8CBJ
Cryo-em structure of otu2-bound cytoplasmic pre-40s ribosome biogenesis complex
PDB DOI: 10.2210/pdb8cbj/pdb
Classification: RIBOSOME Organism(s): Saccharomyces Cerevisiae , Saccharomyces Cerevisiae W303
Deposited: 2023-01-25 Deposition Author(s): Becker, T. , Beckmann, R. , Berninghausen, O. , Buschauer, R. , Cheng, J. , Ikeuchi, K.
Experimental Data Snapshot
Method: ELECTRON MICROSCOPY Resolution: 3.8 Å
Cryo-em structure of otu2-bound cytoplasmic pre-40s ribosome biogenesis complex
Becker, T. , Beckmann, R. , Berninghausen, O. , Buschauer, R. , Cheng, J. , Ikeuchi, K.
Primary Citation of Related Structures: 8CBJ
| Proteins | ||||
|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Sequence |
| 40S ribosomal protein S1-A | B | 255 | Saccharomyces Cerevisiae , Saccharomyces Cerevisiae W303 | MAVGKNKRLSKGKKGQKKRVVDPFTRKEWFDIKAPSTFENRNVGKTLVNKSTGLKSASDALKGRVVEVCLADLQGSEDHSFRKIKLRVDEVQGKNLLTNFHGMDFTTDKLRSMVRKWQTLIEANVTVKTSDDYVLRIFAIAFTRKQANQVKRHSYAQSSHIRAIRKVISEILTKEVQGSTLAQLTSKLIPEVINKEIENATKDIFPLQNIHVRKVKLLKQPKFDVGALMALHGEGSGEEKGKKVTGFKDEVLETV |
| 40S ribosomal protein S11-A | L | 156 | Saccharomyces Cerevisiae , Saccharomyces Cerevisiae W303 | MSTELTVQSERAFQKQPHIFNNPKVKTSKRTKRWYKNAGLGFKTPKTAIEGSYIDKKCPFTGLVSIRGKILTGTVVSTKMHRTIVIRRAYLHYIPKYNRYEKRHKNVPVHVSPAFRVQVGDIVTVGQCRPISKTVRFNVVKVSAAAGKANKQFAKF |
| 20S-pre-rRNA D-site endonuclease NOB1 | A | 459 | Saccharomyces Cerevisiae , Saccharomyces Cerevisiae W303 | MTENQTAHVRALILDATPLITQSYTHYQNYAQSFYTTPTVFQEIKDAQARKNLEIWQSLGTLKLVHPSENSIAKVSTFAKLTGDYSVLSANDLHILALTYELEIKLNNGDWRLRKKPGDALDASKADVGTDGKQKLTEDNKKEEDSESVPKKKNKRRGGKKQKAKREAREAREAENANLELESKAEEHVEEAGSKEQICNDENIKESSDLNEVFEDADDDGDWITPENLTEAIIKDSGEDTTGSLGVEASEEDRHVALNRPENQVALATGDFAVQNVALQMNLNLMNFMSGLKIKRIRNYMLRCHACFKIFPLPKDGKPKHFCASCGGQGTLLRCAVSVDSRTGNVTPHLKSNFQWNNRGNRYSVASPLSKNSQKRYGKKGHVHSKPQENVILREDQKEYEKVIKQEEWTRRHNEKILNNWIGGGSADNYISPFAITGLKQHNVRIGKGRYVNSSKRRS |
| 40S ribosomal protein S28-A | C | 67 | Saccharomyces Cerevisiae , Saccharomyces Cerevisiae W303 | MDNKTPVTLAKVIKVLGRTGSRGGVTQVRVEFLEDTSRTIVRNVKGPVRENDILVLMESEREARRLR |
| RPS29A isoform 1 | D | 56 | Saccharomyces Cerevisiae , Saccharomyces Cerevisiae W303 | MAHENVWFSHPRRYGKGSRQCRVCSSHTGLIRKYGLNICRQCFREKANDIGFNKFR |
| 40S ribosomal protein S30-A | E | 63 | Saccharomyces Cerevisiae , Saccharomyces Cerevisiae W303 | MAKVHGSLARAGKVKSQTPKVEKTEKPKKPKGRAYKRLLYTRRFVNVTLVNGKRRMNPGPSVQ |
| 40S ribosomal protein S5 | F | 225 | Saccharomyces Cerevisiae , Saccharomyces Cerevisiae W303 | MSDTEAPVEVQEDFEVVEEFTPVVLATPIPEEVQQAQTEIKLFNKWSFEEVEVKDASLVDYVQVRQPIFVAHTAGRYANKRFRKAQCPIIERLTNSLMMNGRNNGKKLKAVRIIKHTLDIINVLTDQNPIQVVVDAITNTGPREDTTRVGGGGAARRQAVDVSPLRRVNQAIALLTIGAREAAFRNIKTIAETLAEELINAAKGSSTSYAIKKKDELERVAKSNR |
| Guanine nucleotide-binding protein subunit beta-like protein | G | 319 | Saccharomyces Cerevisiae , Saccharomyces Cerevisiae W303 | MASNEVLVLRGTLEGHNGWVTSLATSAGQPNLLLSASRDKTLISWKLTGDDQKFGVPVRSFKGHSHIVQDCTLTADGAYALSASWDKTLRLWDVATGETYQRFVGHKSDVMSVDIDKKASMIISGSRDKTIKVWTIKGQCLATLLGHNDWVSQVRVVPNEKADDDSVTIISAGNDKMVKAWNLNQFQIEADFIGHNSNINTLTASPDGTLIASAGKDGEIMLWNLAAKKAMYTLSAQDEVFSLAFSPNRYWLAAATATGIKVFSLDPQYLVDDLRPEFAGYSKAAEPHAVSLAWSADGQTLFAGYTDNVIRVWQVMTAN |
| Pre-rRNA-processing protein PNO1 | H | 274 | Saccharomyces Cerevisiae , Saccharomyces Cerevisiae W303 | MVAPTALKKATVTPVSGQDGGSSRIIGINNTESIDEDDDDDVLLDDSDNNTAKEEVEGEEGSRKTHESKTVVVDDQGKPRFTSASKTQGNKIKFESRKIMVPPHRMTPLRNSWTKIYPPLVEHLKLQVRMNLKTKSVELRTNPKFTTDPGALQKGADFIKAFTLGFDLDDSIALLRLDDLYIETFEVKDVKTLTGDHLSRAIGRIAGKDGKTKFAIENATRTRIVLADSKIHILGGFTHIRMARESVVSLILGSPPGKVYGNLRTVASRLKERY |
| ENP1 isoform 1 | I | 483 | Saccharomyces Cerevisiae , Saccharomyces Cerevisiae W303 | MARASSTKARKQRHDPLLKDLDAAQGTLKKINKKKLAQNDAANHDAANEEDGYIDSKASRKILQLAKEQQDEIEGEELAESERNKQFEARFTTMSYDDEDEDEDEDEEAFGEDISDFEPEGDYKEEEEIVEIDEEDAAMFEQYFKKSDDFNSLSGSYNLADKIMASIREKESQVEDMQDDEPLANEQNTSRGNISSGLKSGEGVALPEKVIKAYTTVGSILKTWTHGKLPKLFKVIPSLRNWQDVIYVTNPEEWSPHVVYEATKLFVSNLTAKESQKFINLILLERFRDNIETSEDHSLNYHIYRAVKKSLYKPSAFFKGFLFPLVETGCNVREATIAGSVLAKVSVPALHSSAALSYLLRLPFSPPTTVFIKILLDKKYALPYQTVDDCVYYFMRFRILDDGSNGEDATRVLPVIWHKAFLTFAQRYKNDITQDQRDFLLETVRQRGHKDIGPEIRRELLAGASREFVDPQEANDDLMIDVN |
| LTV1 isoform 1 | J | 463 | Saccharomyces Cerevisiae , Saccharomyces Cerevisiae W303 | MSKKFSSKNSQRYVVVHRPHDDPSFYDTDASAHVLVPVSNPNKTSPEADLRKKDVSSTKPKGRRAHVGEAALYGINFDDSEYDYTQHLKPIGLDPENSIFIASKGNEQKVEKKNIEDLFIEPKYRRDEIEKDDALPVFQRGMAKPEYLLHQQDTTDEIRGFKPDMNPALREVLEALEDEAYVVNDDVVVEDISKKTQLQGDNYGEEEKEDDIFAQLLGSGEAKDEDEFEDEFDEWDIDNVENFEDENYVKEMAQFDNIENLEDLENIDYQADVRRFQKDNSILEKHNSDDEFSNAGLDSVNPSEEEDVLGELPSIQDKSKTGKKKRKSRQKKGAMSDVSGFSMSSSAIARTETMTVLDDQYDQIINGYENYEEELEEDEEQNYQPFDMSAERSDFESMLDDFLDNYELESGGRKLAKKDKEIERLKEAADEVSKGKLSQRRNRERQEKKKLEKVTNTLSSLKF |
| 40S ribosomal protein S12 | M | 143 | Saccharomyces Cerevisiae , Saccharomyces Cerevisiae W303 | MSDVEEVVEVQEETVVEQTAEVTIEDALKVVLRTALVHDGLARGLRESTKALTRGEALLVVLVSSVTEANIIKLVEGLANDPENKVPLIKVADAKQLGEWAGLGKIDREGNARKVVGASVVVVKNWGAETDELSMIMEHFSQQ |
| 40S ribosomal protein S13 | N | 151 | Saccharomyces Cerevisiae , Saccharomyces Cerevisiae W303 | MGRMHSAGKGISSSAIPYSRNAPAWFKLSSESVIEQIVKYARKGLTPSQIGVLLRDAHGVTQARVITGNKIMRILKSNGLAPEIPEDLYYLIKKAVSVRKHLERNRKDKDAKFRLILIESRIHRLARYYRTVAVLPPNWKYESATASALVN |
| 40S ribosomal protein S14-A | O | 137 | Saccharomyces Cerevisiae , Saccharomyces Cerevisiae W303 | MSNVVQARDNSQVFGVARIYASFNDTFVHVTDLSGKETIARVTGGMKVKADRDESSPYAAMLAAQDVAAKCKEVGITAVHVKIRATGGTRTKTPGPGGQAALRALARSGLRIGRIEDVTPVPSDSTRKKGGRRGRRL |
| RPS15 isoform 1 | P | 142 | Saccharomyces Cerevisiae , Saccharomyces Cerevisiae W303 | MSQAVNAKKRVFKTHSYRGVDLEKLLEMSTEDFVKLAPARVRRRFARGMTSKPAGFMKKLRAAKLAAPENEKPAPVRTHMRNMIIVPEMIGSVVGIYNGKAFNQVEIRPEMLGHYLGEFSITYTPVRHGRAGATTSRFIPLK |
| 40S ribosomal protein S16-A | Q | 143 | Saccharomyces Cerevisiae , Saccharomyces Cerevisiae W303 | MSAVPSVQTFGKKKSATAVAHVKAGKGLIKVNGSPITLVEPEILRFKVYEPLLLVGLDKFSNIDIRVRVTGGGHVSQVYAIRQAIAKGLVAYHQKYVDEQSKNELKKAFTSYDRTLLIADSRRPEPKKFGGKGARSRFQKSYR |
| 40S ribosomal protein S17-A | R | 136 | Saccharomyces Cerevisiae , Saccharomyces Cerevisiae W303 | MGRVRTKTVKRASKALIERYYPKLTLDFQTNKRLCDEIATIQSKRLRNKIAGYTTHLMKRIQKGPVRGISFKLQEEERERKDQYVPEVSALDLSRSNGVLNVDNQTSDLVKSLGLKLPLSVINVSAQRDRRYRKRV |
| 40S ribosomal protein S18-A | S | 146 | Saccharomyces Cerevisiae , Saccharomyces Cerevisiae W303 | MSLVVQEQGSFQHILRLLNTNVDGNIKIVYALTTIKGVGRRYSNLVCKKADVDLHKRAGELTQEELERIVQIMQNPTHYKIPAWFLNRQNDITDGKDYHTLANNVESKLRDDLERLKKIRAHRGIRHFWGLRVRGQHTKTTGRRRA |
| 40S ribosomal protein S19-A | T | 144 | Saccharomyces Cerevisiae , Saccharomyces Cerevisiae W303 | MPGVSVRDVAAQDFINAYASFLQRQGKLEVPGYVDIVKTSSGNEMPPQDAEGWFYKRAASVARHIYMRKQVGVGKLNKLYGGAKSRGVRPYKHIDASGSINRKVLQALEKIGIVEISPKGGRRISENGQRDLDRIAAQTLEEDE |
| 40S ribosomal protein S20 | U | 121 | Saccharomyces Cerevisiae , Saccharomyces Cerevisiae W303 | MSDFQKEKVEEQEQQQQQIIKIRITLTSTKVKQLENVSSNIVKNAEQHNLVKKGPVRLPTKVLKISTRKTPNGEGSKTWETYEMRIHKRYIDLEAPVQIVKRITQITIEPGVDVEVVVASN |
| 40S ribosomal protein S21-A | V | 87 | Saccharomyces Cerevisiae , Saccharomyces Cerevisiae W303 | MENDKGQLVELYVPRKCSATNRIIKADDHASVQINVAKVDEEGRAIPGEYVTYALSGYVRSRGESDDSLNRLAQNDGLLKNVWSYSR |
| 40S ribosomal protein S22-A | W | 130 | Saccharomyces Cerevisiae , Saccharomyces Cerevisiae W303 | MTRSSVLADALNAINNAEKTGKRQVLIRPSSKVIIKFLQVMQKHGYIGEFEYIDDHRSGKIVVQLNGRLNKCGVISPRFNVKIGDIEKWTANLLPARQFGYVILTTSAGIMDHEEARRKHVSGKILGFVY |
| 40S ribosomal protein S23-A | X | 145 | Saccharomyces Cerevisiae , Saccharomyces Cerevisiae W303 | MGKGKPRGLNSARKLRVHRRNNRWAENNYKKRLLGTAFKSSPFGGSSHAKGIVLEKLGIESKQPNSAIRKCVRVQLIKNGKKVTAFVPNDGCLNFVDENDEVLLAGFGRKGKAKGDIPGVRFKVVKVSGVSLLALWKEKKEKPRS |
| rRNA adenine N(6)-methyltransferase | Y | 318 | Saccharomyces Cerevisiae , Saccharomyces Cerevisiae W303 | MGKAAKKKYSGATSSKQVSAEKHLSSVFKFNTDLGQHILKNPLVAQGIVDKAQIRPSDVVLEVGPGTGNLTVRILEQAKNVVAVEMDPRMAAELTKRVRGTPVEKKLEIMLGDFMKTELPYFDICISNTPYQISSPLVFKLINQPRPPRVSILMFQREFALRLLARPGDSLYCRLSANVQMWANVTHIMKVGKNNFRPPPQVESSVVRLEIKNPRPQVDYNEWDGLLRIVFVRKNRTISAGFKSTTVMDILEKNYKTFLAMNNEMVDDTKGSMHDVVKEKIDTVLKETDLGDKRAGKCDQNDFLRLLYAFHQVGIHFS |
| 40S ribosomal protein S25-A | Z | 108 | Saccharomyces Cerevisiae , Saccharomyces Cerevisiae W303 | MPPKQQLSKAAKAAAALAGGKKSKKKWSKKSMKDRAQHAVILDQEKYDRILKEVPTYRYVSVSVLVDRLKIGGSLARIALRHLEKEGIIKPISKHSKQAIYTRATASE |
| TSR1 isoform 1 | K | 788 | Saccharomyces Cerevisiae , Saccharomyces Cerevisiae W303 | MAGHSHRSSLKNGHKSYKSKHASKGALKRLYKGKVEKEPVGTGKPDKQVSKLQRKNKAKQLRAQRILDSIENRKLFEGKNGAAKIITIVPLVNDLDPLDILYKLLKCADDEGIMVQEVDSKRIFNVHIKKFKSNLKIIIPDMTNFLNILDCAKVADFVVFGLSGVQEVDEEFGEQIIRALELQGIASYIGVISNLSAVHEKEKFQLDVKQSLESYFKHFFPSEERVYNLEKNSDALNVLRTLCQRLPRSINWRDNRGYVVADFVDFVETSPDSGDLVIEGTVRGIGFNANRLVHIPDFGDFQLNKIEKISESSQKRKIIKEKATDSLSLELDLQTVFESNMNRDTLDEYAPEGTEDWSDYDEDFEYDGLTTARYDDHGFLPGREQTSKKAAVPKGTSDYQAKWYLDDVIDANEEEEAEQTNGKDETMMEIDDEMMVEQDNEEVAGDEEYDIEDNEGFEELSPEEEERQLREFRDMEKEDREFPDEIELEPSESAIERLKRYRGLKNLYNCDWQVDEKDPSSPAEWKRLLRIGNYKNTKNRIIKETKNEAQAIAGDRIRMFIRFPKFLLEKIQDPKQLLFAVYGLLLHEHKNAVVNFSLQRWEQYDKPVPSQEPIVVQYGVRRYTIQPLFSQGSNSPNNVHKYERFLHPDTVSVATCIAPVDFTQSPAIFFKPSPTDAKNIELIGHGTFLNADHSRILAKRAILTGHPFRFHKTVVTVRYMFFRPEDVEWFKSIPLFTKSGRSGFIKESLGTHGYFKATFDGKLSAQDVVAMSLYKRMWPMPSLPWNGM |
| Nucleic Acids / Hybrid | ||||
|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Sequence |
| 20S pre-ribosomal RNA | 2 | 2012 | NA | UAUCUGGUUGAUCCUGCCAGUAGUCAUAUGCUUGUCUCAAAGAUUAAGCCAUGCAUGUCUAAGUAUAAGCAAUUUAUACAGUGAAACUGCGAAUGGCUCAUUAAAUCAGUUAUCGUUUAUUUGAUAGUUCCUUUACUACAUGGUAUAACUGUGGUAAUUCUAGAGCUAAUACAUGCUUAAAAUCUCGACCCUUUGGAAGAGAUGUAUUUAUUAGAUAAAAAAUCAAUGUCUUCGGACUCUUUGAUGAUUCAUAAUAACUUUUCGAAUCGCAUGGCCUUGUGCUGGCGAUGGUUCAUUCAAAUUUCUGCCCUAUCAACUUUCGAUGGUAGGAUAGUGGCCUACCAUGGUUUCAACGGGUAACGGGGAAUAAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGCAAAUUACCCAAUCCUAAUUCAGGGAGGUAGUGACAAUAAAUAACGAUACAGGGCCCAUUCGGGUCUUGUAAUUGGAAUGAGUACAAUGUAAAUACCUUAACGAGGAACAAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAGUUGUUGCAGUUAAAAAGCUCGUAGUUGAACUUUGGGCCCGGUUGGCCGGUCCGAUUUUUUCGUGUACUGGAUUUCCAACGGGGCCUUUCCUUCUGGCUAACCUUGAGUCCUUGUGGCUCUUGGCGAACCAGGACUUUUACUUUGAAAAAAUUAGAGUGUUCAAAGCAGGCGUAUUGCUCGAAUAUAUUAGCAUGGAAUAAUAGAAUAGGACGUUUGGUUCUAUUUUGUUGGUUUCUAGGACCAUCGUAAUGAUUAAUAGGGACGGUCGGGGGCAUCAGUAUUCAAUUGUCAGAGGUGAAAUUCUUGGAUUUAUUGAAGACUAACUACUGCGAAAGCAUUUGCCAAGGACGUUUUCAUUAAUCAAGAACGAAAGUUAGGGGAUCGAAGAUGAUCAGAUACCGUCGUAGUCUUAACCAUAAACUAUGCCGACUAGGGAUCGGGUGGUGUUUUUUUAAUGACCCACUCGGCACCUUACGAGAAAUCAAAGUCUUUGGGUUCUGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGAGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGGAAACUCACCAGGUCCAGACACAAUAAGGAUUGACAGAUUGAGAGCUCUUUCUUGAUUUUGUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGCUUAAUUGCGAUAACGAACGAGACCUUAACCUACUAAAUAGUGGUGCUAGCAUUUGCUGGUUAUCCACUUCUUAGAGGGACUAUCGGUUUCAAGCCGAUGGAAGUUUGAGGCAAUAACAGGUCUGUGAUGCCCUUAGACGUUCUGGGCCGCACGCGCGCUACACUGACGGAGCCAGCGAGUCUAACCUUGGCCGAGAGGUCUUGGUAAUCUUGUGAAACUCCGUCGUGCUGGGGAUAGAGCAUUGUAAUUAUUGCUCUUCAACGAGGAAUUCCUAGUAAGCGCAAGUCAUCAGCUUGCGUUGAUUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUAGUACCGAUUGAAUGGCUUAGUGAGGCCUCAGGAUCUGCUUAGAGAAGGGGGCAACUCCAUCUCAGAGCGGAGAAUUUGGACAAACUUGGUCAUUUAGAGGAACUAAAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCGGAAGGAUCAUUAAAGAAAUUUAAUAAUUUUGAAAAUGGAUUUUUUUGUUUUGGCAAGAGCAUGAGAGCUUUUACUGGGCAAGAAGACAAGAGAUGGAGAGUCCAGCCGGGCCUGCGCUUAAGUGCGCGGUCUUGCUAGGCUUGUAAGUUUCUUUCUUGCUAUUCCAAACGGUGAGAGAUUUCUGUGCUUUUGUUAUAGGACAAUUAAAACCGUUUCAAUACAAC |
Experimental Data
Method: ELECTRON MICROSCOPY
Deposited Date: 2023-01-25 Deposition Author(s): Becker, T. , Beckmann, R. , Berninghausen, O. , Buschauer, R. , Cheng, J. , Ikeuchi, K.