Advanced Search:
7NAD
State e2 nucleolar 60s ribosomal biogenesis intermediate - spb4 local refinement model
PDB DOI: 10.2210/pdb7nad/pdb
Classification: RIBOSOME Organism(s): Saccharomyces Cerevisiae By4741
Deposited: 2021-06-21 Deposition Author(s): Cruz, V.E. , Erzberger, J.P. , Peddada, N. , Sekulski, K.
Experimental Data Snapshot
Method: ELECTRON MICROSCOPY Resolution: 3.04 Å
State e2 nucleolar 60s ribosomal biogenesis intermediate - spb4 local refinement model
Cruz, V.E. , Erzberger, J.P. , Peddada, N. , Sekulski, K.
Primary Citation of Related Structures: 7NAD
| Nucleic Acids / Hybrid | ||||
|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Sequence |
| 25S rRNA | 1 | 697 | NA | AUGCCUGAAUAGGGUGAAGCCAGAGGAAACUCUGGUGGAGGCUCGCGAAUUUGGGUAUAGUAGCAAAUAUUCAAAUGAGAACUUUGAAGACUGAAGUGGGGAAAGGUUCCACGUCAACAGCAGUUGGACGUGGGUUAGUCGAUCCUAAGAGAUGGUUUCAAAGGCCUGACAGGCCACCAUCGAAAGGGAAUCCGGUUAAGAUUCCGGAACCUGGAUAUGGAUUCUUCACGGUAACGUAACUGAAUGUGGAGACGUCGGCGCGAGCCCUGGGAGGAGUUAUCUUUUCUUCUUAACAGCUUAUCACCCCGGAAUUGGUUUAUCCGGAGAUGGGGUCUUAUGGCUGGAAGAGGCCAGCACCUUUGCUGGCUCCGGUGCGCUUGUGACGGCCCGUGAAAAUCCACAGGAAGGAAUAGUUUUCAUGCCAGGUCGUACUGUCUCCAAGGUGAACAGCCUCUAGUUGAUAGAAGAUAAGGGAAGUCGGUCCGUAACUUCGGGAUAAGGAUUGGCUCUAAGGGUCGGGUAGUGAGGGCCUUGGUCACGGCCUUGGCUUGCUACAAUUAACGAUCAACUUAGAACUGGUACGGACAAGGGGAAUCUGACUGUUAACGAGAUUCCCACUGUCCCUAUCUACUAUCUAGCGAGGCUGUCUGAUCAGGCAUUGCGUAAGCAGUAGAGUAGCCGUUACGAUCUGCUGAGA |
| 5.8S rRNA | 2 | 72 | NA | GAACGCGCGAUACUCUUUGAACGCACAUUGCGCCCCUUGGUAUUCCAGGGGGCAUCUUUGAAAGCGUAUUGC |
| Proteins | ||||
|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Sequence |
| Ribosome biogenesis protein RLP24 | U | 199 | Saccharomyces Cerevisiae By4741 | MRIYQCHFCSSPCYPGHGIMFVRNDAKEFRFCRSKCHKAFKQRRNPRKLKWTKAFRKAAGKELAVDSTLTFAQRRNVPVRYNRELVATTLKAMARIEEIRQKRERAFYKNRMRGNKEKDFLRDKKLVESNPELLRIREVEIARKLAKEQERAESVSEQEESEEEEEDMEIDSDEEEEEQLEKQKILLKNRRRNTKKIAF |
| 60S ribosomal protein L23-A | V | 36 | Saccharomyces Cerevisiae By4741 | LPVGAIMNCARNLYIIMATVKKGKPELRKKVMEDNA |
| SPB4 isoform 1 | X | 606 | Saccharomyces Cerevisiae By4741 | MSKSLEWDNLGFSLLPWIRTGLDVMGFETMTPVQASTIPMLAGNKDVVVDSVTGSGKTAAFVIPVLEKVVKEEANTSKFKKAHFHSLIIAPTRELSRQIESVVLSFLEHYPSDLFPIKCQLLVGTNEATVRDDVSNFLRNRPQILIGTPGRVLDFLQMPAVKTSACSMVVMDEADRLLDMSFIKDTEKILRLLPKQRRTGLFSATMRSAGSDIFKTGLRNPVRITVNSKNQAPSSLKLNYCVVNPAEKLQLLVSILNNYKFKKCIVYFPTCVSVSYFYSFIQYLGKRNILVNEVEIFSLHGKLQTSARTKTLTAFTDSLSNSVLFTTDVAARGIDIPDVDLVIQLDPPTNTDMFMHRCGRTGRANRVGKAITFLNEGREEDFIPFMQVKNVELEELDLEVKGITANFYEDFRNWILEDRDRFDKGVKAYVAFIKYYSNHSATSIFRLQSLDYVGIAKLYGLFRLPRMPEITKYLATEKQEGIFPGNWLVDPPVNMDEYKYKDKKREKERQETLKNISLINDKKKLKSELKKKNLAWSDKTLTKERKLERKEKMSLKRKAIEEELKAEELDENAEEERIKEDWKEIVLQNKRKKVSSKAIQGNFDDL |
| 60S ribosomal protein L27-A | Z | 136 | Saccharomyces Cerevisiae By4741 | MAKFLKAGKVAVVVRGRYAGKKVVIVKPHDEGSKSHPFGHALVAGIERYPLKVTKKHGAKKVAKRTKIKPFIKVVNYNHLLPTRYTLDVEAFKSVVSTETFEQPSQREEAKKVVKKAFEERHQAGKNQWFFSKLRF |
| 60S ribosomal protein L3 | B | 387 | Saccharomyces Cerevisiae By4741 | MSHRKYEAPRHGHLGFLPRKRAASIRARVKAFPKDDRSKPVALTSFLGYKAGMTTIVRDLDRPGSKFHKREVVEAVTVVDTPPVVVVGVVGYVETPRGLRSLTTVWAEHLSDEVKRRFYKNWYKSKKKAFTKYSAKYAQDGAGIERELARIKKYASVVRVLVHTQIRKTPLAQKKAHLAEIQLNGGSISEKVDWAREHFEKTVAVDSVFEQNEMIDAIAVTKGHGFEGVTHRWGTKKLPRKTHRGLRKVACIGAWHPAHVMWSVARAGQRGYHSRTSINHKIYRVGKGDDEANGATSFDRTKKTITPMGGFVHYGEIKNDFIMVKGCIPGNRKRIVTLRKSLYTNTSRKALEEVSLKWIDTASKFGKGRFQTPAEKHAFMGTLKKDL |
| 60S ribosomal protein L30 | C | 105 | Saccharomyces Cerevisiae By4741 | MAPVKSQESINQKLALVIKSGKYTLGYKSTVKSLRQGKSKLIIIAANTPVLRKSELEYYAMLSKTKVYYFQGGNNELGTAVGKLFRVGVVSILEAGDSDILTTLA |
| 60S ribosomal protein L31-A | D | 113 | Saccharomyces Cerevisiae By4741 | MAGLKDVVTREYTINLHKRLHGVSFKKRAPRAVKEIKKFAKLHMGTDDVRLAPELNQAIWKRGVKGVEYRLRLRISRKRNEEEDAKNPLFSYVEPVLVASAKGLQTVVVEEDA |
| RPL8A isoform 1 | G | 256 | Saccharomyces Cerevisiae By4741 | MAPGKKVAPAPFGAKSTKSNKTRNPLTHSTPKNFGIGQAVQPKRNLSRYVKWPEYVRVQRQKKILSIRLKVPPTIAQFQYTLDRNTAAETFKLFNKYRPETAAEKKERLTKEAAAVAEGKSKQDASPKPYAVKYGLNHVVALIENKKAKLVLIANDVDPIELVVFLPALCKKMGVPYAIVKGKARLGTLVNQKTSAVAALTEVRAEDEAALAKLVSTIDANFADKYDEVKKHWGGGILGNKAQAKMDKRAKNSDSA |
| RPL38 isoform 1 | K | 78 | Saccharomyces Cerevisiae By4741 | MAREITDIKQFLELTRRADVKTATVKINKKLNKAGKPFRQTKFKVRGSSSLYTLVINDAGKAKKLIQSLPPTLKVNRL |
| Ribosome biogenesis protein ERB1 | M | 429 | Saccharomyces Cerevisiae By4741 | DHVMHLRAPKLPLDLYLAPRVRKNKLNIDPNSLIPELPSPKDLRPFPIRCSTIYAGHKGKVRTLSIDPSGLWLATGSDDGTVRVWEILTGREVYRTTLIDPKDNPDYHIECIEWNPDANNGILAVAVGENIHLIVPPIFGYDIENNGKTKIEDGFGYDTFGTVKKSNLEVNAIEWNPDANNGILAKNAVKKQVAQWNKPSQKQLEKDICITISCKKTVKKLSWHRKGDYFVTVQPDSGNTSVLIHQVSKHLTQSPFKKSKGIIMDAKFHPFKPQLFVCSQRYVRIYDLSQQILVKKLLPGARWLSKIDIHPRGDNLIASSFDKRVLWHDLDLASTPYKTLRYHEKAVRSVNFHKKLPLFSSAADDGTIHVFHATVYDDMMKNPMIVPLKKLTGHKVINSLGVLDAIWHPREAWLFSAGADNTARLWTTI |
| Pescadillo homolog | N | 104 | Saccharomyces Cerevisiae By4741 | MRIKKKNTRGNARNFITRSQAVRKLQVSLADFRRLCIFKGIYPREPRNKKKANKGSTAPTTFYYAKDIQYEEKKLKMIMMSNKQKKLYKKMKYSNAKKEEQAEN |
| 60S ribosomal protein L17-A | P | 184 | Saccharomyces Cerevisiae By4741 | MARYGATSTNPAKSASARGSYLRVSFKNTRETAQAINGWELTKAQKYLEQVLDHQRAIPFRRFNSSIGRTAQGKEFGVTKARWPAKSVKFVQGLLQNAAANAEAKGLDATKLYVSHIQVNQAPKQRRRTYRAHGRINKYESSPSHIELVVTEKEEAVAKAAEKKVVRLTSRQRGRIAAQKRIAA |
| RLP7 isoform 1 | T | 322 | Saccharomyces Cerevisiae By4741 | MSSTQDSKAQTLNSNPEILLRKRRNADRTRIERQELAKKKREEQIKKKRSNKNKFVRAESIVAKTLATSREKERIKRVSILEDKKAKNETQHIASGKDFILKITEKANGAEENSVDLEETEEEEDDGLIREKTTYDGKPALLFIVRVRGPLAVNIPNKAFKILSLLRLVETNTGVFVKLTKNVYPLLKVIAPYVVIGKPSLSSIRSLIQKRGRIIYKGENEAEPHEIVLNDNNIVEEQLGDHGIICVEDIIHEIATMGESFSVCNFFLQPFKLNREVSGFGSLNRLRKIKQREAESRTRQFSNAATAPVIEVDIDSLLAKLN |
| SPB1 isoform 1 | W | 841 | Saccharomyces Cerevisiae By4741 | MGKTQKKNSKGRLDRYYYLAKEKGYRARSSFKIIQINEKYGHFLEKSKVVIDLCAAPGSWCQVASKLCPVNSLIIGVDIVPMKPMPNVITFQSDITTEDCRSKLRGYMKTWKADTVLHDGAPNVGLGWVQDAFTQSQLTLQALKLAVENLVVNGTFVTKIFRSKDYNKLIWVFQQLFEKVEATKPPASRNVSAEIFVVCKGFKAPKRLDPRLLDPKEVFEELPDGQQNMESKIYNPEKKVRKRQGYEEGDNLLYHETSILDFVRTEDPISMLGEMNKFTIDENDHEWKILKKLKQTTDEFRSCIEDLKVLGKKDFKMILRWRKIAREILGIEVKDDAKTEIEVVPLTEEEQIEKDLQGLQEKQRLNVKRERRRKNEMKQKELQRMQMNMITPTDIGIEAASLGKESLFNLKTAEKTGILNDLAKGKKRMIFTDDELAKDNDIYIDENIMIKDKDSAADADDLESELNAMYSDYKTRRSERDAKFRAKQARGGDNEEEWTGFNEGSLEKKEEEGKDYIEDNDDEGVEGDSDDDEAITNLISKLKGQEGDHKLSSKARMIFNDPIFNNVEPDLPVNTVNDGIMSSESVGDISKLNKKRKHEEMHQKQDEADSSDESSSDDSDFEIVANDNASEEFDSDYDSEEEKNQTKKEKHSRDIDIATVEAMTLAHQLALGQKNKHDLVDEGFNRYTFRDTENLPDWFLEDEKEHSKINKPITKEAAMAIKEKIKAMNARPIKKVAEAKARKRMRAVARLEKIKKKAGLINDDSDKTEKDKAEEISRLMRKVTKKPKTKPKVTLVVASGRNKGLAGRPKGVKGKYKMVDGVMKNEQRALRRIAKKHHKKK |
| 60S ribosomal protein L37-A | J | 88 | Saccharomyces Cerevisiae By4741 | MGKGTPSFGKRHNKSHTLCNRCGRRSFHVQKKTCSSCGYPAAKTRSYNWGAKAKRRHTTGTGRMRYLKHVSRRFKNGFQTGSASKASA |
| RRP17 isoform 1 | 5 | 235 | Saccharomyces Cerevisiae By4741 | MAVHTNRQILTRGKNYATKQSKKFGTDEVTFDKDSRLDYLTGFHKRKLQRQKKAQEFIKEQERLRKIEERQKIRQERKEVMEEQLKTFKESLNLEAEIEDAKNDKTEDLQVESDESWHGFDSDKDDGDNDNNESSVKPILKKGAITEIYDDSTTVELETLEPNDNFEYLAQLNNVKLEKAEKVLKQSINRATKYAKFLGVDEKQKKKPRVKKFRYLTKNERRINQRKANDNKRRR |
| NOC2 isoform 1 | 8 | 710 | Saccharomyces Cerevisiae By4741 | MGKVSKSTKKFQSKHLKHTLDQRRKEKIQKKRIQGRRGNKTDQEKADAAGTREQQQLKKSAKEEVFKDMSVETFFEKGIEIPKENKKLKKKTTKEQSDEDSSSSEEEEDMGQSMAKLAEKDPEFYKYLEENDKDLLDFAGTNPLDGIDSQDEGEDAERNSNIEEKSEQMELEKEKIELSLKLVRKWKKQLHDSPSLKLLRNIISAFKVAVNLNKEENIEDYKYAITDEKAFHELMFMVLKDVPQAIQKMAPYKIVKGARTLPNGGNVSRVSSIVKSHAGSLLILLNDITNTETAALVLHSVNELMPYLLSYRRILKELIKSIVGVWSTTRELETQIASFAFLINTTKEFKKSMLETTLKTTYSTFIKSCRKTNMRSMPLINFQKNSAAELFGIDEVLGYQVGFEYIRQLAIHLRNTMNATTKKSSKINSAEAYKIVYNWQFCHSLDFWSRVLSFACQPEKENGSESPLRQLIYPLVQVTLGVIRLIPTPQFFPLRFYLIKSLIRLSQNSGVFIPIYPLLSEILTSTAFTKAPKKSPNLAAFDFEHNIKCTQAYLNTKIYQEGLSEQFVDLLGDYFALYCKNIAFPELVTPVIISLRRYIKTSTNVKLNKRLSTVVEKLNQNSTFIQEKRSDVEFGPTNKSEVSRFLNDVAWNKTPLGSYVAVQREVKEEKARLMRESMEEQDKERETEEAKLLNSLESDDDNEDVEMSDA |
| NOC3 isoform 1 | I | 663 | Saccharomyces Cerevisiae By4741 | MAKRNRSQFRIQERTAKKRKHEDSLLEGNVFQNAPEDMDENTIYSAKGSSWDEEEQDYEMVPRKNRSDTSNLVEGLPIKVNGKVERKLHKAQEKPKDDDEEDEDSNDSSEDDEGPNEEQEAEAKEDEPDTEEKILQLKEDIADLVTKVMEEPEENTAALGRLCKMVESKNPNTCKFSMLALVPVFKSIIPGYRIRPLTETEKKEKVSKEVSKLRNFEQALVYNYKNYVGRLQSLSKTPSNAAPIQVSLGILATQAAKELISTASHFNFRTDIFTLLLRRICKPRISTDPTSIQIIQTFETLLNEDEEGSISFEILRIFNKILKTRNFNIEESVLNMLLSLDVLHDYDPNTKLKGNVSAPKLKKKDRVHLSKKQRKARKEMQQIEEEMRNAEQAVSAEERERNQSEILKIVFTIYLNILKNNAKTLIGSVLEGLTKFGNMANFDLLGDFLEVMKELISDTEFDNLSSAEVRKALLCIVSAFSLISNTQYMKVNVDLSKFVDGLYALLPYICLDADIELSYRSLRLADPLNNEIIKPSVNVSTKAELLLKALDHVFFRSKSGTKERATAFTKRLYMCISHTPEKTSIAILKFIDKLMNRYPEISGLYSSEDRIGNGHFIMEADNPSRSNPEAATLWDNALLEKHYCPVVTKGLRSLSSRSKECSK |
| 60S ribosomal protein L19-A | R | 189 | Saccharomyces Cerevisiae By4741 | MANLRTQKRLAASVVGVGKRKVWLDPNETSEIAQANSRNAIRKLVKNGTIVKKAVTVHSKSRTRAHAQSKREGRHSGYGKRKGTREARLPSQVVWIRRLRVLRRLLAKYRDAGKIDKHLYHVLYKESKGNAFKHKRALVEHIIQAKADAQREKALNEEAEARRLKNRAARDRRAQRVAEKRDALLKEDA |
Experimental Data
Method: ELECTRON MICROSCOPY
Deposited Date: 2021-06-21 Deposition Author(s): Cruz, V.E. , Erzberger, J.P. , Peddada, N. , Sekulski, K.