Late-stage 48S Initiation Complex (LS48S IC) guided by the trans-RNA

2026-09-02 REL PDBe INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY REMEDIATION REPOSITORY Metalloprotein remediation STRUCTURE_SUMMARY em_admin pdbx_entry_details pdbx_modification_feature pdbx_nonpoly_atom_coordination pdbx_nonpoly_atom_coordination_sphere pdbx_nonpoly_atom_coordination_sphere_order _em_admin.last_update _pdbx_entry_details.has_protein_modification EXPERIMENTAL_SUMMARY em_admin _em_admin.last_update PDBe PDBe 2024-10-25 2025-12-10 2025-12-10 2026-09-02 National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) DP1GM142101 United States Howard Hughes Medical Institute (HHMI) 55108556 United States European Research Council (ERC) 101088541 European Union Late-stage 48S Initiation Complex (LS48S IC) guided by the trans-RNA Nguyen TT Hashem Y Rocha REO Boissier F Qian SB Jia L Uematsu S Gu Y Shi S 48S late-stage initiation complex, Programmable mRNA translation initiation, trans-RNA, activation of mRNA translation, TRANSLATION Jia L Nguyen TT Uematsu S Gu Y Shi S Hashem Y Qian SB Programmable initiation of mRNA translation by trans-RNA. Nat.Biotechnol. US 2025 41272315 doi:10.1038/s41587-025-02897-1 1087-0156 2119 NABIF9 9h6y FULLOVERLAP EMDB EMD-51903 associated EM volume

Late-stage 48S Initiation Complex (LS48S IC) guided by the trans-RNA of 15 nt length, purification method of biotinylated DNA-oligo pull-down Late-stage 48S Initiation Complex (LS48S IC) guided by the trans-RNA of 15 nt length, purification method of biotinylated DNA-oligo pull-down 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 37 38 39 40 41 42 Oryctolagus cuniculus 1.3 Initiator methionylated tRNA Oryctolagus cuniculus 0.024721828 1 GAGCAGAGUGGCGCAGCGGAAGCGUGCUGGGCCCAU(T6A)ACCCAGAGGUCGAUGGAUCGAAACCAUCCUCUGCUACCA 18S ribosomal RNA Oryctolagus cuniculus 0.6010156879999999 1 UACCUGGUUGAUCCUGCCAGUAGCAUAUGCUUGUCUCAAAGAUUAAGCCAUGCAUGUCUAAGUACGCACGGCCGGUACAG UGAAACUGCGAAUGGCUCAUUAAAUCAGUUAUGGUUCCUUUGGUCGCUCGCUCCUCUCCUACUUGGAUAACUGUGGUAAU UCUAGAGCUAAUACAUGCCGACGGCGCUGACUCCCUUUGUGUGGGAUGCGUGCAUUUAUCAGAUCAAAACCAACCCGGUC AGCCUCCCCGCCGGCCGGGGGGGUGGGGCGGCGGCUUUGGUGACUCUAGAUAACCUCGGGCCGAUCGCAGCCCUCCGUGG CGGCGACGACCCAUUCGAACGUCUGCCCUAUCAACUUUCGAUGGUAGUCGCCGUGCCUACCAUGGUGACCACGGGUGACG GGGAAUCAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGCAAAUUAC CCACUCCCGACCCGGGGAGGUAGUGACGAAAAAUAACAAUACAGGACUCUUUCGAGGCCCUGUAAUUGGAAUGAGUCCAC UUUAAAUCCUUUAACGAGGAUCCAUUGGAGGGCAAGUCUGGUCGCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUA UUAAAGUUGCUGCAGUUAAAAAGCUCGUAGUUGGAUCUUGUGGAGGGUGCGUAGCGGGCGGUCCGCCGCGAGGCGAGCCA CCGCCCGUCCCCGCCCCUUGCCUCUCGGCGCCCCCUCGAUGCUCUUAGCUGAGUGUCCCGCGGGGCCCGAAGCGUUUACU UUGAAAAAAUUAGAGUGUUCAAAGCAGGCCCGAGCCGCCUGGAUACCGCAGCUAGGAAUAAUGGAAUAGGACCGCGGUUC UAUUUUGUUGGUUUUCGGAACUGAGGCCAUGAUUAAGAGGGACGGCCGGGGGCAUUCGUAUUGCGCCGCUAGAGGUGAAA UUCUUGGACCGGCGCAAGACGGACCAGAGCGAAAGCAUUUGCCAAGAAUGUUUUCAUUAAUCAAGAACGAAAGUCGGAGG UUCGAAGACGAUCAGAUACCGUCGUAGUUCCGACCAUAAACGAUGCCGACUGGCGAUGCGGCGGCGUUAUUCCCAUGACC CGCCGGGCAGCUUCCGGGAAACCAAAGUCUUUGGGUUCCGGGGGGAGUAUGGUUGCAAAGCUGAAACUUAAAGGAAUUGA CGGAAGGGCACCACCAGGAGUGGAGCCUGCGGCUUAAUUUGAC(I2T)CAACACGGGAAACCUCACCCGGCCCGGACACG GACAGGAUUGACAGAUUGAUAGCUCUUUCUCGAUUCUGUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGCGAUUU GUCUGGUUAAUUCCGAUAACGAACGAGACUCUGGCAUGCUAACUAGUUACGCGACCCCCGAGCGGUCGGCGUCCCCCAAC UUCUUAGAGGGACAAGUGGCGUUCAGCCACCCGAGAUUGAGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUCGGGGCUGC ACGCGCGCUACACUGACUGGCUCAGCGUGUGCCUACCCUACGCCGGCAGGCGCGGGUAACCCGUUGAACCCCAUUCGUGA UGGGGAUCGGGGAUUGCAAUUAUUCCCCAUGAACGAGGAAUUCCCAGUAAGUGCGGGUCAUAAGCUUGCGUUGAUUAAGU CCCUGCCCUUUGUACACACCGCCCGUCGCUACUACCGAUUGGAUGGUUUAGUGAGGCCCUCGGAUCGGCCCGCCGGGGUC GGCCCACGGCCCUGGCGGAGCGCUGAGAAGACGGUCGAACUUGACUAUCUAGAGGAAGUAAAAGUCGUAACAAGGUUUCC GUAGGUGAACCUGCGGAAGGAUCAUUA Linear mRNA Oryctolagus cuniculus 0.051665809 1 GGGACAUUUGCUUCUGACACAACAUGGAAUCGAUCAUCAACUUCGAAAAGCUAUAGUAAUGUGUUCACUAGCAACCUCAA ACAGACACCGCCACCAUGGUGAGCGGCUGGCGGCUGUUCAAGAAGAUUAGCCCGCUCGAGAUGGUGAGCAAGGGCGAGGA Eukaryotic translation initiation factor 2 subunit 1 Oryctolagus cuniculus 0.032792866999999996 1 LEVO MPGLSCRFYQHKFPEVEDVVMVNVRSIAEMGAYVSLLEYNNIEGMILLSELSRRRIRSINKLIRIGRNECVVVIRVDKEK GYIDLSKRRVSPEEAIKCEDKFTKSKTVYSILRHVAEVLEYTKDEQLESLFQRTAWVFDDKYKRPGYGAYDAFKHAVSDP SILDSLDLNEDEREVLINNINRRLTPQAVKIRADIEVACYGYEGIDAVKEALRAGLNCSTETMPIKINLIAPPRYVMTTT TLERTEGLSVLNQAMAVIKEKIEEKRGVFNVQMEQVWKTPRRKT G1T2G4 Eukaryotic translation initiation factor 2 subunit 3 Oryctolagus cuniculus 0.052499991999999995

Uniprot ID: A0A5F9C3W2

1 LEVO MRLPGQLPSSPGKMAGGEAGVTLGQPHLSRQDLATLDVTKLTPLSHEVISRQATINIGTIGHVAHGKSTVVKAISGVHTV RFKNELERNITIKLGYANAKIYKLDDPSCPRPECYRSCGSSTPDEFPTDIPGTKGNFKLVRHVSFVDCPGHDILMATMLN GAAVMDAALLLIAGNESCPQPQTSEHLAAIEIMKLKHILILQNKIDLVKESQAKEQYEQILAFVQGTVAEGAPIIPISAQ LKYNIEVVCEYIVKKIPVPPRDFTSEPRLIVIRSFDVNKPGCEVDDLKGGVAGGSILKGVLKVGQEIEVRPGIVSKDSEG KLMCKPIFSKIVSLFAEHNDLQYAAPGGLIGVGTKIDPTLCRADRMVGQVLGAVGALPEIFTELEISYFLLRRLLGVRTE GDKKAAKVQKLSKNEVLMVNIGSLSTGGRVSAVKADLGKIVLTNPVCTEVGEKIALSRRVEKHWRLIGWGQIRRGVTIKP TVDDD Small ribosomal subunit protein uS2 Oryctolagus cuniculus 0.032927988

G1TLT8

1 LEVO MSGALDVLQMKEEDVLKFLAAGTHLGGTNLDFQMEQYIYKRKSDGIYIINLKRTWEKLLLAARAIVAIENPADVSVISSR NTGQRAVLKFAAATGATPIAGRFTPGTFTNQIQAAFREPRLLVVTDPRADHQPLTEASYVNLPTIALCNTDSPLRYVDIA IPCNNKGAHSVGLMWWMLAREVLRMRGTISREHPWEVMPDLYFYRDPEEIEKEEQAAAEKAVTKEEFQGEWTAPAPEFTA TQPEVADWSEGVQVPSVPIQQFPTEDWSAQPATEDWSAAPTAQATEWVGTTTEWS G1TLT8 Small ribosomal subunit protein eS1 Oryctolagus cuniculus 0.029928967

G1TN72

1 LEVO MAVGKNKRLTKGGKKGAKKKVVDPFSKKDWYDVKAPAMFNIRNIGKTLVTRTQGTKIASDGLKGRVFEVSLADLQNDEVA FRKFKLITEDVQGKNCLTNFHGMDLTRDKMCSMVKKWQTMIEAHVDVKTTDGYLLHLFCVGFTKKCNNQIRKTSYAQHQQ VRQIRKKMMEIMTREVQTNDLKEVVNKLIPDSIGKDIEKACQSIYPLHDVFVRKVKMLKKPKFELGKLMELHGEGSSSGK ATGDETGAKVERADGYEPPVQESV G1TN72 Small ribosomal subunit protein uS5 Oryctolagus cuniculus 0.029099955

A0AAA9WW19

1 LEVO LGFGGAEGGGGGRLLGLGSGRGRGRGARGGKAEDKEWLPVTKLGRLVKDVKIKSLEEIYLFSLPIKESEIIDFFLGAALK DEVLKIMPVQKQTRAAQRTRFKAFVAIGDYNGHVGLGVKCSKEVATAIRGAIILAKLSIVPVRRGYWGNKIGKPHTVPCK VTGRCGSVLVHLIPAPRGTGIVSAPVPKKLLLMAGIDDCYTSAWSCTATLGNFAKATFDAISKTYSYLTPDLWKETVFTK SPYQEFTDHLVKTHTRVSVQRTQAPAVATT A0AAA9WW19 Small ribosomal subunit protein uS3 Oryctolagus cuniculus 0.026715344

G1TNM3

1 LEVO MAVQISKKRKFVADGIFKAELNEFLTRELAEDGYSGVEVRVTPTRTEIIILATRTQNVLGEKGRRIRELTAVVQKRFGFP EGSVELYAEKVATRGLCAIAQAESLRYKLLGGLAVRRACYGVLRFIMESGAKGCEVVVSGKLRGQRAKSMKFVDGLMIHS GDPVNYYVDTAVRHVLLRQGVLGIKVKIMLPWDPSGKIGPKKPLPDHVSIVEPKDEILPTTPISEQKGGKPEPPAMPQPV PTA G1TNM3 Small ribosomal subunit protein eS4 Oryctolagus cuniculus 0.02965892

G1TK17

1 LEVO MARGPKKHLKRVAAPKHWMLDKLTSVFAPRPSTGPHKLRECLPLIIFLRNKLKYALTGDEVKKICMQRFIKIDGKVRADI TYPAGFMDVISIDKTGENFRLIYDTKGRFAVHRITPEEAKYKLCKVRKIFVGTKGIPHLVTHDARTIRYPDPLIKMNDTI QIDLETGKITDFIKFDTGNLCMVTGGANLGRIGVITNRERHPGSFDVVHVKDANGNSFATRLSNIFVIGKGNKPWISLPR GKGIRLTIAEERDKRLAAKQSSG G1TK17 Small ribosomal subunit protein uS7 Oryctolagus cuniculus 0.022913453

G1TFM5

1 LEVO MTEWETAAPAVAETPDIKLFGKWSTDDVQINDISLQDYIAVKEKYAKYLPHSAGRYAAKRFRKAQCPIVERLTNSMMMHG RNNGKKLMTVRIVKHAFEIIHLLTGENPLQVLVNAIINSGPREDSTRIGRAGTVRRQAVDVSPLRRVNQAIWLLCTGARE AAFRNIKTIAECLADELINAAKGSSNSYAIKKKDELERVAKSNR G1TFM5 Small ribosomal subunit protein eS6 Oryctolagus cuniculus 0.028755895

G1TM55

1 LEVO MKLNISFPATGCQKLIEVDDERKLRTFYEKRMATEVAADALGEEWKGYVVRISGGNDKQGFPMKQGVLTHGRVRLLLSKG HSCYRPRRTGERKRKSVRGCIVDANLSVLNLVIVKKGEKDIPGLTDTTVTRRLGPKRASRIRKLFNLSKEDDVRQYVVRK PLNKEGKKPRTKAPKIQRLVTPRVLQHKRRRIALKKQRTKKNKEEAAEYAKLLAKRMKEAKEKRQEQIAKRRRLSSLRAS TSKSESSQK G1TM55 Small ribosomal subunit protein eS7 Oryctolagus cuniculus 0.022168914

G1SVB0

1 LEVO MFSSSAKIVKPNGEKPDEFESGISQALLELEMNSDLKAQLRELNITAAKEIEVGGGRKAIIIFVPVPQLKSFQKIQVRLV RELEKKFSGKHVVFIAQRRILPKPTRKSRTKNKQKRPRSRTLTAVHDAILEDLVFPSEIVGKRIRVKLDGSRLIKVHLDK AQQNNVEHKVETFSGVYKKLTGKDVNFEFPEFQL G1SVB0 Small ribosomal subunit protein eS8 Oryctolagus cuniculus 0.024163243999999997

G1TJW1

1 LEVO MGISRDNWHKRRKTGGKRKPYHKKRKYELGRPAANTKIGPRRIHTVGVRGGNKKYRALRLDVGNFSWGSECCTRKTRIID VVYNASNNELVRTKTLVKNCIVLIDSTPYRQWYESHYALPLGRKKGAKLTPEEEEILNKKRSKKIQKKYDERKKNAKISS LLEEQFQQGKLLACIASRPGQCGRADGYVLEGKELEFYLRKIKARKGK G1TJW1 Small ribosomal subunit protein uS4 Oryctolagus cuniculus 0.022641563999999996

B7NZS8

1 LEVO MPVARSWVCRKTYVTPRRPFEKSRLDQELKLIGEYGLRNKREVWRVKFTLAKIRKAARELLTLDEKDPRRLFEGNALLRR LVRIGVLDEGKMKLDYILGLKIEDFLERRLQTQVFKLGLAKSIHHARVLIRQRHIRVRKQVVNIPSFIVRLDSQKHIDFS LRSPYGGGRPGRVKRKNAKKGQGGAGAGDDEEED B7NZS8 Small ribosomal subunit protein eS10 Oryctolagus cuniculus 0.017156865

G1U0Y5

1 LEVO MLMPKKNRIAIYELLFKEGVMVAKKDVHMPKHPELADKNVPNLHVMKAMQSLKSRGYVKEQFAWRHFYWYLTNEGIQYLR DYLHLPPEIVPATLRRSRPETGRPRPKGLEGERPARLTRGEADRDTYRRSAVPPGADKKAEAGAGSATE G1T168 Small ribosomal subunit protein uS17 Oryctolagus cuniculus 0.018468826

G1TRM4

1 LEVO MADIQTERAYQKQPTIFQNKKRVLLGETGKEKLPRYYKNIGLGFKTPKEAIEGTYIDKKCPFTGNVSIRGRILSGVVTKM KMQRTIVIRRDYLHYIRKYNRFEKRHKNMSVHLSPCFRDVQIGDIVTVGECRPLSKTVRFNVLKVTKAAGTKKQFQKF G1TRM4 Small ribosomal subunit protein eS12 Oryctolagus cuniculus 0.014538986999999998

G1SFR8

1 LEVO MAEEGIAAGGVMDVNTALQEVLKTALIHDGLARGIREAAKALDKRQAHLCVLASNCDEPMYVKLVEALCAEHQINLIKVD DNKKLGEWVGLCKIDREGKPRKVVGCSCVVVKDYGKESQAKDVIEEYFKCKK G1SFR8 Small ribosomal subunit protein uS15 Oryctolagus cuniculus 0.017259389

G1SP51

1 LEVO MGRMHAPGKGLSQSALPYRRSVPTWLKLTSDDVKEQIYKLAKKGLTPSQIGVILRDSHGVAQVRFVTGNKILRILKSKGL APDLPEDLYHLIKKAVAVRKHLERNRKDKDAKFRLILIESRIHRLARYYKTKRVLPPNWKYESSTASALVA G1SP51 Small ribosomal subunit protein uS11 Oryctolagus cuniculus 0.016302772

G1T1F0

1 LEVO MAPRKGKEKKEEQVISLGPQVAEGENVFGVCHIFASFNDTFVHVTDLSGKETICRVTGGMKVKADRDESSPYAAMLAAQD VAQRCKELGITALHIKLRATGGNRTKTPGPGAQSALRALARSGMKIGRIEDVTPIPSDSTRRKGGRRGRRL G1T1F0 Small ribosomal subunit protein uS19 Oryctolagus cuniculus 0.017049182

G1U0Q2

1 LEVO MAEVEQKKKRTFRKFTYRGVDLDQLLDMSYEQLMQLYSARQRRRLSRGLRRKQHSLLKRLRKAKKEAPPMEKPEVVKTHL RDMIILPEMVGSMVGVYNGKTFNQVEIKPEMIGHYLGEFSITYKPVKHGRPGIGATHSSRFIPLK G1U0Q2 Small ribosomal subunit protein uS9 Oryctolagus cuniculus 0.016477377

G1SGX4

1 LEVO MPSKGPLQSVQVFGRKKTATAVAHCKRGNGLIKVNGRPLEMIEPRTLQYKLLEPVLLLGKERFAGVDIRVRVKGGGHVAQ IYAIRQSISKALVAYYQKYVDEASKKEIKDILIQYDRTLLVADPRRCESKKFGGPGARARYQKSYR G1SGX4 Small ribosomal subunit protein eS17 Oryctolagus cuniculus 0.015552119

G1TU13

1 LEVO MGRVRTKTVKKAARVIIEKYYTRLGNDFHTNKRVCEEIAIIPSKKLRNKIAGYVTHLMKRIQRGPVRGISIKLQEEERER RDNYVPEVSALDQEIIEVDPDTKEMLKLLDFGSLSNLQVTQPTVGMNFKTPRGAV G1TU13 Small ribosomal subunit protein uS13 Oryctolagus cuniculus 0.017759776999999997

G1TPG3

1 LEVO MSLVIPEKFQHILRVLNTNIDGRRKIAFAITAIKGVGRRYAHVVLRKADIDLTKRAGELTEDEVERVITIMQNPRQYKIP DWFLNRQKDVKDGKYSQVLANGLDNKLREDLERLKKIRAHRGLRHFWGLRVRGQHTKTTGRRGRTVGVSKKK G1TPG3 Small ribosomal subunit protein eS19 Oryctolagus cuniculus 0.016235796

G1TN62

1 LEVO MPGVTVKDVNQQEFVRALAAFLKKSGKLKVPEWVDTVKLAKHKELAPYDENWFYTRAASTARHLYLRGGAGVGSMTKIYG GRQRNGVMPSHFSRGSKSVARRVLQALEGLKMVEKDQDWGRKLTPQGQRDLDRIAGQVAAAKKKH G1TN62 Small ribosomal subunit protein uS10 Oryctolagus cuniculus 0.013398763000000001

G1SIZ2

1 LEVO MAFKDTGKTPVEPEVAIHRIRITLTSRNVKSLEKVCADLIRGAKEKNLKVKGPVRMPTKTLRITTRKTPCGEGSKTWDRF QMRIHKRLIDLHSPSEIVKQITSISIEPGVEVEVTIADA G1SIZ2 Small ribosomal subunit protein eS21 Oryctolagus cuniculus 0.009124388999999998

G1TM82

1 LEVO MQNDAGEFVDLYVPRKCSASNRIIGAKDHASIQMNVAEVDKVTGRFNGQFKTYAICGAIRRMGESDDSILRLAKADGIVS KNF Q32PB8 Small ribosomal subunit protein uS8 Oryctolagus cuniculus 0.014865554999999999

G1TG89

1 LEVO MVRMNVLADALKSINNAEKRGKRQVLIRPCSKVIVRFLTVMMKHGYIGEFEIIDDHRAGKIVVNLTGRLNKCGVISPRFD VQLKDLEKWQNNLLPSRQFGFIVLTTSAGIMDHEEARRKHTGGKILGFFF G1TG89 Small ribosomal subunit protein uS12 Oryctolagus cuniculus 0.015844665999999997

G1SZ47

1 LEVO MGKCRGLRTARKLRSHRRDQKWHDKQYKKAHLGTALKANPFGGASHAKGIVLEKVGVEAKQPNSAIRKCVRVQLIKNGKK ITAFVPNDGCLNFIEENDEVLVAGFGRKGHAVGDIPGVRFKVVKVANVSLLALYKGKKERPRS G1SZ47 40S ribosomal protein S24 Oryctolagus cuniculus 0.015434267

G1TS40

1 LEVO MNDTVTIRTRKFMTNRLLQRKQMVIDVLHPGKATVPKTEIQEKLAKMYKTTPDVIFVFGFRTHFGGGKTTGFGMIYDSLD YAKKNEPKHRLARHGLYEKKKTSRKQRKERKNRMKKVRGTAKANVGAGKKPKE G1TS40 Small ribosomal subunit protein eS26 Oryctolagus cuniculus 0.012961455

G1TFE8

1 LEVO MTKKRRNNGRAKKGRGHVQPIRCTNCACCVPKDKAIKKFVIRNIVEAAAVRDISEVSVFDAYVLPKLYVKLHYCVSCAIH SKVVRNRSREARKDRTPPPRFRPAGAAPPPPPKPM G1TFE8 Small ribosomal subunit protein eS27 Oryctolagus cuniculus 0.009480186

G1TZ76

1 LEVO MPLAKDLLHPSPEEEKRKHKKKRLVQSPNSYFMDVKCPGCYKITTVFSHAQTVVLCVGCSTVLCQPTGGKARLTEGCSFR RKQH G1TZ76 Small ribosomal subunit protein eS28 Oryctolagus cuniculus 0.007855052

G1TIB4

1 LEVO MDTSRVQPIKLARVTKVLGRTGSQGQCTQVRVEFMDDTSRSIIRNVKGPVREGDVLTLLESEREARRLR G1TIB4 Small ribosomal subunit protein uS14 Oryctolagus cuniculus 0.006690821

G1U7M4

1 LEVO MGHQQLYWSHPRKFGQGSRSCRVCSNRHGLIRKYGLNMCRQCFRQYAKDIGFIKLD G1U7M4 Ubiquitin-ribosomal protein eS31 fusion protein Oryctolagus cuniculus 0.018004041000000002

G1SK22

1 LEVO MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGAKKR KKKSYTTPKKNKHKRKKVKLAVLKYYKVDENGKISRLRRECPSDECGAGVFMASHFDRHYCGKCCLTYCFNKPEDK G1SK22 Small ribosomal subunit protein RACK1 Oryctolagus cuniculus 0.035115652

G1SJB4

1 LEVO MTEQMTLRGTLKGHNGWVTQIATTPQFPDMILSASRDKTIIMWKLTRDETNYGIPQRALRGHSHFVSDVVISSDGQFALS GSWDGTLRLWDLTTGTTTRRFVGHTKDVLSVAFSSDNRQIVSGSRDKTIKLWNTLGVCKYTVQDESHSEWVSCVRFSPNS SNPIIVSCGWDKLVKVWNLANCKLKTNHIGHTGYLNTVTVSPDGSLCASGGKDGQAMLWDLNEGKHLYTLDGGDIINALC FSPNRYWLCAATGPSIKIWDLEGKIIVDELKQEVISTSSKAEPPQCTSLAWSADGQTLFAGYTDNLVRVWQVTIGTR G1SJB4 Ubiquitin-like FUBI-ribosomal protein eS30 fusion protein Oryctolagus cuniculus 0.014498884

G1T8A2

1 LEVO MQLFVRAQELHTLEVTGRETVAQIKAHVASLEGIAPEDQVVLLAGTPLEDEATLGQCGVEALSTLEVAGRMLGGKVHGSL ARVGKVRGQTLKVAKQEKKKKRTGRAKRRMQYNRRFVNVVPTFGKKKGPNANS G1T8A2 Eukaryotic translation initiation factor 4C Oryctolagus cuniculus 0.016476395

Uniprot: G1SYS4, Eukaryotic translation initiation factor 4C. Many last papers called this protein as Eukaryotic translation initiation factor 1A

1 LEVO MPKNKGKGGKNRRRGKNENESEKRELVFKEDGQEYAQVIKMLGNGRLEAMCFDGVKRLCHIRGKLRKKVWINTSDIILVG LRDYQDNKADVILKYNADEARSLKAYGELPEHAKINETDTFGPGDDDEIQFDDIGDDDEDTDDI G1SYS4 ATP binding cassette subfamily E member 1 Oryctolagus cuniculus 0.067419258

G1SG72

1 LEVO MADKLTRIAIVNHDKCKPKKCRQECKKSCPVVRMGKLCIEVTPQSKIAWISETLCIGCGICIKKCPFGALSIVNLPSNLE KETTHRYCANAFKLHRLPIPRPGEVLGLVGTNGIGKSTALKILAGKQKPNLGKYDDPPDWQEILTYFRGSELQNYFTKIL EDDLKAIIKPQYVDQIPKAAKGTVGSILDRKDETKTQAIVCQQLDLTHLKERNVEDLSGGELQRFACAVVCIQKADIFMF DEPSSYLDVKQRLKAAITIRSLINPDRYIIVVEHDLSVLDYLSDFICCLYGVPSAYGVVTMPFSVREGINIFLDGYVPTE NLRFRDASLVFKVAETANEEEVKKMCMYKYPGMKKKMGEFELAIVAGEFTDSEIMVMLGENGTGKTTFIRMLAGRLKPDE GGEVPVLNVSYKPQKISPKSTGSVRQLLHEKIRDAYTHPQFVTDVMKPLQIENIIDQEVQTLSGGELQRVALALCLGKPA DVYLIDEPSAYLDSEQRLMAARVVKRFILHAKKTAFVVEHDFIMATYLADRVIVFDGIPSKNTVANSPQTLLAGMNKFLS QLEITFRRDPNNYRPRINKLNSIKDVEQKKSGNYFFLDD G1SG72 Small ribosomal subunit protein eS32 Oryctolagus cuniculus 0.003473451

A0A087WNH4

1 LEVO MRAKWRKKRMRRLKRKRRKMRQRSK A0A087WNH4 Small ribosomal subunit protein eS25 Oryctolagus cuniculus 0.013645028

G1TDB3

1 LEVO PPKDDKKKKDAGKSAKKDKDPVNKSGGKAKKKKWSKGKVRDKLNNLVLFDKATYDKLCKEVPNYKLITPAVVSERLKIRG SLARAALQELLSKGLIKLVSKHRAQVIYTRNTKGGDAPAAGEDA G1TDB3 Eukaryotic translation initiation factor 5 Oryctolagus cuniculus 0.04913152

G1TGW1 (2019-12-11 v2) (430 aa) and A0A5F9C5D3 (2019-12-11 v1) (398 aa). Different the C-ter of two protein isoform from the position 354

1 LEVO MSVNVNRSVSDQFYRYKMPRLIAKVEGKGNGIKTVIVNMVDVAKALNRPPTYPTKYFGCELGAQTQFDVKNDRYIVNGSH EANKLQDMLDGFIKKFVLCPECENPETDLHVNPKKQTIGNSCKACGYRGMLDTHHKLCTFILKNPPENSDSATGKKEKEK KNRKGKDKENGSVSSSETPPPPPPNEISPPPHAVEEEEDDDWGEDTTEEAQRRRMDEISDHAKVLTLSDDLERTVEERVN ILFDFVKKKKEEGVIDSSDKEIVAEAERLDVKAMGPLVLTEVLFNEKIREQIKKYRRHFLRFCHNNKKAQRYLLHGLECV VAMHQAQLISKIPHILKEMYDADLLEEEVIISWSEKASKKYVSKELAKEIRVKAEPFIKWLKEAEEESSGGEEDDEDENI EVVYSKTASVPKVETVKSDNKDDDIDIDAI G1TGW1 IRON/SULFUR CLUSTER 0.00035163999999999996 2 SF4 singleParticle particle 0.4 7.4 10.0 HEPES-KOH HEPES Buffer 5.0 Mg(OAc)2 Magnesium Acetate 50.0 KOAc Potassium Acetate 10.0 NH4Cl Ammonium Chloride 2.0 DTT Dithiothreitol

10 mM HEPES-KOH pH 7.4, 5 mM Mg(OAc)2, 50 mM KOAc, 10 mM NH4Cl, 2 mM DTT and Roche cOmplete protease inhibitor cocktail

Quantifoil R2/2 COPPER 300 CARBON HOLEY 2.0 GLOW DISCHARGE 20

glow-discharged at 2.5 mA for 20 s

ETHANE 100 277 FEI VITROBOT MARK IV

The sample was incubated on the grid for 30 s and then blotted with filter paper from both sides for 1.5 s with the blot force 5.

late-stage 48S initiation translation complex was dissolved in 20 microlitre buffer containing 10 mM HEPES-KOH pH 7.4, 5 mM Mg(OAc)2, 50 mM KOAc, 10 mM NH4Cl, 2 mM DTT and Roche cOmplete protease inhibitor cocktail

FEI TALOS ARCTICA FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 200 30.0 2.7 0.5 2.5 59000.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN 90.0 95.0 GATAN K2 SUMMIT (4k x 4k) COUNTING 4096 4096 1-40 1 9524 6.0 50.0 1 CTFFIND 4 PHASE FLIPPING AND AMPLITUDE CORRECTION 2.9 OTHER cryoSPARC 4.5.1 1000 COMMON LINE PROJECTION MATCHING emd_51903.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 500 500 500 0 0 0 500 500 500 465.0 465.0 465.0 90.0 90.0 90.0 X Y Z -1.1440256 2.1109765 -0.0006061282 0.052475207 0.93 0.93 0.93 0.246 AUTHOR ::::EMDATABANK.org::::EMD-51903:::: main map of the mammalian late-stage 48S initiation complex 8P09 PDB experimental model 6YAM PDB experimental model 6FYX PDB experimental model G1TGW1 o 1-147 AlphaFold in silico model

Eukaryotic translation initiation factor 5 (N-terminal domain)

RIGID BODY FIT

The atomic model of LS48S IC complex (PDB: 8P09) was initially rigid body fitted in density using ChimeraX and further model building was done for mRNA, eIF5 N-terminal domain, eIF2gamma, eIF3d and eIF3 octamer in ChimeraX. Densities for eIF5 N-terminal domain, eIF2gamma, eIF3d and eIF3 octamer were observed in the map and therefore were included in the model. The 3D structure of the eIF5-N terminal domain was generated by Alphafold2 (PDB: G1TGW1). It was then accommodated into the model by aligning structurally to its counterparts in the yeast atomic model of the py48S-eIF5N pre-initiation complex (PDB: 6FYX). IF3d and eIF3 octamer were taken from the atomic model of LS48S IC complex with eIF3 proteins (PDB: 6YAM) and placed into density by rigid-body fitting. The atomic models with and without eIF3 proteins were inspected visually and performed stereochemical, torsional, angle refinement and optimization by using ISOLDE v1.6. Figures featuring cryo-EM densities and atomic models were visualized by using ChimeraX.

emd_51903_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 500 500 500 0 0 0 500 500 500 465.0 465.0 465.0 90.0 90.0 90.0 X Y Z -0.08701938 2.3285406 0.0013896395 0.024707252 0.93 0.93 0.93 AUTHOR ::::EMDATABANK.org::::EMD-51903:::: EMhanced map of the mammalian late-stage 48S initiation complex emd_51903_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 500 500 500 0 0 0 500 500 500 465.0 465.0 465.0 90.0 90.0 90.0 X Y Z -0.6728217 1.1360123 0.0006306706 0.085040554 0.93 0.93 0.93 AUTHOR ::::EMDATABANK.org::::EMD-51903:::: half map A of the mammalian late-stage 48S initiation complex emd_51903_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 500 500 500 0 0 0 500 500 500 465.0 465.0 465.0 90.0 90.0 90.0 X Y Z -0.657675 1.198344 0.0006324271 0.085194424 0.93 0.93 0.93 AUTHOR ::::EMDATABANK.org::::EMD-51903:::: half map B of the mammalian late-stage 48S initiation complex