Yeast mitochondrial small subunit assembly intermediate (State 1)

2026-08-12 REL RCSB INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY EXPERIMENTAL_SUMMARY em_admin _em_admin.last_update REFINEMENT_DESCRIPTION chem_comp_atom chem_comp_bond em_3d_fitting_list _em_3d_fitting_list.accession_code _em_3d_fitting_list.initial_refinement_model_id _em_3d_fitting_list.source_name _em_3d_fitting_list.type 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 RCSB RCSB 2022-06-08 2022-12-21 2022-12-21 2026-08-12 Other private National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) 5T32GM136640-02 United States Yeast mitochondrial small subunit assembly intermediate (State 1) Burnside C Harper N Klinge S Ribonucleoprotein complex Mitochondria Biogenesis, RIBOSOME Harper NJ Burnside C Klinge S Principles of mitoribosomal small subunit assembly in eukaryotes. Nature UK 614 175 181 2023 36482135 doi:10.1038/s41586-022-05621-0 1476-4687 0006 NATUAS 8d8j FULLOVERLAP EMDB EMD-27249 associated EM volume

Yeast mitochondrial small subunit assembly intermediate (State 3) Yeast mitochondrial small subunit assembly intermediate (State 3) 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 Saccharomyces cerevisiae 1.26 Probable S-adenosyl-L-methionine-dependent RNA methyltransferase RSM22, mitochondrial Saccharomyces cerevisiae 0.07230832799999999 1 LEVO MMKRCFSILPQNVRFSSKFTSLNLPKLDLADFIDSNKRGINVLPSYRDETASTTQATNSKELRLLSKTLQGQSYRDQLEL NPDVSKAINNNIMAVHIPNNLRRVATNYYKEIQEPNSLHRPCRTKMEVDAHIASIFLQNYGSIFQSLKELQKRVGPDNFK PQRILDVGYGPATGIVALNDILGPNYRPDLKDAVILGNAEMQERAKIILSRQLNEVVDTVEENVSTEKEQETDRRNKNFQ EDEHIGEVMTKKINIMTNLRSSIPASKEYDLIILTHQLLHDGNQFPIQVDENIEHYLNILAPGGHIVIIERGNPMGFEII ARARQITLRPENFPDEFGKIPRPWSRGVTVRGKKDAELGNISSNYFLKVIAPCPHQRKCPLQVGNPNFYTHKEGKDLKFC NFQKSIKRPKFSIELKKGKLLATSWDGSQGNASRLKGTGRRNGRDYEILNYSYLIFERSHKDENTLKEIKKLRNENVNGK YDIGSLGDDTQNSWPRIINDPVKRKGHVMMDLCAPSGELEKWTVSRSFSKQIYHDARKSKKGDLWASAAKTQIKGLGDLN VKKFHKLEKERIKQLKKEERQKARKAMESYNELEDSLQFDDHQFSNFEVMKKLSTFHGNDFLQHVNRK P36056 2.1.1.- 37S ribosomal protein MRP13, mitochondrial Saccharomyces cerevisiae ATCC 204508 / S288c 0.039045031 1 LEVO MGTITVVINEGPILLIRALHRATTNKKMFRSTVWRRFASTGEIAKAKLDEFLIYHKTDAKLKPFIYRPKNAQILLTKDIR DPKTREPLQPRPPVKPLSKQTLNDFIYSVEPNSTELLDWFKEWTGTSIRKRAIWTYISPIHVQKMLTASFFKIGKYAHMV GLLYGIEHKFLKAQNPSVFDIEHFFNTNIMCALHRNRLKDYKDAEIAQRKLQVAWKKVLNRKNNTGLANILVATLGRQIG FTPELTGLQPVDISLPDIPNSSSGAELKDLLSKYEGIYLIARTLLDIDQHNAQYLELQEFIRQYQNALSESSDPYDTHLK ALGLLETPPPQESTEKEEK P12686 Mitochondrial group I intron splicing factor CCM1 Saccharomyces cerevisiae 0.101568547 1 LEVO MYMARCGPKNNVLCFPFQLSFLFSKRLINKRFKYTLQTEDEKNMMGSLSKNKIITPEDVEFKLAQLREFSNTLKERIHNT KSVNSDGHQSNSIAPISEDSRNVNVTKTSSVPNEEKSKNLSDLIHSSFLEKMDHLVPKVIRERVADDDILAKNLFDRSHS NWAPVIDRLYVSEKRFMDIDSREFSVWLNGTVKYLPFHSILHLDEMLLEQINGDVVKFNTHMYECIFNNLGNLKPTNFNQ DGTNDKVILKMKELLERYDKALKITEERINKKEGFPSKVPKMTQAILNNCLKYSTKCSSFHDMDYFITKFRDDYGITPNK QNLTTVIQFYSRKEMTKQAWNTFDTMKFLSTKHFPDICTYNTMLRICEKERNFPKALDLFQEIQDHNIKPTTNTYIMMAR VLASSSSNAVVSEGKSDSLRLLGWKYLHELEDKNLYRHKKDDLNLFLAMMALAAFDGDIELSRALYYLFIAKKYKTLCAN WKGNILVDQDTIWKSTLMPEMLNYLMLAYARFDPRNLPVLSGYEKGIELRRKFLREFDSSMRLDDTDKLVKFKLPFLPIS DLNSEAQVLAESNAIWSFNMENGGTRNTLTSSNEAALEDIKKYRQLLDSFAQEAEDFNEFKFKVMYEVTKMQRESINVNV FNKISLHTYLSIPINLKQQKEFLRRLTFFTFQQHEFEAVIKRLYEGYRNIPSSHTRDQNSISTEAISVSKPETTEDLNLI MHDIWYITCLRHKIMMDTTLYELVMKAAIEFQNEDLAKKVWNDRGKFRTTVPFLKMDQRIRIAKDQKFAHLMVEFFTKQG KYSDAIAIILSSKNRFNWTYSMVRNLHKALEEIEDRNSVEILLDVVNKKSHAKALKWEEQELNM A0A8H4FBQ6 37S ribosomal protein S28, mitochondrial Saccharomyces cerevisiae ATCC 204508 / S288c 0.033116383 1 LEVO MSIVGRNAILNLRISLCPLFMGKRSFVSSPVSNSAKAVKFLKAQRRKQKNEAKQATLKASTDKVDPVLGRADTPFITRIM AELKEPLVLSKGYNIEEVDKFLAAIESAKRERAELSGLNTEVVGIEDIEKLEDRREAILRILSMRNSENKNAIKMAVELA RKEFERFPGDTGSSEVQAACMTVRIQNMANHIKEHRKDFANTRNLRILVQQRQAILRYLKRDNPEKYYWTIQKLGLNDAA ITDEFNMDRRYMQDYEFFGDKILIRDSKKVANQKRKEIRKQKRATF P21771 37S ribosomal protein S16, mitochondrial Saccharomyces cerevisiae ATCC 204508 / S288c 0.013663011 1 LEVO MTCGLVRIRLARFGRKNSPVYNIVVANSRKARDAKPIEVLGTYVPVPSPVTKRELKRGVVPIKDVKLDFDRTKYWIGVGA QPSETVTKLLRKAGILNDAWATSKNSNVNRKVVFERMETLE Q02608 37S ribosomal protein S17, mitochondrial Saccharomyces cerevisiae ATCC 204508 / S288c 0.027683986 1 LEVO MARQNFLGLVVSQGKMQKTVKVRVETKVFNKKINKELFHRRDYLVHDEGEISREGDLVRIEATRPLSKRKFFAIAEIIRN KGQQFALYESEAQLSVAKEEAQKAKEFLDKRSVRENKLNEKTTLLRDIRTIQDALSSGSTPKELLEIKQRYGIQDFSQET VRQLLQLDISGLEVNLEKQRSLIDRIQTRLSELLSNDLKCDQFLKDHGVEDPLTLKKNIKKNLLRKHVMMDMQQPSQ Q03246 37S ribosomal protein RSM18, mitochondrial Saccharomyces cerevisiae ATCC 204508 / S288c 0.01586649 1 LEVO MQPIIKGAVSSTFKRALYNFGIKEKKSVNIEMGRTQQTKKIDQSLSKKLPKGTIYDPFDFSMGRIHLDRKYQANKNSNRN DIMKSGANPLEFYARPRILSRYVTSTGRIQHRDITGLSAKNQRRLSKAIRRCQAIGLM P40033 37S ribosomal protein PET123, mitochondrial Saccharomyces cerevisiae ATCC 204508 / S288c 0.036059281 1 LEVO MGKGAAKYGFKSGVFPTTRSILKSPTTKQTDIINKVKSPKPKGVLGIGYAKGVKHPKGSHRLSPKVNFIDVDNLIAKTVA EPQSIKSSNGSAQKVRLQKAELRRKFLIEAFRKEEARLLHKHEYLQKRTKELEKAKELELEKLNKEKSSDLTIMTLDKMM SQPLLRNRSPEESELLKLKRNYNRSLLNFQAHKKKLNELLNLYHVANEFIVTESQLLKKIDKVFNDETEEFTDAYDVTSN FTQFGNRKLLLSGNTTLQTQINNAIMGSLSNEKFFDISLVDSYLNKDLKNISNKIDSKLNPTSNGAGNNGNNNNTTNL P17558 Protein FYV4, mitochondrial Saccharomyces cerevisiae ATCC 204508 / S288c 0.015321683999999999 1 LEVO MIPSRISHKFPLFLRSSLAAPKAAYRFSSTIPKPSDQVPDVDAFLNKIGRNCNELKDTFENNWNNLFQWDSKILKEKGVN IQQRKYILKQVHNYRNNRPIHEIKLGKKSFFGGERKRKAFTAKWKAENKQ P38783 37S ribosomal protein NAM9, mitochondrial Saccharomyces cerevisiae ATCC 204508 / S288c 0.056450949 1 LEVO MPRKANLLKSLARGRVRTSFNKYNLFNLYKKGGVDLKSKSLYQQKWTAKQETRAYHGEHLTEKRWQTVFKPKLDSVAQLD ASLRGGEIKETPFLLQTFAVLEKRLDFALFRAMFASSVRQARQFILHGNVRVNGVKIKHPSYTLKPGDMFSVKPDKVLEA LGAKKPSFQEALKIDKTQIVLWNKYVKEAKTEPKEVWEKKLENFEKMSDSNPKKLQFQEFLRQYNKNLESQQYNALKGCT QEGILRKLLNVEKEIGKSNNEPLSIDELKQGLPEIQDSQLLESLNNAYQEFFKSGEIRREIISKCQPDELISLATEMMNP NETTKKELSDGAKSALRSGKRIIAESVKLWTKNITDHFKTRMSDISDGSLTFDPKWAKNLKYHDPIKLSELEGDEPKARK LINLPWQKNYVYGRQDPKKPFFTPWKPRPFLSPFAILPHHLEISFKTCHAVYLRDPVARPGQSEVISPFDVPVHERAYMY YLRNGK P27929 37S ribosomal protein S5, mitochondrial Saccharomyces cerevisiae ATCC 204508 / S288c 0.034941101999999995 1 LEVO MFKRQLSTSVRYLQHYDESLLSRYYPESLLKSIKLAQQTIPEDTKFRVSRNVEFAPPYLDDFTKIHPFWDYKPGMPHLHA QEENNNFSIFRWDQVQQPLPGEGNILPPGVSLPNDGGRKSKSADVAAGLHKQTGVDPDYITRKLTMKPLVMKRVSNQTGK GKIASFYALVVVGDKNGMVGLGEGKSREEMSKAIFKAHWDAVRNLKEIPRYENRTIYGDIDFRYHGVKLHLRSAKPGFGL RVNHVIFEICECAGIKDLSGKVYKSRNDMNIAKGTIEAFTKAQKTLDEVALGRGKKLVDVRKVYYSS P33759 37S ribosomal protein MRP17, mitochondrial Saccharomyces cerevisiae ATCC 204508 / S288c 0.015046701999999999 1 LEVO MLYELIGLVRITNSNAPKLEAKELSSTIGKLIIQNRGVVRDIVPMGIRYLPKIMKKDQEKHFRAYHFLMLFDSSAAVQSE ILRTLKKDPRVIRSSIVKVDLDKQLDRASSLHRSLGKKSILELVNEDYQSI P28778 37S ribosomal protein S35, mitochondrial Saccharomyces cerevisiae ATCC 204508 / S288c 0.039638172 1 LEVO MSYGLTGTSSKLRGTSSIFSWTQVRHFSRRRIAYPFYPFKKLGRQHPKKHDTNLKTAMRQFLGPKNYKGEYVMNKYFTVP TNHVPNYIKPDLERGQSLEHPVTKKPLQLRYDGTLGPPPVENKRLQNIFKDRLLQPFPSNPHCKTNYVLSPQLKQSIFEE ITVEGLSAQQVSQKYGLKIPRVEAIVKLVSVENSWNRRNRVSSDLKTMDETLYRMFPVFDSDASFKRENLSEIPVPQKTL ASRFLTIAESEPFGPVDAAHVLELEPAVETLRNLSTVGEHSSGHQQSTNKNTKVIYGELVEGERSQYKFTNAKVGKVGYR YGSGNRDNKKDRRIGFNKLGQMVYI P53292 37S ribosomal protein S8, mitochondrial Saccharomyces cerevisiae ATCC 204508 / S288c 0.017496601999999997 1 LEVO MSLVKLANTCAHLQNCSKVRVALTSIPYTKLQLQFAYNLYQQGFLSSLQKGSTMGPDKDFVEVTPDNISTRRLWVGLKYR DNKPVLSSCKLISKPNSRIHLPMEDMKKLCSGVTIRNIKPLQPGELILVRAHNNIMDINEAISKKLDGEVLCRVK Q03799 15S ribosomal RNA Saccharomyces cerevisiae 0.549234062 1 UUUUAUAUAAUAAUAAUAAUAUAUAUAUAUAUAUAUUAUUAUAUUAGUUAUAUAAUAAGGAAAAGUAAAAAAUUUAUAAG AAUAUGAUGUUGGUUCAGAUUAAGCGCUAAAUAAGGACAUGACACAUGCGAAUCAUACGUUUAUUAUUGAUAAGAUAAUA AAUAUGUGGUGUAAACGUGAGUAAUUUUAUUAGGAAUUAAUGAACUAUAGAAUAAGCUAAAUACUUAAUAUAUUAUUAUA UAAAAAUAAUUUAUAUAAUAAAAAGGAUAUAUAUAUAAUAUAUAUUUAUCUAUAGUCAAGCCAAUAAUGGUUUAGGUAGU AGGUUUAUUAAGAGUUAAACCUAGCCAACGAUCCAUAAUCGAUAAUGAAAGUUAGAACGAUCACGUUGACUCUGAAAUAU AGUCAAUAUCUAUAAGAUACAGCAGUGAGGAAUAUUGGACAAUGAUCGAAAGAUUGAUCCAGUUACUUAUUAGGAUGAUA UAUAAAAAUAUUUUAUUUUAUUUAUAAAUAUUAAAUAUUUAUAAUAAUAAUAAUAAUAAUAUAUAUAUAUAAAUUGAUUA AAAAUAAAAUCCAUAAAUAAUUAAAAUAAUGAUAUUAAUUACCAUAUAUAUUUUUAUAUGGAUAUAUAUAUUAAUAAUAA UAUUAAUUUUAUUAUUAUUAAUAAUAUAUUUUAAUAGUCCUGACUAAUAUUUGUGCCAGCAGUCGCGGUAACACAAAGAG GGCGAGCGUUAAUCAUAAUGGUUUAAAGGAUCCGUAGAAUGAAUUAUAUAUUAUAAUUUAGAGUUAAUAAAAUAUAAUUA AAGAAUUAUAAUAGUAAAGAUGAAAUAAUAAUAAUAAUUAUAAGACUAAUAUAUGUGAAAAUAUUAAUUAAAUAUUAACU GACAUUGAGGGAUUAAAACUAGAGUAGCGAAACGGAUUCGAUACCCGUGUAGUUCUAGUAGUAAACUAUGAAUACAAUUA UUUAUAAUAUAUAUUAUAUAUAAAUAAUAAAUGAAAAUGAAAGUAUUCCACCUGAAGAGUACGUUAGCAAUAAUGAAACU CAAAACAAUAGACGGUUACAGACUUAAGCAGUGGAGCAUGUUAUUUAAUUCGAUAAUCCACGACUAACCUUACCAUAUUU UGAAUAUUAUAAUAAUUAUUAUAAUUAUUAUAUUACAGGCGUUACAUUGUUGUCUUUAGUUCGUGCUGCAAAGUUUUAGA UUAAGUUCAUAAACGAACAAAACUCCAUAUAUAUAAUUUUAAUUAUAUAUAAUUUUAUAUUAUUUAUUAAUAUAAAGAAA GGAAUUAAGACAAAUCAUAAUGAUCCUUAUAAUAUGGGUAAUAGACGUGCUAUAAUAAAAUGAUAAUAAAAUUAUAUAAA AUAUAUUUAAUUAUAUUUAAUUAAUAAUAUAAAACAUUUUAAUUUUUAAUAUAUUUUUUUAUUAUAUAUUAAUAUGAAUU AUAAUCUGAAAUUCGAUUAUAUGAAAAAAGAAUUGCUAGUAAUACGUAAAUUAGUAUGUUACGGUGAAUAUUCUAACUGU UUCGCACUAAUCACUCAUCACGCGUUGAAACAUAUUAUUAUCUUAUUAUUUAUAUAAUAUUUUUUAAUAAAUAUUAAUAA UUAUUAAUUUAUAUUUAUUUAUAUCAGAAAUAAUAUGAAUUAAUGCGAAGUUGAAAUACAGUUACCGUAGGGGAACCUGC GGUGGGCUUAUAAAUAUCUUAAAUAUUCUUACA CP059539.1 uS12m Saccharomyces cerevisiae 0.01694874 1 LEVO MLSRFMSNTWCTPLRQAQRLFSSTTTMQATLNQIKRGSGPPRRKKISTAPQLDQCPQRKGVVLRVMVLKPKKPNSAQRKA CRVRLTNGNVVSAYIPGEGHDAQEHSIVYVRGGRCQDLPGVKYHVIRGAGDLSGVVNRISSRSKYGAKKPSKS A0A6A5Q5F6 IRON/SULFUR CLUSTER 0.00035163999999999996 1 SF4 MAGNESIUM ION 2.4305e-05 29 MG singleParticle particle 7.5 ETHANE FEI VITROBOT MARK IV FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 1.0 2.5 64000.0 FEI TITAN KRIOS AUTOGRID HOLDER GATAN K3 (6k x 4k) 1 14111 61.73 1 3286640 Gctf 1.18 PHASE FLIPPING AND AMPLITUDE CORRECTION

Ab Initio (Cryosparc)

3.8 FSC 0.143 CUT-OFF PHENIX 1.19 19720 MAXIMUM LIKELIHOOD RELION 3.1.1 MAXIMUM LIKELIHOOD RELION 3.1.1 emd_27249.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 400 400 400 0 0 0 400 400 400 422.80002 422.80002 422.80002 90.0 90.0 90.0 X Y Z -10.443467 27.062866 0.027765708 1.0685806 1.057 1.057 1.057 4.3 AUTHOR ::::EMDATABANK.org::::EMD-27249:::: Full map 5MRC PDB experimental model REAL emd_27249_msk_1.map emd_27249_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 400 400 400 0 0 0 400 400 400 422.80002 422.80002 422.80002 90.0 90.0 90.0 X Y Z -7.958602 17.001298999999999 0.027731253 1.0031481 1.057 1.057 1.057 AUTHOR ::::EMDATABANK.org::::EMD-27249:::: Half map 1 emd_27249_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 400 400 400 0 0 0 400 400 400 422.80002 422.80002 422.80002 90.0 90.0 90.0 X Y Z -7.9956346 16.316382999999998 0.031038208 1.0207887 1.057 1.057 1.057 AUTHOR ::::EMDATABANK.org::::EMD-27249::::