2026-09-02 REL PDBe INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY REFINEMENT_DESCRIPTION atom_site chem_comp_atom chem_comp_bond em_3d_fitting_list pdbx_validate_rmsd_angle pdbx_validate_torsion struct_conn _atom_site.auth_atom_id _atom_site.label_atom_id _em_3d_fitting_list.initial_refinement_model_id _struct_conn.pdbx_leaving_atom_flag _struct_conn.ptnr1_label_atom_id STRUCTURE_SUMMARY chem_comp chem_comp_atom chem_comp_bond _chem_comp.pdbx_synonyms _chem_comp_atom.atom_id _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.pdbx_aromatic_flag _chem_comp_bond.value_order REMEDIATION REPOSITORY Metalloprotein remediation STRUCTURE_SUMMARY atom_site chem_comp chem_comp_atom chem_comp_bond em_admin entity pdbx_entity_nonpoly pdbx_entry_details pdbx_modification_feature pdbx_nonpoly_atom_coordination pdbx_nonpoly_atom_coordination_sphere pdbx_nonpoly_atom_coordination_sphere_order pdbx_nonpoly_scheme pdbx_struct_conn_angle struct_conn _atom_site.auth_atom_id _atom_site.auth_comp_id _atom_site.label_atom_id _atom_site.label_comp_id _chem_comp.formula _chem_comp.formula_weight _chem_comp.id _chem_comp.name _em_admin.last_update _entity.formula_weight _entity.pdbx_description _pdbx_entity_nonpoly.comp_id _pdbx_entity_nonpoly.name _pdbx_entry_details.has_protein_modification _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.pdb_mon_id STRUCTURE_SUMMARY em_admin entity _chem_comp.name _em_admin.last_update _entity.formula_weight _entity.pdbx_description PDBe PDBe 2023-03-23 2023-06-14 2023-06-14 2026-09-02 Swiss National Science Foundation 182341 Switzerland Swiss National Science Foundation 179190 Switzerland European Molecular Biology Organization (EMBO) 1074-2019 European Union Saurer M Leibundgut M Scaiola A Schoenhut T Ban N human mitochondrial ribosome, release factor mtRF1, non-canonical stop codon, RIBOSOME Saurer M Leibundgut M Nadimpalli HP Scaiola A Schonhut T Lee RG Siira SJ Rackham O Dreos R Lenarcic T Kummer E Gatfield D Filipovska A Ban N Science US 380 531 536 2023 37141370 doi:10.1126/science.adf9890 1095-9203 0038 SCIEAS EMD-16894 other EM volume EMD-16895 other EM volume EMD-16896 other EM volume EMD-16897 other EM volume EMD-16899 other EM volume 8ois FULLOVERLAP EMDB EMD-16894 other EM volume EMDB EMD-16895 other EM volume EMDB EMD-16896 other EM volume EMDB EMD-16897 other EM volume EMDB EMD-16899 other EM volume EMDB EMD-16898 associated EM volume

28S human mitochondrial small ribosomal subunit with mtRF1 and P-site tRNA

28S human mitochondrial small ribosomal subunit with mtRF1, mRNA, and P-site tRNA 28S human mitochondrial small ribosomal subunit with mtRF1, mRNA, and P-site tRNA 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

28S human mitochondrial small ribosomal subunit in complex with mtRF1(AAQ)-3xFLAG, human methionine-tRNA(Met), and an mRNA containing a non-canonical stop codon, purified from HEK293 EBNA cells.

Homo sapiens Mitochondrion Mitochondrial matrix 0.05 39S ribosomal protein L19, mitochondrial Homo sapiens 0.033584996 1 LEVO MAACIAAGHWAAMGLGRSFQAARTLLPPPASIACRVHAGPVRQQSTGPSEPGAFQPPPKPVIVDKHRPVEPERRFLSPEF IPRRGRTDPLKFQIERKDMLERRKVLHIPEFYVGSILRVTTADPYASGKISQFLGICIQRSGRGLGATFILRNVIEGQGV EICFELYNPRVQEIQVVKLEKRLDDSLLYLRDALPEYSTFDVNMKPVVQEPNQKVPVNELKVKMKPKPWSKRWERPNFNI KGIRFDLCLTEQQMKEAQKWNQPWLEFDMMREYDTSKIEAAIWKEIEASKRS P49406 39S ribosomal protein L55, mitochondrial Homo sapiens 0.015160433000000001 1 LEVO MAAVGSLLGRLRQSTVKATGPALRRLHTSSWRADSSRASLTRVHRQAYARLYPVLLVKQDGSTIHIRYREPRRMLAMPID LDTLSPEERRARLRKREAQLQSRKEYEQELSDDLHVERYRQFWTRTKK Q7Z7F7 12S rRNA Homo sapiens 0.306547531

NCBI Reference Sequence: NC_012920.1 + one C at 3'-end (encoded but not annotated as part of the sequence), a A103>G and A791>G as found in e.g. GenBank: OM714795.1

1 AAUAGGUUUGGUCCUAGCCUUUCUAUUAGCUCUUAGUAAGAUUACACAUGCAAGCAUCCCCGUUCCAGUGAGUUCACCCU CUAAAUCACCACGAUCAAAAGGGACAAGCAUCAAGCACGCAGCAAUGCAGCUCAAAACGCUUAGCCUAGCCACACCCCCA CGGGAAACAGCAGUGAUUAACCUUUAGCAAUAAACGAAAGUUUAACUAAGCUAUACUAACCCCAGGGUUGGUCAAUUUCG UGCCAGCCACCGCGGUCACACGAUUAACCCAAGUCAAUAGAAGCCGGCGUAAAGAGUGUUUUAGAUCACCCCCUCCCCAA UAAAGCUAAAACUCACCUGAGUUGUAAAAAACUCCAGUUGACACAAAAUAGACUACGAAAGUGGCUUUAACAUAUCUGAA CACACAAUAGCUAAGACCCAAACUGGGA(5MU)UAGAUACCCCACUAUGCUUAGCCCUAAACCUCAACAGUUAAAUCAAC AAAACUGCUCGCCAGAACACUACGAGCCACAGCUUAAAACUCAAAGGACCUGGCGGUGCUUCAUAUCCCUCUAGAGGAGC CUGUUCUGUAAUCGAUAAACCCCGAUCAACCUCACCACCUCUUGCUCAGCCUAUAUACCGCCAUCUUCAGCAAACCCUGA UGAAGGCUACAAAGUAAGCGCAAGUACCCACGUAAAGACGUUAGGUCAAGGUGUAGCCCAUGAGGUGGCAAGAAAUGGGC UACAUUUUCUACCCCAGAAAACUACGAUAGCCCUUAUGAAACUUAAGGGUCGAAGGUGGAUUUAGCAGUAAACUGAGAGU AGAGUGCUUAGUUGAACAGGGCCCUGAAGCGCGUACACACCG(B8T)C(5MC)GUCACCCUCCUCAAGUAUACUUCAAAG GACAUUUAACUAAAACCCCUACGCAUUUAUAUAGAGGAGACAAGUCGUAACAUGGUAAGUGUACUGG(MA6)(MA6)AGU GCACUUGGACGAACC OM714795.1 28S ribosomal protein S35, mitochondrial Homo sapiens 0.036898328 1 LEVO MAAAALPAWLSLQSRARTLRAFSTAVYSATPVPTPSLPERTPGNERPPRRKALPPRTEKMAVDQDWPSVYPVAAPFKPSA VPLPVRMGYPVKKGVPMAKEGNLELLKIPNFLHLTPVAIKKHCEALKDFCTEWPAALDSDEKCEKHFPIEIDSTDYVSSG PSVRNPRARVVVLRVKLSSLNLDDHAKKKLIKLVGERYCKTTDVLTIKTDRCPLRRQNYDYAVYLLTVLYHESWNTEEWE KSKTEADMEEYIWENSSSERNILETLLQMKAAEKNMEINKEELLGTKEIEEYKKSVVSLKNEEENENSISQYKESVKRLL NVT P82673 28S ribosomal protein S24, mitochondrial Homo sapiens 0.019046164 1 LEVO MAASVCSGLLGPRVLSWSRELPCAWRALHTSPVCAKNRAARVRVSKGDKPVTYEEAHAPHYIAHRKGWLSLHTGNLDGED HAAERTVEDVFLRKFMWGTFPGCLADQLVLKRRGNQLEICAVVLRQLSPHKYYFLVGYSETLLSYFYKCPVRLHLQTVPS KVVYKYL Q96EL2 Aurora kinase A-interacting protein Homo sapiens 0.022395326 1 LEVO MLLGRLTSQLLRAVPWAGGRPPWPVSGVLGSRVCGPLYSTSPAGPGRAASLPRKGAQLELEEMLVPRKMSVSPLESWLTA RCFLPRLDTGTAGTVAPPQSYQCPPSQIGEGAEQGDEGVADAPQIQCKNVLKIRRRKMNHHKYRKLVKKTRFLRRKVQEG RLRRKQIKFEKDLRRIWLKAGLKEAPEGWQTPKIYLRGK Q9NWT8 28S ribosomal protein S6, mitochondrial Homo sapiens 0.014250588 1 LEVO MPRYELALILKAMQRPETAATLKRTIEALMDRGAIVRDLENLGERALPYRISAHSQQHNRGGYFLVDFYAPTAAVESMVE HLSRDIDVIRGNIVKHPLTQELKECEGIVPVPLAEKLYSTKKRKK P82932 28S ribosomal protein S7, mitochondrial Homo sapiens 0.028186153999999998 1 LEVO MAAPAVKVARGWSGLALGVRRAVLQLPGLTQVRWSRYSPEFKDPLIDKEYYRKPVEELTEEEKYVRELKKTQLIKAAPAG KTSSVFEDPVISKFTNMMMIGGNKVLARSLMIQTLEAVKRKQFEKYHAASAEEQATIERNPYTIFHQALKNCEPMIGLVP ILKGGRFYQVPVPLPDRRRRFLAMKWMITECRDKKHQRTLMPEKLSHKLLEAFHNQGPVIKRKHDLHKMAEANRALAHYR WW Q9Y2R9 P-site Met-tRNA(Met) Homo sapiens 0.022692508

NCBI Reference Sequence: NC_012920.1 + aminoacylated CCA-end

1 AGUAAGGUCAGCUAAAUAAGCUA(PSU)CGGGCC(RSQ)AUACCCCGAAAAUG(PSU)UGGU(PSU)AUACCCUUCCCGU ACUACCA NC_012920.1 28S ribosomal protein S10, mitochondrial Homo sapiens 0.0230335 1 LEVO MAARTAFGAVCRRLWQGLGNFSVNTSKGNTAKNGGLLLSTNMKWVQFSNLHVDVPKDLTKPVVTISDEPDILYKRLSVLV KGHDKAVLDSYEYFAVLAAKELGISIKVHEPPRKIERFTLLQSVHIYKKHRVQYEMRTLYRCLELEHLTGSTADVYLEYI QRNLPEGVAMEVTKTQLEQLPEHIKEPIWETLSEEKEESKS P82664 mRNA Homo sapiens 0.007329883

Sequence as observed in the cryo-EM density map.

1 (N)(N)(N)(N)AUGAGG(Y5P)(N)(N)(N)(N)(N)(N)(N)(N)(N)(N)(N)(N)(N)(N)(N)(N)(N)(N)(N) (N)(N)(N) 28S ribosomal protein S12, mitochondrial Homo sapiens 0.015200947 1 LEVO MSWSGLLHGLNTSLTCGPALVPRLWATCSMATLNQMHRLGPPKRPPRKLGPTEGRPQLKGVVLCTFTRKPKKPNSANRKC CRVRLSTGREAVCFIPGEGHTLQEHQIVLVEGGRTQDLPGVKLTVVRGKYDCGHVQKK O15235 28S ribosomal protein S14, mitochondrial Homo sapiens 0.015168787999999999 1 LEVO MAAFMLGSLLRTFKQMVPSSASGQVRSHYVDWRMWRDVKRRKMAYEYADERLRINSLRKNTILPKILQDVADEEIAALPR DSCPVRIRNRCVMTSRPRGVKRRWRLSRIVFRHLADHGQLSGIQRATW O60783 28S ribosomal protein S15, mitochondrial Homo sapiens 0.029903293 1 LEVO MLRVAWRTLSLIRTRAVTQVLVPGLPGGGSAKFPFNQWGLQPRSLLLQAARGYVVRKPAQSRLDDDPPPSTLLKDYQNVP GIEKVDDVVKRLLSLEMANKKEMLKIKQEQFMKKIVANPEDTRSLEARIIALSVKIRSYEEHLEKHRKDKAHKRYLLMSI DQRKKMLKNLRNTNYDVFEKICWGLGIEYTFPPLYYRRAHRRFVTKKALCIRVFQETQKLKKRRRALKAAAAAQKQAKRR NPDSPAKAIPKTLKDSQ P82914 28S ribosomal protein S16, mitochondrial Homo sapiens 0.015371898999999998 1 LEVO MVHLTTLLCKAYRGGHLTIRLALGGCTNRPFYRIVAAHNKCPRDGRFVEQLGSYDPLPNSHGEKLVALNLDRIRHWIGCG AHLSKPMEKLLGLAGFFPLHPMMITNAERLRRKRAREVLLASQKTDAEATDTEATET Q9Y3D3 28S ribosomal protein S17, mitochondrial Homo sapiens 0.014526078 1 LEVO MSVVRSSVHARWIVGKVIGTKMQKTAKVRVTRLVLDPYLLKYFNKRKTYFAHDALQQCTVGDIVLLRALPVPRAKHVKHE LAEIVFKVGKVIDPVTGKPCAGTTYLESPLSSETTQLSKNLEELNISSAQ Q9Y2R5 28S ribosomal protein S18b, mitochondrial Homo sapiens 0.029440629 1 LEVO MAASVLNTVLRRLPMLSLFRGSHRVQVPLQTLCTKAPSEEDSLSSVPISPYKDEPWKYLESEEYQERYGSRPVWADYRRN HKGGVPPQRTRKTCIRRNKVVGNPCPICRDHKLHVDFRNVKLLEQFVCAHTGIIFYAPYTGVCVKQHKRLTQAIQKARDH GLLIYHIPQVEPRDLDFSTSHGAVSATPPAPTLVSGDPWYPWYNWKQPPERELSRLRRLYQGHLQEESGPPPESMPKMPP RTPAEASSTGQTGPQSAL Q9Y676 28S ribosomal protein S18c, mitochondrial Homo sapiens 0.015876786 1 LEVO MAAVVAVCGGLGRKKLTHLVTAAVSLTHPGTHTVLWRRGCSQQVSSNEDLPISMENPYKEPLKKCILCGKHVDYKNVQLL SQFVSPFTGCIYGRHITGLCGKKQKEITKAIKRAQIMGFMPVTYKDPAYLKDPKVCNIRYRE Q9Y3D5 28S ribosomal protein S21, mitochondrial Homo sapiens 0.010806689

GenBank: AAH04566.2

1 LEVO M(AYA)KHLKFIARTVMVQEGNVESAYRTLNRILTMDGLIEDIKHRRYYEKPCRRRQRESYERCRRIYNMEMARKINFLM RKNRADPWQGC P82921 28S ribosomal protein S22, mitochondrial Homo sapiens 0.041337316 1 LEVO MAPLGTTVLLWSLLRSSPGVERVCFRARIQPWHGGLLQPLPCSFEMGLPRRRFSSEAAESGSPETKKPTFMDEEVQSILT KMTGLNLQKTFKPAIQELKPPTYKLMTQAQLEEATRQAVEAAKVRLKMPPVLEERVPINDVLAEDKILEGTETTKYVFTD ISYSIPHRERFIVVREPSGTLRKASWEERDRMIQVYFPKEGRKILTPIIFKEENLRTMYSQDRHVDVLNLCFAQFEPDST EYIKVHHKTYEDIDKRGKYDLLRSTRYFGGMVWYFVNNKKIDGLLIDQIQRDLIDDATNLVQLYHVLHPDGQSAQGAKDQ AAEGINLIKVFAKTEAQKGAYIELTLQTYQEALSRHSAAS P82650 28S ribosomal protein S23, mitochondrial Homo sapiens 0.021805664 1 LEVO MAGSRLETVGSIFSRTRDLVRAGVLKEKPLWFDVYDAFPPLREPVFQRPRVRYGKAKAPIQDIWYHEDRIRAKFYSVYGS GQRAFDLFNPNFKSTCQRFVEKYTELQKLGETDEEKLFVETGKALLAEGVILRRVGEARTQHGGSHVSRKSEHLSVRPQT ALEENETQKEVPQDQHLEAPADQSKGLLPP Q9Y3D9 28S ribosomal protein S25, mitochondrial Homo sapiens 0.020146427999999997 1 LEVO MPMKGRFPIRRTLQYLSQGNVVFKDSVKVMTVNYNTHGELGEGARKFVFFNIPQIQYKNPWVQIMMFKNMTPSPFLRFYL DSGEQVLVDVETKSNKEIMEHIRKILGKNEETLREEEEEKKQLSHPANFGPRKYCLRECICEVEGQVPCPSLVPLPKEMR GKYKAALKADAQD P82663 28S ribosomal protein S26, mitochondrial Homo sapiens 0.024259819999999998 1 LEVO MLRALSRLGAGTPCRPRAPLVLPARGRKTRHDPLAKSKIERVNMPPAVDPAEFFVLMERYQHYRQTVRALRMEFVSEVQR KVHEARAGVLAERKALKDAAEHRELMAWNQAENRRLHELRIARLRQEEREQEQRQALEQARKAEEVQAWAQRKEREVLQL QEEVKNFITRENLEARVEAALDSRKNYNWAITREGLVVRPQRRDS Q9BYN8 28S ribosomal protein S27, mitochondrial Homo sapiens 0.047669262 1 LEVO MAASIVRRGMLLARQVVLPQLSPAGKRYLLSSAYVDSHKWEAREKEHYCLADLASLMDKTFERKLPVSSLTISRLIDNIS SREEIDHAEYYLYKFRHSPNCWYLRNWTIHTWIRQCLKYDAQDKALYTLVNKVQYGIFPDNFTFNLLMDSFIKKENYKDA LSVVFEVMMQEAFEVPSTQLLSLYVLFHCLAKKTDFSWEEERNFGASLLLPGLKQKNSVGFSSQLYGYALLGKVELQQGL RAVYHNMPLIWKPGYLDRALQVMEKVAASPEDIKLCREALDVLGAVLKALTSADGASEEQSQNDEDNQGSEKLVEQLDIE ETEQSKLPQYLERFKALHSKLQALGKIESEGLLSLTTQLVKEKLSTCEAEDIATYEQNLQQWHLDLVQLIQREQQQREQA KQEYQAQKAAKASA Q92552 28S ribosomal protein S28, mitochondrial Homo sapiens 0.020878846 1 LEVO MAALCRTRAVAAESHFLRVFLFFRPFRGVGTESGSESGSSNAKEPKTRAGGFASALERHSELLQKVEPLQKGSPKNVESF ASMLRHSPLTQMGPAKDKLVIGRIFHIVENDLYIDFGGKFHCVCRRPEVDGEKYQKGTRVRLRLLDLELTSRFLGATTDT TVLEANAVLLGIQESKDSRSKEEHHEK Q9Y2Q9 28S ribosomal protein S29, mitochondrial Homo sapiens 0.045634406 1 LEVO MMLKGITRLISRIHKLDPGRFLHMGTQARQSIAAHLDNQVPVESPRAISRTNENDPAKHGDQHEGQHYNISPQDLETVFP HGLPPRFVMQVKTFSEACLMVRKPALELLHYLKNTSFAYPAIRYLLYGEKGTGKTLSLCHVIHFCAKQDWLILHIPDAHL WVKNCRDLLQSSYNKQRFDQPLEASTWLKNFKTTNERFLNQIKVQEKYVWNKRESTEKGSPLGEVVEQGITRVRNATDAV GIVLKELKRQSSLGMFHLLVAVDGINALWGRTTLKREDKSPIAPEELALVHNLRKMMKNDWHGGAIVSALSQTGSLFKPR KAYLPQELLGKEGFDALDPFIPILVSNYNPKEFESCIQYYLENNWLQHEKAPTEEGKKELLFLSNANPSLLERHCAYL P51398 28S ribosomal protein S31, mitochondrial Homo sapiens 0.045391472999999995 1 LEVO MFPRVSTFLPLRPLSRHPLSSGSPETSAAAIMLLTVRHGTVRYRSSALLARTKNNIQRYFGTNSVICSKKDKQSVRTEET SKETSESQDSEKENTKKDLLGIIKGMKVELSTVNVRTTKPPKRRPLKSLEATLGRLRRATEYAPKKRIEPLSPELVAAAS AVADSLPFDKQTTKSELLSQLQQHEEESRAQRDAKRPKISFSNIISDMKVARSATARVRSRPELRIQFDEGYDNYPGQEK TDDLKKRKNIFTGKRLNIFDMMAVTKEAPETDTSPSLWDVEFAKQLATVNEQPLQNGFEELIQWTKEGKLWEFPINNEAG FDDDGSEFHEHIFLEKHLESFPKQGPIRHFMELVTCGLSKNPYLSVKQKVEHIEWFRNYFNEKKDILKESNIQFN Q92665 28S ribosomal protein S33, mitochondrial Homo sapiens 0.012657775999999999 1 LEVO MSSLSEYAFRMSRLSARLFGEVTRPTNSKSMKVVKLFSELPLAKKKETYDWYPNHHTYAELMQTLRFLGLYRDEHQDFMD EQKRLKKLRGKEKPKKGEGKRAAKRK Q9Y291 Peptide chain release factor 1, mitochondrial,mtRF1(AAQ) Homo sapiens 0.056258391

Human mitochondrial release factor 1 (mtRF1), containing a 311GGQ>AAQ mutation, a C-terminal linker (GGSGGSGGSGGSGGSGG) and a 3xFLAG-tag (DYKDHDGDYKDHDIDYKDDDDK), expressed from a pcDNA3.1(+) plasmid in HEK293 EBNA cells.,Human mitochondrial release factor 1 (mtRF1), containing a 311GGQ>AAQ mutation, a C-terminal linker (GGSGGSGGSGGSGGSGG) and a 3xFLAG-tag (DYKDHDGDYKDHDIDYKDDDDK), expressed from a pcDNA3.1(+) plasmid in HEK293 EBNA cells.

1 LEVO MNRHLCVWLFRHPSLNGYLQCHIQLHSHQFRQIHLDTRLQVFRQNRNCILHLLSKNWSRRYCHQDTKMLWKHKALQKYME NLSKEYQTLEQCLQHIPVNEENRRSLNRRHAELAPLAAIYQEIQETEQAIEELESMCKSLNKQDEKQLQELALEERQTID QKINMLYNELFQSLVPKEKYDKNDVILEVTAGRTTGGDICQQFTREIFDMYQNYSCYKHWQFELLNYTPADYGGLHHAAA RISGDGVYKHLKYEGGIHRVQRIPEVGLSSRMQRIHTGTMSVIVLPQPDEVDVKLDPKDLRIDTFRAKGAAAQHVNKTDS AVRLVHIPTGLVVECQQERSQIKNKEIAFRVLRARLYQQIIEKDKRQQQSARKLQVGTRAQSERIRTYNFTQDRVSDHRI AYEVRDIKEFLCGGKGLDQLIQRLLQSADEEAIAELLDEHLKSAKGGSGGSGGSGGSGGSGGDYKDHDGDYKDHDIDYKD DDDK O75570 28S ribosomal protein S2, mitochondrial Homo sapiens 0.033298237999999994 1 LEVO MATSSAALPRILGAGARAPSRWLGFLGKATPRPARPSRRTLGSATALMIRESEDSTDFNDKILNEPLKHSDFFNVKELFS VRSLFDARVHLGHKAGCRHRFMEPYIFGSRLDHDIIDLEQTATHLQLALNFTAHMAYRKGIILFISRNRQFSYLIENMAR DCGEYAHTRYFRGGMLTNARLLFGPTVRLPDLIIFLHTLNNIFEPHVAVRDAAKMNIPTVGIVDTNCNPCLITYPVPGND DSPLAVHLYCRLFQTAITRAKEKRQQVEALYRLQGQKEPGDQGPAHPPGADMSHSL Q9Y399 Coiled-coil-helix-coiled-coil-helix domain-containing protein 1 Homo sapiens 0.013540855999999999 1 LEVO M(AYA)TPSLRGRLARFGNPRKPVLKPNKPLILANRVGERRREKGEATCITEMSVMMACWKQNEFRDDACRKEIQGFLDC AARAQEARKMRSIQETLGESGSLLPNKLNKLLQRFPNKPYLS Q96BP2 28S ribosomal protein S5, mitochondrial Homo sapiens 0.048094594 1 LEVO MATAVRAVGCLPVLCSGTAGHLLGRQCSLNTLPAASILAWKSVLGNGHLSSLGTRDTHPYASLSRALQTQCCISSPSHLM SQQYRPYSFFTKLTADELWKGALAETGAGAKKGRGKRTKKKKRKDLNRGQIIGEGRYGFLWPGLNVPLMKNGAVQTIAQR SKEEQEKVEADMIQQREEWDRKKKMKVKRERGWSGNSWGGISLGPPDPGPCGETYEDFDTRILEVRNVFTMTAKEGRKKS IRVLVAVGNGKGAAGFSIGKATDRMDAFRKAKNRAVHHLHYIERYEDHTIFHDISLRFKRTHIKMKKQPKGYGLRCHRAI ITICRLIGIKDMYAKVSGSINMLSLTQGLFRGLSRQETHQQLADKKGLHVVEIREECGPLPIVVASPRGPLRKDPEPEDE VPDVKLDWEDVKTAQGMKRSVWSNLKRAAT P82675 Pentatricopeptide repeat domain-containing protein 3, mitochondrial Homo sapiens 0.078648547 1 LEVO MAVVSAVRWLGLRSRLGQPLTGRRAGLCEQARSCRFYSGSATLSKVEGTDVTGIEEVVIPKKKTWDKVAVLQALASTVNR DTTAVPYVFQDDPYLMPASSLESRSFLLAKKSGENVAKFIINSYPKYFQKDIAEPHIPCLMPEYFEPQIKDISEAALKER IELRKVKASVDMFDQLLQAGTTVSLETTNSLLDLLCYYGDQEPSTDYHFQQTGQSEALEEENDETSRRKAGHQFGVTWRA KNNAERIFSLMPEKNEHSYCTMIRGMVKHRAYEQALNLYTELLNNRLHADVYTFNALIEATVCAINEKFEEKWSKILELL RHMVAQKVKPNLQTFNTILKCLRRFHVFARSPALQVLREMKAIGIEPSLATYHHIIRLFDQPGDPLKRSSFIIYDIMNEL MGKRFSPKDPDDDKFFQSAMSICSSLRDLELAYQVHGLLKTGDNWKFIGPDQHRNFYYSKFFDLICLMEQIDVTLKWYED LIPSAYFPHSQTMIHLLQALDVANRLEVIPKIWKDSKEYGHTFRSDLREEILMLMARDKHPPELQVAFADCAADIKSAYE SQPIRQTAQDWPATSLNCIAILFLRAGRTQEAWKMLGLFRKHNKIPRSELLNELMDSAKVSNSPSQAIEVVELASAFSLP ICEGLTQRVMSDFAINQEQKEALSNLTALTSDSDTDSSSDSDSDTSEGK Q96EY7 28S ribosomal protein S9, mitochondrial Homo sapiens 0.045909859 1 LEVO MAAPCVSYGGAVSYRLLLWGRGSLARKQGLWKTAAPELQTNVRSQILRLRHTAFVIPKKNVPTSKRETYTEDFIKKQIEE FNIGKRHLANMMGEDPETFTQEDIDRAIAYLFPSGLFEKRARPVMKHPEQIFPRQRAIQWGEDGRPFHYLFYTGKQSYYS LMHDVYGMLLNLEKHQSHLQAKSLLPEKTVTRDVIGSRWLIKEELEEMLVEKLSDLDYMQFIRLLEKLLTSQCGAAEEEF VQRFRRSVTLESKKQLIEPVQYDEQGMAFSKSEGKRKTAKAEAIVYKHGSGRIKVNGIDYQLYFPITQDREQLMFPFHFV DRLGKHDVTCTVSGGGRSAQAGAIRLAMAKALCSFVTEDEVEWMRQAGLLTTDPRVRERKKPGQEGARRKFTWKKR P82933 28S ribosomal protein S11, mitochondrial Homo sapiens 0.020663805 1 LEVO MQAVRNAGSRFLRSWTWPQTAGRVVARTPAGTICTGARQLQDAAAKQKVEQNAAPSHTKFSIYPPIPGEESSLRWAGKKF EEIPIAHIKASHNNTQIQVVSASNEPLAFASCGTEGFRNAKKGTGIAAQTAGIAAAARAKQKGVIHIRVVVKGLGPGRLS AMHGLIMGGLEVISITDNTPIPH(5F0)GCRPRKARKL P82912 28S ribosomal protein S34, mitochondrial Homo sapiens 0.025695548999999998 1 LEVO MARKKVRPRLIAELARRVRALREQLNRPRDSQLYAVDYETLTRPFSGRRLPVRAWADVRRESRLLQLLGRLPLFGLGRLV TRKSWLWQHDEPCYWRLTRVRPDYTAQNLDHGKAWGILTFKGKTESEAREIEHVMYHDWRLVPKHEEEAFTAFTPAPEDS LASVPYPPLLRAMIIAERQKNGDTSTEEPMLNVQRIRMEPWDYPAKQEDKGRAKGTPV P82930 POTASSIUM ION 3.9098e-05 17 K MAGNESIUM ION 2.4305e-05 126 MG METHIONINE 0.000149211 1 MET ZINC ION 6.5409e-05 1 ZN FE2/S2 (INORGANIC) CLUSTER 0.00017581999999999998 2 FES ADENOSINE-5'-TRIPHOSPHATE 0.000507181 1 ATP GUANOSINE-5'-DIPHOSPHATE 0.000443201 1 GDP water 1.8015e-05 3 HOH singleParticle particle 7.5 20.0 C8H18N2O4S HEPES 100.0 KCl potassium chloride 20.0 MgCl2 magnesium chloride 1.0 HSCH2CH(OH)CH(OH)CH2SH DTT Quantifoil R2/2 COPPER CARBON HOLEY CARBON CONTINUOUS GLOW DISCHARGE ETHANE-PROPANE 100 277.15 FEI VITROBOT MARK IV

Affinity-purified 55S mitoribosome. Refinement focused on 28S small subunit.

FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 100.0 2.7 0.6 3.0 81000.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN 20 GATAN K3 (6k x 4k) 2 43882 60.0 1

Micrographs were motion corrected and CTF parameters were estimated using Cryosparc.

5423665

Particles were picked with blob picker in Cryosparc.

cryoSPARC 4 PHASE FLIPPING AND AMPLITUDE CORRECTION EMD-2914

low-pass filtered to 40A

3.0 FSC 0.143 CUT-OFF cryoSPARC 4 41288 MAXIMUM LIKELIHOOD cryoSPARC 4

Homogeneous refinement (Cryosparc) of all particles with EMD-2914 (low-pass filtered to 40A) as initial reference

MAXIMUM LIKELIHOOD cryoSPARC 4 7QI4 PDB experimental model

High-res mammalian mitoribosome

UniProt AF-O75570-F1 AlphaFold in silico model

human mtRF1 model prediction

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