9HCD
Mouse mitoribosome large subunit assembly intermediate (with ul16m) bound to mrm3-dimer, ddx28 and the malsu-l0r8f8-mt-acp complex, state a2 (samc knock-out)
PDB DOI: 10.2210/pdb9hcd/pdb
Classification: RIBOSOME Organism(s): Enterobacter Aerogenes
Deposited: 2024-11-08 Deposition Author(s): Amunts, A. , Freyer, C. , Rorbach, J. , Singh, V. , Wredenberg, A.
Experimental Data Snapshot
Method: ELECTRON MICROSCOPY Resolution: 4.63 Å
Mouse mitoribosome large subunit assembly intermediate (with ul16m) bound to mrm3-dimer, ddx28 and the malsu-l0r8f8-mt-acp complex, state a2 (samc knock-out)
Amunts, A. , Freyer, C. , Rorbach, J. , Singh, V. , Wredenberg, A.
Primary Citation of Related Structures: 9HCD
| Proteins | ||||
|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Sequence |
| Large ribosomal subunit protein mL42 | A | 142 | Enterobacter Aerogenes | MAAAVKWAISNRTIWKHLLPIQNGALSSACHKSTYSSLPDDYNCQVDLALTADGRTIVCYHPSVDIPYEHTKPIPQPDLLHNNEETHEQILKAKLEVRKSKQLEQGPMIEQLSKVFYTTKHRWYPHGQYHNRRKKLNPPRDR |
| Large ribosomal subunit protein mL54 | L | 135 | Enterobacter Aerogenes | MAAAHLLRASRVWARWHPRALPVLRRPGGFSIREYAKKPVGKGGKGGVAAEALKDPEVCTDPTQLTTHAMGVNIYKEGQDVALKADSEYPTWLFQVNLGPPKKLEELEPESREYWRLLRKQNIWRHNRLSKNKKL |
| Large ribosomal subunit protein uL15m | M | 295 | Enterobacter Aerogenes | MAGTARGCGTSLDLLRSLPRVSLANLKPSPNSRKRERRPRDRRRGRKCGRGHKGERQRGTRPRLGFEGGQTPFYIRIPKYGFNEGHSFRHQYQPLSLRRLQYLIDLGRVDPTQPIDLTQLVNGRGVTIQPLKRDYGVQLVEEGADTFQAKINIEVQLASELAIAAIEKNGGVVTTAFYDPRSLEILCKPIPFFLRGQPIPKRMLPPESLVPYYTDAKNRGYLADPAKFPEARLELAMKFGYVLPDITKDELFRMLSARKDPRQIFFGLAPGWVVNMADKKILKPTDENLLKYYSS |
| Large ribosomal subunit protein uL16m | N | 251 | Enterobacter Aerogenes | MWRLLTRVPAPLLRMHFSDSWAALPTSAGLKTLLPVPTFENVSIPERSKLKFVERVPLVPKVRREPKNLKDIRGPSTEATDFTEGNFAILALGGGYLHWGHFEMMRLTINRFMDPKNMFAIWRVPAPFKPITRKGVGQRMGGGKGAIDHYVTPVKTGCLVVEMGGRCEFEEVKGILNQVAHKLPFPAKAVSRKTLERMHQNQRERELNNQNPWTFEHIATANMFGIRKFLSPYDLTQKGRYWGKFYMPKRV |
| Large ribosomal subunit protein mL63 | O | 102 | Enterobacter Aerogenes | MFLTAVLLRGRIPGRQWIGKHRRPRTVSFQAKESMIRRLEVEAENHYWLSMPYMTAEQECGHAAERRAQAFEAIKAAATSKFPKHRYIADQLDHLNISKKWS |
| Large ribosomal subunit protein mL62 | P | 206 | Enterobacter Aerogenes | MATAWGLRWGLSRTGTLLLAPPARCARRALHRQVDGTTFQSIYSLDKLYPESKGADTAWKVPEHAKQASSYIPLDRLSISYCRSSGPGGQNVNKVNSKAEVRFHLASADWIEEPVRQKIALTHKNKINKAGELVLTSESSRYQFRNLAECLQKIRDMIAEASQVPKEPSKEDARLQRLRIEKMNRERLRQKRLNSALKTSRRMTMD |
| Large ribosomal subunit protein mL64 | Q | 222 | Enterobacter Aerogenes | MAALAMRSGYLLRLSVALGPRSRSYRAPPPPRRRPGPHSPDPENLLTPRWQLTPRYVAKQFGRHGAISGVPPASLWPTPEQLRELEAEEQEWYPSLATMQESLRLQQQALEARRQAREQRIAECMAKMPQMIENWRKQKRERWEKIQADKERRARLQAEAQERLGYHVDPRSARFQELLQDLDKQQRKRLKEERQRQKKEARIAAMASAEAQDSAVSGEPSS |
| Large ribosomal subunit protein mL66 | R | 196 | Enterobacter Aerogenes | MAALRRLVSGCGRQLQAFLAGPAATGWLWLPARGLREVVKIQEGKTTVIEGRITETPKATPDPPNPSGQCPICRWNLKHKYTYEDVLLLSQFIRPYGGMLPRRVTGLCREEHRKIEECVKMAHRAGLLPNHRPQLPEGCLPKDKPKLNRYLTRWAPKSVKPIYKKGHRWNKVGMAVGSPLLKDNVCYSRRPLKMMH |
| Large ribosomal subunit protein mL65 | S | 442 | Enterobacter Aerogenes | MAAARYWKLVPRGRGLSQNAAAKASATAPEVRDLEVVATPVARYPPIVASMTADSKAARQRRVQRWQATVHAAPSVDEKIRILTKMQFKKYVVHPQISALNADRWYQSFTKTVFVSGLPPAPALSPPPPSLDLAALRAAVCDCILQEQVYVRRRRPRSLFDRRQALASSILDQVVRTLVNLLAPLNPVLSTAALDCKRSVDFYWLRGEERIPAGHRKGHIDALRYQINDKPHNQIRISKQLPEFVPLDYSIPTEIPVMKCKPDKLPLFRRQYENSIFTGSKTADPCCYGHTQFHLIPDRLKRERLIRQNQAEQVEAVFRANAIASLFAWTGAQAMYQGFWSEADVTRPFVSQAVITDGKYFSFFCYQLNTLALTVQADQNNPRKNLCWGSQSQPLYETVEDNDVKGFDDGTLLQIVHFLLNKPREDGAQLLASQEKELDLGP |
| Large ribosomal subunit protein uL22m | T | 206 | Enterobacter Aerogenes | MAAALLRELGALRVPNLRIWATQTLRVLPPSCIHTSASLDISRKWEKKNKIVYPPQLPGEPRRPAEIYHCRRQIKYSKDKMWYLAKMIRGMSIDQALAQLEFNDKKGAQIIKEVLLEAQDMAVRDHNVEFRSNLHIAESTSGRGQCLKRIRYHGRGRFGIMEKVYCHYFVKLVEGPPPPPEVPKTAVDHAKDYIQQLRSRTIIHTL |
| Mitochondrial assembly of ribosomal large subunit protein 1 | U | 228 | Enterobacter Aerogenes | MGPGWSPARRLWPLLWRRAVFQRAGPAMASVPWLPRLAERWLPARPATCLTPSLTRGLHHGPQPEERTAGDARLQPGPADHIGAKFDIDMLVSLLRQENARDICVIQVPPEMRYTDYFVIGSGTSTRHLHAMVHYLVKMYKHLKCRSDPYVKIEGKDADDWLCVDFGSMVIHLMLPETRETYELEKLWTLRSFDDQLAQIAAETLPEDFILGLEDDTSSLTPVEFKCK |
| Large ribosomal subunit protein mL43 | B | 159 | Enterobacter Aerogenes | MTGRGTSSRFLTSVLHNGLGRYVQQLQRLSLSLSRDAPSSRGAREFVEREVTDFARRNPGVVVYVNPRPCAMPRIVAEYLNGAVREENVNSKSVEEIKSLVQKLADQSGLDVIRIRKPFHTDNPSIQGQWHPFTNKRTALHGLRPRELRDSAPASMQAQ |
| Predicted gene, 55359 | V | 70 | Enterobacter Aerogenes | MAPWSREAVLCLYRALLRQGRELRYTDRDFYFASIRREFRKNQKLENLEAREKQLEKGLVFLHSKLGGLI |
| rRNA methyltransferase 3, mitochondrial | X | 418 | Enterobacter Aerogenes | MAAPAKGMWCSLGSLLRVVQTRDLNARRWVRALRRSPVRVLSPSGQVEERKRAPDQQPRKAVPKASSQGQRQKQPLETSPSQTPHTWEEAGLRYDKAFPGDRRLSSVMTIVKSRPFREKQGKILLEGRRLIADALKAGAVPKAFFFSRLEYVKELPVDKLKDVSLIKVKFEDIKDWSDLVTPQGIMGIFAKPDPVKMTYPETPLHHTLPLVLICDNLRDPGNLGTILRSAAGAGCSKVLLTKGCVDAWEPKVLRAGMGAHFQVPIVNNVEWETVPNHLPPDTRVYVADNCGHYAQVQMSDKTGDRDWACDRRFLKFHKYEEDLDTKTRKDWLPKLEVQSYDLDWTGAPAAVVIGGETHGVSLESLQLAESTGGKRLLIPVVPGVDSLNSAMAASILLFEGKRQLRIKVEDLSRDRSYH |
| rRNA methyltransferase 3, mitochondrial | Y | 418 | Enterobacter Aerogenes | MAAPAKGMWCSLGSLLRVVQTRDLNARRWVRALRRSPVRVLSPSGQVEERKRAPDQQPRKAVPKASSQGQRQKQPLETSPSQTPHTWEEAGLRYDKAFPGDRRLSSVMTIVKSRPFREKQGKILLEGRRLIADALKAGAVPKAFFFSRLEYVKELPVDKLKDVSLIKVKFEDIKDWSDLVTPQGIMGIFAKPDPVKMTYPETPLHHTLPLVLICDNLRDPGNLGTILRSAAGAGCSKVLLTKGCVDAWEPKVLRAGMGAHFQVPIVNNVEWETVPNHLPPDTRVYVADNCGHYAQVQMSDKTGDRDWACDRRFLKFHKYEEDLDTKTRKDWLPKLEVQSYDLDWTGAPAAVVIGGETHGVSLESLQLAESTGGKRLLIPVVPGVDSLNSAMAASILLFEGKRQLRIKVEDLSRDRSYH |
| Probable ATP-dependent RNA helicase DDX28 | Z | 540 | Enterobacter Aerogenes | MALAGPSRLLALAVRLLLEPRRNLVVRGSDQSLPVVRVPRALQRRQEQRQSGRGSLQRPVLVRPGPLLVSARRPELNQPARLTLGRWERAPLASRGWKHRRSRQDHFSIERVQQEAPALRNLSSRGSFVDLGLEPRVLLALQEAVPEVVQPTSVQSKTIPPLLRGRHLLCAAETGSGKTLSYLLPLFQRLLRGSDLDSRSFTAPRGLVLVPSRELAEQVQAVAQSLGGYLGLQVIELGGGLGMSRLKLQLYRRPAADVLVATPGALWKALKSQLISLQHLNFIVLDEVDTLLDESFLELVDYILEKSPIAESPAELEDPFNPKAQLVLVGATFPEGLNQLLSKVTSPDSLTTITSSKLHCLMPHVRQTFMRLKGADKVTELVQILKQQDKASKTEPSGTVLVFCNSASTVNWLGYILDDHKIQHLRLQGQMPASMRAGIFQSFQKGSQNILVCTDIASRGLDSVHVEVVINYDFPPTLQDYIHRAGRVGRVGSEVPGSVISFVTHPWDVSLVQKIELAARRRRSLPGLASSVGDPLPQKA |
| Large ribosomal subunit protein bL32m | 0 | 187 | Enterobacter Aerogenes | MAPSLLLLSLPWPVRPGPLQRCWELLQRQLQQSWSRFVSPPWAPALAVQRPSILTELAHDTCENKENSSFLDSIFWMAAPKNRRTIEVNRCRRRNPQKLIKIKNNIDICPECGHLKQKHVLCGYCYEKVRQETTKIRQQIGAQEGGPFRAPSVETMVLYTGEKPSEKDQGKRIVERNIKRPSWFTQN |
| Large ribosomal subunit protein mL37 | 5 | 423 | Enterobacter Aerogenes | MALASGPALRALAGSGRLGLGGYGTPKRGAYEWGVRSTRKPEPRPLDRVYEIPGLEPITYEGKKHFVPWLARPIFPPWERGWNDPRFHRAAPIHEQTLYKEEPCYIFHQRCRLLEGMKQALWLTKTKLIEGLPKKVLSLVDDPANHIENQEQRVLDIISHARLWHSTEDIPKRETYCPLIVDSLIQLCKSQILKHPSLARRTSAQNCTLATTWNRESLLLQVRGTSSTILSAKDPLPVIASREEVEATRSHVLETFYPISPTIDLQECHVYEVKDDTGFQEGYPYPHPHTLYFLEKANLRPQRFLPEQLRAKMLLFAFANALAQARLLYGNTAKVLEQPIVVQSVGTDGRVFQFLVLQLNTTDLASSEGVKNLVWTDSDQLLYRHFWCRPVIKKKVVVEPVGPVDFQPETFRKFLALYLHGVV |
| Large ribosomal subunit protein mL38 | 6 | 380 | Enterobacter Aerogenes | MAAPWWRAAFFGIGRCRGFSTSAFLSRRTPPLGPMPNEDIDVSNLERLEKYRSFERYRRRAEQEARAPHWWRTYREHFVKETDPKDKIDIGLPPPRVSRTQKLLERKHFLRELRANVEEERAARLRTASIPLEAVRAEWERTCGPYHKQRLAEYYGLYRDLFHGATFVPWVPLHVAYAVGEEDLIPVYHGNEVTPTEASRAPEVTYEADKDSLWTLLFINLDGHLLEPDAEYVHWLLTNIPSNRVAEGQETCPYLPPFPARGSGFHRFAFLLFKQDKPINFSEDTRPSPCYQLAQRTFRTFDFYKRHQEAMTPAGLAFFQCRWDDSVTHTFHQLLDMREPVFEFVRPPPYHPKQKRFPHEQPLRYLDRYRDSHEPTYGIY |
| Large ribosomal subunit protein mL39 | 7 | 336 | Enterobacter Aerogenes | MATAVGRLVLRRPGAGGGARWRFIATSPAAELSPTELTEMRNDLFNREKSRQLSLTPRTEKIEVKHVGKTDPGTVFVMNKNISTPYSCAMHLSEWYCSKSILALVDGQPWDMYKPLTKSCEIKFLTFKDPDPKEVNKAYWRSCAMMLGCVIERAFKDDYVVSLVRAPEVPVIAGAFCYDVTLDKRLDEWMPTKENLRSFTKDAHALIYRDLPFETLDVDARVALEIFQHNKYKVDFIEEKASQNPERIVKLHRIGDFIDVSEGPLIPRTSVCFQYEVSAVHNLNPSQPNLIRRFQGLSLPTHLRAQFTIWDKLVERSRKMVTEDEVRQTENTESTQ |
| Large ribosomal subunit protein mL40 | 8 | 206 | Enterobacter Aerogenes | MATGVMLCAARALRPRSWIPGTCQAHVRHTHQRASLLAFWDLIPMRAEPLRKKKKVDPRKDQAAKDRLKKRIRKLEKASQELIPIEDFITPVRFLDKSRQRPQEEHSPEESERRALLLKRWALFKQQEHEMERDAIRSMLEAQQEALEELKLESAELYAEAIKRDTSLFPFEKEGPHYTPPISNYQAPEGRYNDITKVYTQVEFKR |
| Large ribosomal subunit protein mL41 | 9 | 135 | Enterobacter Aerogenes | MGFLTAVTQGLVRGADRMSKWTSKRGPRTFTKSRGAKKTGIYTSDRKFVQIKEMVPEFVVPDLTGFKLKPYVNYRAPAGIDTPLTAKALFQETVAPAIEKDFKEGTFDANNLEKYGFEPTQEGKLFQLYPKNFPR |
| Large ribosomal subunit protein mL45 | D | 306 | Enterobacter Aerogenes | MAAPVPRGLSSLYRTLGWWSRQPILVTQSTTVVQVKTKSRFRPPTPEPKYKTEKEFLEYARKAGLVIPQERLERPIHLACTAGIFDPYVPPEGDARMSSLSKEGLTQRTERLRKNAASQLAIRKIREFDANFKTKDFPEKAKDIFIEAHLCLNNSDHDRLHTLVTEHCFPDMVWDLKYKTVRWGFVESLEPAQVVHVRCSGLVNQSNMYGQVTVRLHTRQTLAIYDRFGRLMYGQEDVPKDVLEYVVFERHLMNPYGSWRMHAKIVPAWAPPKQPILKTLMIPGPQLKPWEEYEETQGEAQKPQLA |
| Large ribosomal subunit protein mL44 | C | 308 | Enterobacter Aerogenes | PPVRGVKKGFRAAFRFQKELERWRLLRCPPPPVRRSEKPNWDYHAEVQAFGSRLQETFSLDLLKTAFINSCYIKSEEAKRQSLGIEKEAALLNLKDNQELFEQGLSFSHRCLTQFLEDEFPDLPAEGTESLVSFLTGEAVVCHVARNLAVEQLTLSAEFPVPLPVLRQTFFAVIGALLQSSGPERAALFIRDFLITQMTGKELFEMWTVVNPMGLLVEELKKRNISAPESRLTRQSGSTTALPLYFVGLYCDRKLIAEGPGETVLVAEEEAARVALRKLYGFTENRRPWDYSKPKESPKRAEQTSVAS |
| Large ribosomal subunit protein uL3m | E | 348 | Enterobacter Aerogenes | MPGWRLLAQAGARVLGCGARGLGADPGLERRKNILFFVRNLHSKSSTWWDEHLSEENLSFVKQLVSDENKTQLTSKLNPLKDEPWPLHPWEPGSFRVGLIALKLGMMPLWTKDGQKHAVTLLQVQDCHVLKYTPKEDHNGKIAALTVGGKTVSRFYKPDSRLEFYRDLGLPPKQIHKIFHVTDNAVIKPGTPLYAAHFRPGQYVDVTAKTIGKGFQGVMKRWGFKGQPASHGQTKTHRRPGAISTGDIARVWPGTKMPGRMGNQNRTVYGLKVWRVNTKHNIIYVNGSVPGHKNCLVKIKDSTLPAYKDSCKNLPFPTYFPDGDEEELPEDLFDESVWQPSEPSITFA |
| Large ribosomal subunit protein uL4m | F | 294 | Enterobacter Aerogenes | MLRLFQAASRASLRLSGSRVIHSLAEGAERPAEISEPRDSAGLLDPVLRKCELRIPVHRRPVQAWVESLRGFEQERIGLAELHPDVFATAPRLDIVHQVAIWQRNFRRISYANTKTRAEVSGGGRKPWQQKGSGRARHGSIRSPLWRGGGVAHGPRGPTSYYYMLPMKVRALGLKVALTVKLMQDDLHIVDSLELPTADPQYLTELAQYRHWGSSVLLVDLTHEEMPKNVVAATSGLNSFNLIPAVGLNVYSMLKHQTLVLTLPSVAFLEDKLLWQDSRYTPLYPFRLPYSDFP |
| Large ribosomal subunit protein mL49 | G | 166 | Enterobacter Aerogenes | MAAAVLRAALQDWRSCLGRSYGRRKLSQTQGPPDNPGFVESVDEYQFVERLLPPTKIPEPPKHKHYPTPSGWQPPRDPLPSLPYFVRRSRMHNIPVYKEITHGNRQMTLIRKVEGDIWALQKDVEEFLSPLLGKTPITQVNEVTGTLRIKGYFDEQLKAWLLEKGF |
| Large ribosomal subunit protein bL9m | H | 268 | Enterobacter Aerogenes | MAASVAPGVRTLWWAGAAWLRQGGIRELFRPRIEGSTPGRDFSLSHYQSTVIVERWWKVPLAGEGRKPHLHRRHRVYKLVEDTKHRPKDNLELILTQSVDEIGVRGDLVSVKKSVGRNKLLSQGLAVYASPENRKLFEEEKSLRREGKLEKIQTKAGEATVKFLRSCHLEVGMKNNVKWELNPEIVARHFFKNLGVVVAPHALRLPEEPITRWGEYWCDVTTRGHQGIRNRTITRLKMEANMEADRKKILILCGFQQPQVAKTFTRLE |
| Large ribosomal subunit protein uL10m | I | 262 | Enterobacter Aerogenes | MAAAVAGILRGGLPPRAAWLPTLQTVRHGSKAVTRHWRVMHFQRQKLMAITEYIPPKPAINPRCLPPPPKPPKEESGLVRLLRQDIVAVFRDNRMIAVCQNVALSAEDKLLLRHQLRKHKIFIKVFPSQVLKPFLENSKYRNLLPLFVGHNLLLVSEEPKVKEMVRVLKSVPFLPLLGGCVDDTILSRQGLVDYAKLPSLDQLQGQLVGGLTHLMAQTRYLLQHQPVQLTSLLDQYVKEQNEGDCATSANEKLHPPDPAPDA |
| Large ribosomal subunit protein uL11m | J | 192 | Enterobacter Aerogenes | MSKLSRATRTLKKPEAGGVIRSIVRAGQAIPGPPLGPILGQRGVSINQFCKEFNEKTKDIKEGIPLPTKIFIKPDRTFELKIGQPTVSYFLKAAAGIEKGARHTGKEVAGLVSLKHVYEIACVKAKDDAFAMQDVPLSSVVRSIIGSARSLGIRVVKDLSAEELEAFQKERAVFLAAQKEADLAAQAEAAKK |
| Large ribosomal subunit protein uL13m | K | 178 | Enterobacter Aerogenes | MSSFSRAPQQWATFARMWYLLDGKMQPPGKLAVIASNKLQGLNKPVYHQLSDCGDHVVIINTRHIAFSGNKWEQKVYSSHTGYPGGFRQVTAAQLHRKDPVAIVKLAIYGMLPKNLHRRTMMQRLHLFPDEDIPEDILKNLVEELPQPRRVPKRLDEYTQEEIEAFPRVWTPPDDFRM |
| Acyl carrier protein, mitochondrial | W | 156 | Enterobacter Aerogenes | MASRVLCACVRRLPAAFAPLPRLPTLALARPLSTTLCPEGIRRRPGALQSALALAQVPGTVTHLCRQYSDAPPLTLDGIKDRVLYVLKLYDKIDPEKLSVNSHFMKDLGLDSLDQVEIIMAMEDEFGFEIPDIDAEKLMCPQEIVDYIADKKDVYE |
Experimental Data
Method: ELECTRON MICROSCOPY
Deposited Date: 2024-11-08 Deposition Author(s): Amunts, A. , Freyer, C. , Rorbach, J. , Singh, V. , Wredenberg, A.