIT YPAGFMDVISIDKTGENFRLIYDTKGRFAVHRITPEEAKYKLCKVRKIFVGTKGIPHLVTHDARTIRYPDPLIKVNDTIQ IDLETGKITDFIKFDTGNLCMVTGGANLGRIGVITNRERHPGSFDVVHVKDANGNSFATRLSNIFVIGKGNKPWISLPRG KGIRLTIAEERDKRLAAKQSSG P62701 40S ribosomal protein S3 Homo sapiens 0.024970289 1 LEVO VQISKKRKFVADGIFKAELNEFLTRELAEDGYSGVEVRVTPTRTEIIILATRTQNVLGEKGRRIRELTAVVQKRFGFPEG SVELYAEKVATRGLCAIAQAESLRYKLLGGLAVRRACYGVLRFIMESGAKGCEVVVSGKLRGQRAKSMKFVDGLMIHSGD PVNYYVDTAVRHVLLRQGVLGIKVKIMLPWDPTGKIGPKKPLPDHVSIVEPKDEILPTTPISEQK P23396 4.2.99.18 40S ribosomal protein S6 Homo sapiens 0.026599479999999998 1 LEVO MKLNISFPATGCQKLIEVDDERKLRTFYEKRMATEVAADALGEEWKGYVVRISGGNDKQGFPMKQGVLTHGRVRLLLSKG HSCYRPRRTGERKRKSVRGCIVDANLSVLNLVIVKKGEKDIPGLTDTTVPRRLGPKRASRIRKLFNLSKEDDVRQYVVRK PLNKEGKKPRTKAPKIQRLVTPRVLQHKRRRIALKKQRTKKNKEEAAEYAKLLAKRMKEAKEKRQEQIAK P62753 40S ribosomal protein S7 Homo sapiens 0.021315891 1 LEVO IVKPNGEKPDEFESGISQALLELEMNSDLKAQLRELNITAAKEIEVGGGRKAIIIFVPVPQLKSFQKIQVRLVRELEKKF SGKHVVFIAQRRILPKPTRKSRTKNKQKRPRSRTLTAVHDAILEDLVFPSEIVGKRIRVKLDGSRLIKVHLDKAQQNNVE HKVETFSGVYKKLTGKDVNFEFPEFQ P62081 40S ribosomal protein S8 Homo sapiens 0.023945959 1 LEVO GISRDNWHKRRKTGGKRKPYHKKRKYELGRPAANTKIGPRRIHTVRVRGGNKKYRALRLDVGNFSWGSECCTRKTRIIDV VYNASNNELVRTKTLVKNCIVLIDSTPYRQWYESHYALPLGRKKGAKLTPEEEEILNKKRSKKIQKKYDERKKNAKISSL LEEQFQQGKLLACIASRPGQCGRADGYVLEGKELEFYLRKIKARK P62241 40S ribosomal protein S9 Homo sapiens 0.021279271 1 LEVO PVARSWVCRKTYVTPRRPFEKSRLDQELKLIGEYGLRNKREVWRVKFTLAKIRKAARELLTLDEKDPRRLFEGNALLRRL VRIGVLDEGKMKLDYILGLKIEDFLERRLQTQVFKLGLAKSIHHARVLIRQRHIRVRKQVVNIPSFIVRLDSQKHIDFSL RSPYGGGRPGRVKRKNAKKG P46781 40S ribosomal protein S5 Homo sapiens 0.021327723 1 LEVO DIKLFGKWSTDDVQINDISLQDYIAVKEKYAKYLPHSAGRYAAKRFRKAQCPIVERLTNSMMMHGRNNGKKLMTVRIVKH AFEIIHLLTGENPLQVLVNAIINSGPREDSTRIGRAGTVRRQAVDVSPLRRVNQAIWLLCTGAREAAFRNIKTIAECLAD ELINAAKGSSNSYAIKKKDELERVAKSNR P46782 40S ribosomal protein S11 Homo sapiens 0.017528662 1 LEVO ADIQTERAYQKQPTIFQNKKRVLLGETGKEKLPRYYKNIGLGFKTPKEAIEGTYIDKKCPFTGNVSIRGRILSGVVTKMK MQRTIVIRRDYLHYIRKYNRFEKRHKNMSVHLSPCFRDVQIGDIVTVGECRPLSKTVRFNVLKVTKAAGTK P62280 40S ribosomal protein S10 Homo sapiens 0.011372406 1 LEVO MPKKNRIAIYELLFKEGVMVAKKDVHMPKHPELADKNVPNLHVMKAMQSLKSRGYVKEQFAWRHFYWYLTNEGIQYLRDY LHLPPEIVPATLRRS P46783 40S ribosomal protein S13 Homo sapiens 0.017057113 1 LEVO GRMHAPGKGLSQSALPYRRSVPTWLKLTSDDVKEQIYKLAKKGLTPSQIGVILRDSHGVAQVRFVTGNKILRILKSKGLA PDLPEDLYHLIKKAVAVRKHLERNRKDKDAKFRLILIESRIHRLARYYKTKRVLPPNWKYESSTASALV P62277 40S ribosomal protein S12 Homo sapiens 0.013709069999999999 1 LEVO GVMDVNTALQEVLKTALIHDGLARGIREAAKALDKRQAHLCVLASNCDEPMYVKLVEALCAEHQINLIKVDDNKKLGEWV GLCKIDREGKPRKVVGCSCVVVKDYGKESQAKDVIEEYFKCKK P25398 40S ribosomal protein S14 Homo sapiens 0.01445758 1 LEVO LGPQVAEGENVFGVCHIFASFNDTFVHVTDLSGKETICRVTGGMKVKADRDESSPYAAMLAAQDVAQRCKELGITALHIK LRATGGNRTKTPGPGAQSALRALARSGMKIGRIEDVTPIPSDSTRRKGGRRGRRL P62263 40S ribosomal protein S15 Homo sapiens 0.014067593 1 LEVO FTYRGVDLDQLLDMSYEQLMQLYSARQRRRLNRGLRRKQHSLLKRLRKAKKEAPPMEKPEVVKTHLRDMIILPEMVGSMV GVYNGKTFNQVEIKPEMIGHYLGEFSITYKPVKHGRPGIG P62841 40S ribosomal protein S16 Homo sapiens 0.01576548 1 LEVO QSVQVFGRKKTATAVAHCKRGNGLIKVNGRPLEMIEPRTLQYKLLEPVLLLGKERFAGVDIRVRVKGGGHVAQIYAIRQS ISKALVAYYQKYVDEASKKEIKDILIQYDRTLLVADPRRCESKKFGGPGARARYQKSYR P62249 40S ribosomal protein S17 Homo sapiens 0.015250713999999999 1 LEVO GRVRTKTVKKAARVIIEKYYTRLGNDFHTNKRVCEEIAIIPSKKLRNKIAGYVTHLMKRIQRGPVRGISIKLQEEERERR DNYVPEVSALDQEIIEVDPDTKEMLKLLDFGSLSNLQVTQPTVGMNFKTPRG P08708 40S ribosomal protein S18 Homo sapiens 0.016811572 1 LEVO LVIPEKFQHILRVLNTNIDGRRKIAFAITAIKGVGRRYAHVVLRKADIDLTKRAGELTEDEVERVITIMQNPRQYKIPDW FLNRQKDVKDGKYSQVLANGLDNKLREDLERLKKIRAHRGLRHFWGLRVRGQHTKTTGRRGRT P62269 40S ribosomal protein S19 Homo sapiens 0.015960365 1 LEVO PGVTVKDVNQQEFVRALAAFLKKSGKLKVPEWVDTVKLAKHKELAPYDENWFYTRAASTARHLYLRGGAGVGSMTKIYGG RQRNGVMPSHFSRGSKSVARRVLQALEGLKMVEKDQDGGRKLTPQGQRDLDRIAGQVAAANKKH P39019 40S ribosomal protein S20 Homo sapiens 0.011508647999999998 1 LEVO IHRIRITLTSRNVKSLEKVCADLIRGAKEKNLKVKGPVRMPTKTLRITTRKTPCGEGSKTWDRFQMRIHKRLIDLHSPSE IVKQITSISIEPGVEVEVTIA P60866 40S ribosomal protein S15a Homo sapiens 0.014734357 1 LEVO VRMNVLADALKSINNAEKRGKRQVLIRPCSKVIVRFLTVMMKHGYIGEFEIIDDHRAGKIVVNLTGRLNKCGVISPRFDV QLKDLEKWQNNLLPSRQFGFIVLTTSAGIMDHEEARRKHTGGKILGFFF P62244 40S ribosomal protein S23 Homo sapiens 0.015626392 1 LEVO GKCRGLRTARKLRSHRRDQKWHDKQYKKAHLGTALKANPFGGASHAKGIVLEKVGVEAKQPNSAIRKCVRVQLIKNGKKI TAFVPNDGCLNFIEENDEVLVAGFGRKGHAVGDIPGVRFKVVKVANVSLLALYKGKKERPR P62266 40S ribosomal protein S24 Homo sapiens 0.014476135 1 LEVO DTVTIRTRKFMTNRLLQRKQMVIDVLHPGKATVPKTEIREKLAKMYKTTPDVIFVFGFRTHFGGGKTTGFGMIYDSLDYA KKNEPKHRLARHGLYEKKKTSRKQRKERKNRMKKVRGTAKANVG P62847 40S ribosomal protein S21 Homo sapiens 0.008977213999999999 1 LEVO MQNDAGEFVDLYVPRKCSASNRIIGAKDHASIQMNVAEVDKVTGRFNGQFKTYAICGAIRRMGESDDSILRLAKADGIVS KN P63220 40S ribosomal protein S25 Homo sapiens 0.008182693 1 LEVO DKLNNLVLFDKATYDKLCKEVPNYKLITPAVVSERLKIRGSLARAALQELLSKGLIKLVSKHRAQVIYTRNT P62851 40S ribosomal protein S27 Homo sapiens 0.009210843 1 LEVO PLAKDLLHPSPEEEKRKHKKKRLVQSPNSYFMDVKCPGCYKITTVFSHAQTVVLCVGCSTVLCQPTGGKARLTEGCSFRR KQ P42677 40S ribosomal protein S26 Homo sapiens 0.011645794 1 LEVO TKKRRNNGRAKKGRGHVQPIRCTNCARCVPKDKAIKKFVIRNIVEAAAVRDISEASVFDAYVLPKLYVKLHYCVSCAIHS KVVRNRSREARKDRTPPPRFR P62854 40S ribosomal protein S28 Homo sapiens 0.006878939999999999 1 LEVO PIKLARVTKVLGRTGSQGQCTQVRVEFMDDTSRSIIRNVKGPVREGDVLTLLESEREARRL P62857 40S ribosomal protein S30 Homo sapiens 0.006302479999999999 1 LEVO GSLARAGKVRGQTPKVAKQEKKKKKTGRAKRRMQYNRRFVNVVPTFGKKKGPNANS P62861 40S ribosomal protein S29 Homo sapiens 0.006502573 1 LEVO HQQLYWSHPRKFGQGSRSCRVCSNRHGLIRKYGLNMCRQCFRQYAKDIGFIKLD P62273 Ribosomal protein S27a Homo sapiens 0.00845315 1 LEVO KKRKKKSCTTPKKNKHKRKKVKLAVLKYYKVDENGKISRLRRECPSDECGAGVFMASHFDRHYCGKCCLTYC Q5RKT7 Receptor of activated protein C kinase 1 Homo sapiens 0.034726164 1 LEVO TEQMTLRGTLKGHNGWVTQIATTPQFPDMILSASRDKTIIMWKLTRDETNYGIPQRALRGHSHFVSDVVISSDGQFALSG SWDGTLRLWDLTTGTTTRRFVGHTKDVLSVAFSSDNRQIVSGSRDKTIKLWNTLGVCKYTVQDESHSEWVSCVRFSPNSS NPIIVSCGWDKLVKVWNLANCKLKTNHIGHTGYLNTVTVSPDGSLCASGGKDGQAMLWDLNEGKHLYTLDGGDIINALCF SPNRYWLCAATGPSIKIWDLEGKIIVDELKQEVISTSSKAEPPQCTSLAWSADGQTLFAGYTDNLVRVWQVTIG P63244 18S ribosomal RNA Homo sapiens 0.6024326249999999 1 UACCUGGUUGAUCCUGCCAGUAGCAUAUGCUUGUCUCAAAGAUUAAGCCAUGCAUGUCUAAGUACGCACGGCCGGUACAG UGAAACUGCGAAUGGCUCAUUAAAUCAGUUAUGGUUCCUUUGGUCGCUCGCUCCUCUCCUACUUGGAUAACUGUGGUAAU UCUAGAGCUAAUACAUGCCGACGGGCGCUGACCCCCUUCGCGGGGGGGAUGCGUGCAUUUAUCAGAUCAAAACCAACCCG GUCAGCCCCUCUCCGGCCCCGGCCGGGGGGCGGGCCGCGGCGGCUUUGGUGACUCUAGAUAACCUCGGGCCGAUCGCACG CCCCCCGUGGCGGCGACGACCCAUUCGAACGUCUGCCCUAUCAACUUUCGAUGGUAGUCGCCGUGCCUACCAUGGUGACC ACGGGUGACGGGGAAUCAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCCAAGGAAGGCAGCAGGCG CGCAAAUUACCCACUCCCGACCCGGGGAGGUAGUGACGAAAAAUAACAAUACAGGACUCUUUCGAGGCCCUGUAAUUGGA AUGAGUCCACUUUAAAUCCUUUAACGAGGAUCCAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCA AUAGCGUAUAUUAAAGUUGCUGCAGUUAAAAAGCUCGUAGUUGGAUCUUGGGAGCGGGCGGGCGGUCCGCCGCGAGGCGA GCCACCGCCCGUCCCCGCCCCUUGCCUCUCGGCGCCCCCUCGAUGCUCUUAGCUGAGUGUCCCGCGGGGCCCGAAGCGUU UACUUUGAAAAAAUUAGAGUGUUCAAAGCAGGCCCGAGCCGCCUGGAUACCGCAGCUAGGAAUAAUGGAAUAGGACCGCG GUUCUAUUUUGUUGGUUUUCGGAACUGAGGCCAUGAUUAAGAGGGACGGCCGGGGGCAUUCGUAUUGCGCCGCUAGAGGU GAAAUUCUUGGACCGGCGCAAGACGGACCAGAGCGAAAGCAUUUGCCAAGAAUGUUUUCAUUAAUCAAGAACGAAAGUCG GAGGUUCGAAGACGAUCAGAUACCGUCGUAGUUCCGACCAUAAACGAUGCCGACCGGCGAUGCGGCGGCGUUAUUCCCAU GACCCGCCGGGCAGCUUCCGGGAAACCAAAGUCUUUGGGUUCCGGGGGGAGUAUGGUUGCAAAGCUGAAACUUAAAGGAA UUGACGGAAGGGCACCACCAGGAGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGAAACCUCACCCGGCCCGGACACG GACAGGAUUGACAGAUUGAUAGCUCUUUCUCGAUUCCGUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGCGAUUU GUCUGGUUAAUUCCGAUAACGAACGAGACUCUGGCAUGCUAACUAGUUACGCGACCCCCGAGCGGUCGGCGUCCCCCAAC UUCUUAGAGGGACAAGUGGCGUUCAGCCACCCGAGAUUGAGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUCCGGGGCUG CACGCGCGCUACACUGACUGGCUCAGCGUGUGCCUACCCUACGCCGGCAGGCGCGGGUAACCCGUUGAACCCCAUUCGUG AUGGGGAUCGGGGAUUGCAAUUAUUCCCCAUGAACGAGGAAUUCCCAGUAAGUGCGGGUCAUAAGCUUGCGUUGAUUAAG UCCCUGCCCUUUGUACACACCGCCCGUCGCUACUACCGAUUGGAUGGUUUAGUGAGGCCCUCGGAUCGGCCCCGCCGGGG UCGGCCCACGCCCUGGCGGAGCGCUGAGAAGACGGUCGAACUUGACUAUCUAGAGGAAGUAAAAGUCGUAACAAGGUUUC CGUAGGUGAACCUGCGGAAGGAUCAUUA M10098.1 Non-structural protein 1 Severe acute respiratory syndrome coronavirus 2 0.019801287
Non-structural protein 1
1 LEVO MESLVPGFNEKTHVQLSLPVLQVRDVLVRGFGDSVEEVLSEARQHLKDGTCGLVEVEKGVLPQLEQPYVFIKRSDARTAP HGHVMVELVAELEGIQYGRSGETLGVLVPHVGEIPVAYRKVLLRKNGNKGAGGHSYGADLKSFDLGDELGTDPYEDFQEN WNTKHSSGVTRELMRELNGG P0DTD1 3.4.19.12 Pre-rRNA-processing protein TSR1 homolog Homo sapiens 0.09195118799999999 1 LEVO MAAHRPGPLKQQNKAHKGGRHRGRGSAQRDGKGRLALKTLSKKVRKELSRVDQRHRASQLRKQKKEAVLAEKRQLGGKDG PPHQVLVVPLHSRISLPEAMQLLQDRDTGTVHLNELGNTQNFMLLCPRLKHRWFFTSARPGDLHVVLDMAKVADTILFLL DPLEGWDSTGDYCLSCLFAQGLPTYTLAVQGISGLPLKKQIDTRKKLSKAVEKRFPHDKLLLLDTQQEAGMLLRQLANQK QQHLAFRDRRAYLFAHAVDFVPSEENNLVGTLKISGYVRGQTLNVNRLLHIVGYGDFQMKQIDAPGDPFPLNPRGIKPQK DPDMAMEICATDAVDDMEEGLKVLMKADPGRQESLQAEVIPDPMEGEQTWPTEEELSEAKDFLKESSKVVKKVPKGTSSY QAEWILDGGSQSGGEGDEYEYDDMEHEDFMEEESQDESSEEEEEYETMTIGESVHDDLYDKKVDEEAEAKMLEKYKQERL EEMFPDEVDTPRDVAARIRFQKYRGLKSFRTSPWDPKENLPQDYARIFQFQNFTNTRKSIFKEVEEKEVEGAEVGWYVTL HVSEVPVSVVECFRQGTPLIAFSLLPHEQKMSVLNMVVRRDPGNTEPVKAKEELIFHCGFRRFRASPLFSQHTAADKHKL QRFLTADMALVATVYAPITFPPASVLLFKQKSNGMHSLIATGHLMSVDPDRMVIKRVVLSGHPFKIFTKMAVVRYMFFNR EDVLWFKPVELRTKWGRRGHIKEPLGTHGHMKCSFDGKLKSQDTVLMNLYKRVFPKWTYDPYVPEPVPWLKSEISSTVPQ GGME Q2NL82 ZINC ION 6.5409e-05 3 ZN singleParticle particle 7.5 ETHANE FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 GATAN K2 SUMMIT (4k x 4k) 44.8 1 3.2 FSC 0.143 CUT-OFF 20087 MAXIMUM LIKELIHOOD MAXIMUM LIKELIHOOD emd_11310.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 360 360 360 0 0 0 360 360 360 381.24 381.24 381.24 90.0 90.0 90.0 X Y Z -0.24749759 0.50266933 0.00019237022 0.010561777 1.059 1.059 1.059 0.038 AUTHOR SARS-CoV-2 bound to a human pre-40S-like ribosome complex state 2