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FASTA Sequence PDB Format mmCIF Format
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5Z3G

Cryo-em structure of a nucleolar pre-60s ribosome (rpf1-tap)

PDB DOI: 10.2210/pdb5z3g/pdb

Classification: RIBOSOME
Organism(s): Grouper Iridovirus , Burkholderia Vietnamiensis (Strain G4 / Lmg 22486)

Deposited: 2018-01-06
Deposition Author(s): Ye, K. , Zhou, D. , Zhu, X.

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.65 Å

5z3g
Literature

Cryo-em structure of a nucleolar pre-60s ribosome (rpf1-tap)

Ye, K. , Zhou, D. , Zhu, X.

Primary Citation of Related Structures: 5Z3G


Proteins
Molecule Chains Sequence Length Organism Sequence
Ribosome biogenesis protein BRX1 A 291 Grouper Iridovirus , Burkholderia Vietnamiensis (Strain G4 / Lmg 22486) MSSIYKALAGKSKDNKSEKKQGNVKQFMNKQRTLLISSRGVNYRHRHLIQDLSGLLPHSRKEPKLDTKKDLQQLNEIAELYNCNNVLFFEARKHQDLYLWLSKPPNGPTIKFYIQNLHTMDELNFTGNCLKGSRPVLSFDQRFESSPHYQLIKELLVHNFGVPPNARKSKPFIDHVMSFSIVDDKIWVRTYEISHSTKNKEEYEDGEEDISLVEIGPRFVMTVILILEGSFGGPKIYENKQYVSPNVVRAQIKQQAAEEAKSRAEAAVERKIKRRENVLAADPLSNDALFK
60S ribosomal protein L33-A J 107 Grouper Iridovirus , Burkholderia Vietnamiensis (Strain G4 / Lmg 22486) MAESHRLYVKGKHLSYQRSKRVNNPNVSLIKIEGVATPQDAQFYLGKRIAYVYRASKEVRGSKIRVMWGKVTRTHGNSGVVRATFRNNLPAKTFGASVRIFLYPSNI
60S ribosomal protein L8-A K 256 Grouper Iridovirus , Burkholderia Vietnamiensis (Strain G4 / Lmg 22486) MAPGKKVAPAPFGAKSTKSNKTRNPLTHSTPKNFGIGQAVQPKRNLSRYVKWPEYVRVQRQKKILSIRLKVPPTIAQFQYTLDRNTAAETFKLFNKYRPETAAEKKERLTKEAAAVAEGKSKQDASPKPYAVKYGLNHVVALIENKKAKLVLIANDVDPIELVVFLPALCKKMGVPYAIVKGKARLGTLVNQKTSAVAALTEVRAEDEAALAKLVSTIDANFADKYDEVKKHWGGGILGNKAQAKMDKRAKNSDSA
60S ribosomal protein L35-A L 120 Grouper Iridovirus , Burkholderia Vietnamiensis (Strain G4 / Lmg 22486) MAGVKAYELRTKSKEQLASQLVDLKKELAELKVQKLSRPSLPKIKTVRKSIACVLTVINEQQREAVRQLYKGKKYQPKDLRAKKTRALRRALTKFEASQVTEKQRKKQIAFPQRKYAIKA
60S ribosomal protein L36-A M 100 Grouper Iridovirus , Burkholderia Vietnamiensis (Strain G4 / Lmg 22486) MTVKTGIAIGLNKGKKVTSMTPAPKISYKKGAASNRTKFVRSLVREIAGLSPYERRLIDLIRNSGEKRARKVAKKRLGSFTRAKAKVEEMNNIIAASRRH
60S ribosomal protein L37-A N 88 Grouper Iridovirus , Burkholderia Vietnamiensis (Strain G4 / Lmg 22486) MGKGTPSFGKRHNKSHTLCNRCGRRSFHVQKKTCSSCGYPAAKTRSYNWGAKAKRRHTTGTGRMRYLKHVSRRFKNGFQTGSASKASA
Ribosome production factor 1 O 295 Grouper Iridovirus , Burkholderia Vietnamiensis (Strain G4 / Lmg 22486) MALGNEINITNKLKRQEIFADIKHEKNKERHTMRRKRAKEERENPELREQRLKENVTQTIENTRVYDETINKEVEGDEDDLMRYFNSNSNEPPKIFLTTNVNAKKSAYEFANILIEILPNVTFVKRKFGYKLKEISDICIKRNFTDIVIINEDKKKVTGLTFIHLPEGPTFYFKLSSFVEVKKIVGHGRPTSHIPELILNNFQTRLGQTVGRLFQSILPQNPDIEGRQVITLHNQRDYIFFRRHRYVFKDNERVGLQELGPQFTLKLKRLQRGIKEETEWEHKPEMDKEKKKFYL
60S ribosomal protein L13-A P 199 Grouper Iridovirus , Burkholderia Vietnamiensis (Strain G4 / Lmg 22486) MAISKNLPILKNHFRKHWQERVKVHFDQAGKKVSRRNARATRAAKIAPRPLDLLRPVVRAPTVKYNRKVRAGRGFTLAEVKAAGLTAAYARTIGIAVDHRRQNRNQEIFDANVQRLKEYQSKIIVFPRNGKAPEAEQVLSAAATFPIAQPATDVEARAVQDNGESAFRTLRLARSEKKFRGIREKRAREKAEAEAEKKK
60S ribosomal protein L14-A Q 138 Grouper Iridovirus , Burkholderia Vietnamiensis (Strain G4 / Lmg 22486) MSTDSIVKASNWRLVEVGRVVLIKKGQSAGKLAAIVEIIDQKKVLIDGPKAGVPRQAINLGQVVLTPLTFALPRGARTATVSKKWAAAAVCEKWAASSWAKKIAQRERRAALTDFERFQVMVLRKQKRYTVKKALAKA
60S ribosomal protein L15-A R 204 Grouper Iridovirus , Burkholderia Vietnamiensis (Strain G4 / Lmg 22486) MGAYKYLEELQRKKQSDVLRFLQRVRVWEYRQKNVIHRAARPTRPDKARRLGYKAKQGFVIYRVRVRRGNRKRPVPKGATYGKPTNQGVNELKYQRSLRATAEERVGRRAANLRVLNSYWVNQDSTYKYFEVILVDPQHKAIRRDARYNWICDPVHKHREARGLTATGKKSRGINKGHKFNNTKAGRRKTWKRQNTLSLWRYRK
60S ribosomal protein L16-A S 199 Grouper Iridovirus , Burkholderia Vietnamiensis (Strain G4 / Lmg 22486) MSVEPVVVIDGKGHLVGRLASVVAKQLLNGQKIVVVRAEELNISGEFFRNKLKYHDFLRKATAFNKTRGPFHFRAPSRIFYKALRGMVSHKTARGKAALERLKVFEGIPPPYDKKKRVVVPQALRVLRLKPGRKYTTLGKLSTSVGWKYEDVVAKLEAKRKVSSAEYYAKKRAFTKKVASANATAAESDVAKQLAALGY
rRNA-processing protein EBP2 B 427 Grouper Iridovirus , Burkholderia Vietnamiensis (Strain G4 / Lmg 22486) MAKGFKLKELLSHQKEIEKAEKLENDLKKKKSQELKKEEPTIVTASNLKKLEKKEKKADVKKEVAADTEEYQSQALSKKEKRKLKKELKKMQEQDATEAQKHMSGDEDESGDDREEEEEEEEEEEGRLDLEKLAKSDSESEDDSESENDSEEDEDVVAKEESEEKEEQEEEQDVPLSDVEFDSDADVVPHHKLTVNNTKAMKHALERVQLPWKKHSFQEHQSVTSETNTDEHIKDIYDDTERELAFYKQSLDAVLVARDELKRLKVPFKRPLDYFAEMVKSDEHMDKIKGKLIEEASDKKAREEARRQRQLKKFGKQVQNATLQKRQLEKRETLEKIKSLKNKRKHNEIDHSEFNVGVEEEVEGKRFDRGRPNGKRAAKNAKYGQGGMKRFKRKNDATSSADVSGFSSRKMKGKTNRPGKSRRARRF
60S ribosomal protein L17-A T 184 Grouper Iridovirus , Burkholderia Vietnamiensis (Strain G4 / Lmg 22486) MARYGATSTNPAKSASARGSYLRVSFKNTRETAQAINGWELTKAQKYLEQVLDHQRAIPFRRFNSSIGRTAQGKEFGVTKARWPAKSVKFVQGLLQNAAANAEAKGLDATKLYVSHIQVNQAPKQRRRTYRAHGRINKYESSPSHIELVVTEKEEAVAKAAEKKVVRLTSRQRGRIAAQKRIAA
60S ribosomal protein L18-A U 186 Grouper Iridovirus , Burkholderia Vietnamiensis (Strain G4 / Lmg 22486) MGIDHTSKQHKRSGHRTAPKSDNVYLKLLVKLYTFLARRTDAPFNKVVLKALFLSKINRPPVSVSRIARALKQEGAANKTVVVVGTVTDDARIFEFPKTTVAALRFTAGARAKIVKAGGECITLDQLAVRAPKGQNTLILRGPRNSREAVRHFGMGPHKGKAPRILSTGRKFERARGRRRSKGFKV
Ribosome biogenesis protein NSA1 V 463 Grouper Iridovirus , Burkholderia Vietnamiensis (Strain G4 / Lmg 22486) MRLLVSCVDSGSIKEVLCNIGTDTSVQSALQPFHVAPHLAEGLKAYVDRMWVISEDEAILARNSGVVELVKISKHLKENEALQVDPKGESKNEKSLSDDLPKFDISEFEITSSVSDLFDDAKLESLSSKSVKRTKLVDGFVTLCPIKKDSSNNTFVAATKSGLLHIIKKGEDKKLIKLASLGLKAPVEFLQLYDLEDTDTDKYIFAYGGEENLIKLVEIDSSFQSLKQIWEAKNVKNDRLDMRVPVWPMALRFLEPSPGKTEKGKLNYQFAAITRWSHLTKYSTQHGRKPFAQIDLLPNREPLSQMEVFDAKGENVVSSLGNFQSETFNELNVITTDYKKNVFKFDGNGRMLGKVGRDDITGSSTYIHVHDGKYLLQGGLDRYVRIFDIKTNKMLVKVYVGSRINFIVMLDDVEIEMPLSPSAKAAKGKQKRKVTELEEDADELWNKLEGKVAASKASKKSKI
60S ribosomal protein L20-A W 172 Grouper Iridovirus , Burkholderia Vietnamiensis (Strain G4 / Lmg 22486) MAHFKEYQVIGRRLPTESVPEPKLFRMRIFASNEVIAKSRYWYFLQKLHKVKKASGEIVSINQINEAHPTKVKNFGVWVRYDSRSGTHNMYKEIRDVSRVAAVETLYQDMAARHRARFRSIHILKVAEIEKTADVKRQYVKQFLTKDLKFPLPHRVQKSTKTFSYKRPSTFY
Ribosomal RNA-processing protein 1 X 278 Grouper Iridovirus , Burkholderia Vietnamiensis (Strain G4 / Lmg 22486) METSNFVKQLSSNNRKTRVNALEALKKYLTAKQFKENKQIEFNKLWKGLYYAMWFSDRPRPQQRLANELGELHGLYFDPKDNSTADELTTNDKAFIKFSRGFWKVMCFEWFNIDRYRLDKYLLLIRRVLFSQLKYLQSRNWDKKLVDEYIKKVLRWLPLSGSPKVYTGIPIHIVDILLDEWERLLKDGDEDDEDEENKEEEMRKIAESAKKTPLADVIAIFQDIVADYNNSKVLREKIKEDLFSDTRLVSWDILEGETQHNDSSNESEEEEEEEWKGF
ATP-dependent RNA helicase HAS1 Y 505 Grouper Iridovirus , Burkholderia Vietnamiensis (Strain G4 / Lmg 22486) MATPSNKRSRDSESTEEPVVDEKSTSKQNNAAPEGEQTTCVEKFEELKLSQPTLKAIEKMGFTTMTSVQARTIPPLLAGRDVLGAAKTGSGKTLAFLIPAIELLHSLKFKPRNGTGIIVITPTRELALQIFGVARELMEFHSQTFGIVIGGANRRQEAEKLMKGVNMLIATPGRLLDHLQNTKGFVFKNLKALIIDEADRILEIGFEDEMRQIIKILPNEDRQSMLFSATQTTKVEDLARISLRPGPLFINVVPETDNSTADGLEQGYVVCDSDKRFLLLFSFLKRNQKKKIIVFLSSCNSVKYYAELLNYIDLPVLELHGKQKQQKRTNTFFEFCNAERGILICTDVAARGLDIPAVDWIIQFDPPDDPRDYIHRVGRTARGTKGKGKSLMFLTPNELGFLRYLKASKVPLNEYEFPENKIANVQSQLEKLIKSNYYLHQTAKDGYRSYLQAYASHSLKTVYQIDKLDLAKVAKSYGFPVPPKVNITIGASGKTPNTKRRKTHK
Protein MAK16 Z 306 Grouper Iridovirus , Burkholderia Vietnamiensis (Strain G4 / Lmg 22486) MSDEIVWQVINQSFCSHRIKAPNGQNFCRNEYNVTGLCTRQSCPLANSKYATVKCDNGKLYLYMKTPERAHTPAKLWERIKLSKNYTKALQQIDEHLLHWSKFFRHKCKQRFTKLTQVMITERRLALREEERHYVGVAPKVKRREQNRERKALVAAKIEKAIEKELMDRLKSGAYGDKPLNVDEKVWKKIMGQMEEENSQDEEEDWDEEEESDDGEVEYVADDGEGEYVDVDDLEKWLADSDREASSASESESDSESESDSDSDEENKNSAKRRKKGTSAKTKRPKVEIEYEEEHEVQNAEQEVAQ
Ribosome biogenesis protein RLP7 D 322 Grouper Iridovirus , Burkholderia Vietnamiensis (Strain G4 / Lmg 22486) MSSTQDSKAQTLNSNPEILLRKRRNADRTRIERQELAKKKREEQIKKKRSNKNKFVRAESIVAKTLATSREKERIKRVSILEDKKAKNETQHIASGKDFILKITEKANGAEENSVDLEETEEEEDDGLIREKTTYDGKPALLFIVRVRGPLAVNIPNKAFKILSLLRLVETNTGVFVKLTKNVYPLLKVIAPYVVIGKPSLSSIRSLIQKRGRIIYKGENEAEPHEIVLNDNNIVEEQLGDHGIICVEDIIHEIATMGESFSVCNFFLQPFKLNREVSGFGSLNRLRKIKQREAESRTRQFSNAATAPVIEVDIDSLLAKLN
60S ribosomal protein L6-A I 176 Grouper Iridovirus , Burkholderia Vietnamiensis (Strain G4 / Lmg 22486) MSAQKAPKWYPSEDVAALKKTRKAARPQKLRASLVPGTVLILLAGRFRGKRVVYLKHLEDNTLLISGPFKVNGVPLRRVNARYVIATSTKVSVEGVNVEKFNVEYFAKEKLTKKEKKEANLFPEQQNKEIKAERVEDQKVVDKALIAEIKKTPLLKQYLSASFSLKNGDKPHMLKF
Ribosome biogenesis protein 15 E 220 Grouper Iridovirus , Burkholderia Vietnamiensis (Strain G4 / Lmg 22486) MVKSTSKTSTKETVTKQPTEEKPIQEKEELALETSSSSSDEEDEKDEDEIEGLAASDDEQSGTHKIKRLNPKKQANEKKSKDKKTLEEYSGIIYVSRLPHGFHEKELSKYFAQFGDLKEVRLARNKKTGNSRHYGFLEFVNKEDAMIAQESMNNYLLMGHLLQVRVLPKGAKIEKLYKYKKRVLVEKGITKPVKQLKDNMKQKHEERIKKLAKSGIEFKW
60S ribosomal protein L3 F 387 Grouper Iridovirus , Burkholderia Vietnamiensis (Strain G4 / Lmg 22486) MSHRKYEAPRHGHLGFLPRKRAASIRARVKAFPKDDRSKPVALTSFLGYKAGMTTIVRDLDRPGSKFHKREVVEAVTVVDTPPVVVVGVVGYVETPRGLRSLTTVWAEHLSDEVKRRFYKNWYKSKKKAFTKYSAKYAQDGAGIERELARIKKYASVVRVLVHTQIRKTPLAQKKAHLAEIQLNGGSISEKVDWAREHFEKTVAVDSVFEQNEMIDAIAVTKGHGFEGVTHRWGTKKLPRKTHRGLRKVACIGAWHPAHVMWSVARAGQRGYHSRTSINHKIYRVGKGDDEANGATSFDRTKKTITPMGGFVHYGEIKNDFIMVKGCIPGNRKRIVTLRKSLYTNTSRKALEEVSLKWIDTASKFGKGRFQTPAEKHAFMGTLKKDL
60S ribosomal protein L4-A G 362 Grouper Iridovirus , Burkholderia Vietnamiensis (Strain G4 / Lmg 22486) MSRPQVTVHSLTGEATANALPLPAVFSAPIRPDIVHTVFTSVNKNKRQAYAVSEKAGHQTSAESWGTGRAVARIPRVGGGGTGRSGQGAFGNMCRGGRMFAPTKTWRKWNVKVNHNEKRYATASAIAATAVASLVLARGHRVEKIPEIPLVVSTDLESIQKTKEAVAALKAVGAHSDLLKVLKSKKLRAGKGKYRNRRWTQRRGPLVVYAEDNGIVKALRNVPGVETANVASLNLLQLAPGAHLGRFVIWTEAAFTKLDQVWGSETVASSKVGYTLPSHIISTSDVTRIINSSEIQSAIRPAGQATQKRTHVLKKNPLKNKQVLLRLNPYAKVFAAEKLGSKKAEKTGTKPAAVFTETLKHD
Proteasome-interacting protein CIC1 H 376 Grouper Iridovirus , Burkholderia Vietnamiensis (Strain G4 / Lmg 22486) MAKKSNSKKSTPVSTPSKEKKKVIEKKSSTAIPRERVIKAVNELIKFTSKPQDENNEEGNNGKKNLLEDDEEELKKDLQLIVVNNKSFTGTSKSFKLKLLNVKHSFYKPWKEASATAVKDFKVLLILKDSDIKKVSEDDLFDQLDSEGIKVDEIICGKDLKTVYKAYEARNAFISQFSLILADDSIVTSLPKLMGGKAYNKVETTPISIRTHANKEFSLTTLTNNIKKVYMNQLPVKLPRGTTLNVHLGNLEWLRPEEFVDNVELISEQLIKAYQIRSIFIKTNRSPVLPLYYNQDVLDELEAKKDKIEETHEDDMVTIDGVQVHLSTFNKGLMEIANPSELGSIFSKQINNAKKRSSSELEKESSESEAVKKAKS

Nucleic Acids / Hybrid
Molecule Chains Sequence Length Organism Sequence
ITS2 RNA c 232 NA CCUUCUCAAACAUUCUGUUUGGUAGUGAGUGAUACUCUUUGGAGUUAACUUGAAAUUGCUGGCCUUUUCAUUGGAUGUUUUUUUUCCAAAGAGAGGUUUCUCUGCGUGCUUGAGGUAUAAUGCAAGUACGGUCGUUUUAGGUUUUACCAACUGCGGCUAAUCUUUUUUUAUACUGAGCGUAUUGGAACGUUAUCGAUAAGAAGAGAGCGUCUAGGCGAACAAUGUUCUUAAA
Experimental Data

Method: ELECTRON MICROSCOPY

Deposited Date: 2018-01-06
Deposition Author(s): Ye, K. , Zhou, D. , Zhu, X.