8V83: 60S ribosome biogenesis intermediate

60S ribosome biogenesis intermediate (Dbp10 pre-catalytic structure - Overall map). Determined by electron microscopy at 2.53 Å resolution. Released 1 May 2024.

Method
Electron microscopy
Resolution
2.53 Å
Organism
Saccharomyces cerevisiae BY4741
Chains
48
Atoms
119,224
Mol. weight
2681.05 kDa
Ligands
ZN
Released
1 May 2024

Explore 8V83 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8V83 contains 463 α-helices and 406 β-strands across 45 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain 7: 1 helix, 0 β-strands

ElementResiduesLengthSheet
α-helix106-1149
Chain 8: 5 helices, 6 β-strands
ElementResiduesLengthSheet
β-strand263-265311
β-strand268115
β-strand269116
β-strand275116
β-strand276117
β-strand283117
α-helix297-31317
α-helix316-33621
α-helix344-39350
α-helix398-4003
α-helix401-4088
Chain a: 9 helices, 9 β-strands
ElementResiduesLengthSheet
α-helix9-2214
β-strand32-37612
β-strand53113
β-strand65-69514
α-helix71-8010
β-strand85-86214
α-helix87-915
α-helix97-10610
β-strand109-112414
α-helix120-1245
α-helix127-1315
α-helix144-1529
β-strand155113
β-strand164-170712
α-helix176-19318
β-strand205-208412
α-helix211-2133
β-strand214-215212
Chain A: 10 helices, 14 β-strands
ElementResiduesLengthSheet
β-strand33-37520
β-strand38121
α-helix43-5513
β-strand59-61320
α-helix63-642
β-strand65121
α-helix73-819
β-strand85-92820
β-strand96-102720
β-strand109-1181020
β-strand130122
α-helix1331
β-strand134-140720
α-helix141-1444
α-helix147-16014
α-helix162-1632
β-strand173-1821020
β-strand185-1951120
β-strand210-214520
β-strand218-2271020
β-strand235-238420
α-helix245-27632
α-helix280-2823
α-helix286-2894
Chain b: 22 helices, 8 β-strands
ElementResiduesLengthSheet
α-helix8-103
α-helix14-2815
α-helix39-6628
α-helix71-733
α-helix76-8510
α-helix88-11730
α-helix122-14221
α-helix144-15714
β-strand169-174618
α-helix180-1878
β-strand205-211718
β-strand214-220718
α-helix221-2233
α-helix234-24512
β-strand248-253618
α-helix264-27411
α-helix275-2784
β-strand283-286418
α-helix306-3116
β-strand315-318418
α-helix325-34016
α-helix380-3834
α-helix386-3883
α-helix396-3972
α-helix399-4068
α-helix416-4194
β-strand435-436219
β-strand439-440219
α-helix441-4444
α-helix449-46618
Chain B: 13 helices, 17 β-strands
ElementResiduesLengthSheet
α-helix33-353
β-strand42-43224
β-strand45-601625
β-strand70-801125
α-helix82-832
β-strand84-951226
β-strand98-106926
α-helix112-1154
α-helix116-1183
α-helix131-1399
α-helix142-15413
β-strand157-163726
α-helix176-1772
β-strand178-182526
β-strand183-184224
α-helix188-19811
β-strand202-203226
α-helix205-2073
β-strand214-220725
α-helix221-2233
β-strand274-2861325
β-strand299119
α-helix3071
β-strand311127
β-strand315127
β-strand321-325525
β-strand335-340625
α-helix348-3514
β-strand356-359425
α-helix373-3808
Chain C: 24 helices, 12 β-strands
ElementResiduesLengthSheet
β-strand5-9529
β-strand15-21729
α-helix22-232
α-helix24-274
α-helix32-4211
α-helix47-493
β-strand62-64330
β-strand75-77330
β-strand88130
α-helix98-992
α-helix115-12915
α-helix132-1387
β-strand150-152329
α-helix154-1585
α-helix162-17110
α-helix175-1839
β-strand186-187231
α-helix1881
α-helix191-1944
β-strand199-200231
β-strand206-209429
α-helix215-2195
β-strand226-229429
α-helix235-2384
α-helix240-2423
β-strand248-251429
α-helix252-26211
β-strand267132
α-helix276-2794
α-helix286-2905
α-helix293-2964
α-helix300-3023
α-helix307-3093
α-helix321-3277
α-helix330-3378
α-helix339-3413
Chain D: 24 helices, 16 β-strands
ElementResiduesLengthSheet
β-strand43134
α-helix51-6010
β-strand64134
α-helix67-7812
β-strand82-85435
α-helix92-10716
α-helix111-1133
β-strand117-120435
α-helix124-13714
α-helix138-1403
β-strand145-148435
α-helix154-16310
β-strand167-170435
α-helix172-18110
β-strand192-196535
α-helix198-2047
α-helix207-21610
β-strand223-228635
α-helix233-24210
α-helix2441
β-strand248-251435
β-strand267-270436
α-helix273-28614
β-strand291-296636
α-helix299-31113
β-strand317-319336
α-helix325-33713
β-strand341-346636
α-helix347-3504
β-strand360-363436
α-helix366-3672
α-helix370-3734
β-strand389-394636
α-helix396-3983
α-helix401-4077
β-strand414136
α-helix426-43510
α-helix437-45620
α-helix470-4778
α-helix482-4843

37 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

MoleculeChainsTypeLengthOrganismUniProt
Saccharomyces cerevisiae S288C 25S ribosomal RNA1RNA3396Saccharomyces cerevisiae BY4741
Saccharomyces cerevisiae S288C 5.8S ribosomal RNA2RNA158Saccharomyces cerevisiae BY4741
Saccharomyces cerevisiae ITS-26RNA232Saccharomyces cerevisiae BY4741
60S ribosomal subunit assembly/export protein LOC17protein204Saccharomyces cerevisiae BY4741P43586 (AlphaFold model)
Ribosomal RNA-processing protein 148protein434Saccharomyces cerevisiae BY4741P36080 (AlphaFold model)
Ribosome biogenesis protein BRX1Aprotein291Saccharomyces cerevisiae BY4741Q08235 (AlphaFold model)
60S ribosomal protein L3Bprotein387Saccharomyces cerevisiae BY4741P14126 (AlphaFold model)
60S ribosomal protein L4-ACprotein362Saccharomyces cerevisiae BY4741P10664
ATP-dependent RNA helicase HAS1Dprotein505Saccharomyces cerevisiae BY4741Q03532
60S ribosomal protein L6-AEprotein176Saccharomyces cerevisiae BY4741Q02326
60S ribosomal protein L7-AFprotein244Saccharomyces cerevisiae BY4741P05737
Large ribosomal subunit protein eL8AGprotein256Saccharomyces cerevisiae BY4741P17076

36 more molecules are not listed.

Sequence of entity 1 (1), FASTA
>8V83_1 Saccharomyces cerevisiae S288C 25S ribosomal RNA (chains 1)
GUUUGACCUCAAAUCAGGUAGGAGUACCCGCUGAACUUAAGCAUAUCAAUAAGCGGAGGA
AAAGAAACCAACCGGGAUUGCCUUAGUAACGGCGAGUGAAGCGGCAAAAGCUCAAAUUUG
AAAUCUGGUACCUUCGGUGCCCGAGUUGUAAUUUGGAGAGGGCAACUUUGGGGCCGUUCC
UUGUCUAUGUUCCUUGGAACAGGACGUCAUAGAGGGUGAGAAUCCCGUGUGGCGAGGAGU
GCGGUUCUUUGUAAAGUGCCUUCGAAGAGUCGAGUUGUUUGGGAAUGCAGCUCUAAGUGG
GUGGUAAAUUCCAUCUAAAGCUAAAUAUUGGCGAGAGACCGAUAGCGAACAAGUACAGUG
AUGGAAAGAUGAAAAGAACUUUGAAAAGAGAGUGAAAAAGUACGUGAAAUUGUUGAAAGG
GAAGGGCAUUUGAUCAGACAUGGUGUUUUGUGCCCUCUGCUCCUUGUGGGUAGGGGAAUC
UCGCAUUUCACUGGGCCAGCAUCAGUUUUGGUGGCAGGAUAAAUCCAUAGGAAUGUAGCU
UGCCUCGGUAAGUAUUAUAGCCUGUGGGAAUACUGCCAGCUGGGACUGAGGACUGCGACG
UAAGUCAAGGAUGCUGGCAUAAUGGUUAUAUGCCGCCCGUCUUGAAACACGGACCAAGGA
GUCUAACGUCUAUGCGAGUGUUUGGGUGUAAAACCCAUACGCGUAAUGAAAGUGAACGUA
GGUUGGGGCCUCGCAAGAGGUGCACAAUCGACCGAUCCUGAUGUCUUCGGAUGGAUUUGA
GUAAGAGCAUAGCUGUUGGGACCCGAAAGAUGGUGAACUAUGCCUGAAUAGGGUGAAGCC
AGAGGAAACUCUGGUGGAGGCUCGUAGCGGUUCUGACGUGCAAAUCGAUCGUCGAAUUUG
GGUAUAGGGGCGAAAGACUAAUCGAACCAUCUAGUAGCUGGUUCCUGCCGAAGUUUCCCU
CAGGAUAGCAGAAGCUCGUAUCAGUUUUAUGAGGUAAAGCGAAUGAUUAGAGGUUCCGGG
GUCGAAAUGACCUUGACCUAUUCUCAAACUUUAAAUAUGUAAGAAGUCCUUGUUACUUAA
UUGAACGUGGACAUUUGAAUGAAGAGCUUUUAGUGGGCCAUUUUUGGUAAGCAGAACUGG
CGAUGCGGGAUGAACCGAACGUAGAGUUAAGGUGCCGGAAUACACGCUCAUCAGACACCA
CAAAAGGUGUUAGUUCAUCUAGACAGCCGGACGGUGGCCAUGGAAGUCGGAAUCCGCUAA
GGAGUGUGUAACAACUCACCGGCCGAAUGAACUAGCCCUGAAAAUGGAUGGCGCUCAAGC
GUGUUACCUAUACUCUACCGUCAGGGUUGAUAUGAUGCCCUGACGAGUAGGCAGGCGUGG
AGGUCAGUGACGAAGCCUAGACCGUAAGGUCGGGUCGAACGGCCUCUAGUGCAGAUCUUG
GUGGUAGUAGCAAAUAUUCAAAUGAGAACUUUGAAGACUGAAGUGGGGAAAGGUUCCACG
UCAACAGCAGUUGGACGUGGGUUAGUCGAUCCUAAGAGAUGGGGAAGCUCCGUUUCAAAG
GCCUGAUUUUAUGCAGGCCACCAUCGAAAGGGAAUCCGGUUAAGAUUCCGGAACCUGGAU
AUGGAUUCUUCACGGUAACGUAACUGAAUGUGGAGACGUCGGCGCGAGCCCUGGGAGGAG
UUAUCUUUUCUUCUUAACAGCUUAUCACCCCGGAAUUGGUUUAUCCGGAGAUGGGGUCUU
AUGGCUGGAAGAGGCCAGCACCUUUGCUGGCUCCGGUGCGCUUGUGACGGCCCGUGAAAA
UCCACAGGAAGGAAUAGUUUUCAUGCCAGGUCGUACUGAUAACCGCAGCAGGUCUCCAAG
GUGAACAGCCUCUAGUUGAUAGAAUAAUGUAGAUAAGGGAAGUCGGCAAAAUAGAUCCGU
AACUUCGGGAUAAGGAUUGGCUCUAAGGGUCGGGUAGUGAGGGCCUUGGUCAGACGCAGC
GGGCGUGCUUGUGGACUGCUUGGUGGGGCUUGCUCUGCUAGGCGGACUACUUGCGUGCCU
UGUUGUAGACGGCCUUGGUAGGUCUCUUGUAGACCGUCGCUUGCUACAAUUAACGAUCAA
CUUAGAACUGGUACGGACAAGGGGAAUCUGACUGUCUAAUUAAAACAUAGCAUUGCGAUG
GUCAGAAAGUGAUGUUGACGCAAUGUGAUUUCUGCCCAGUGCUCUGAAUGUCAAAGUGAA
GAAAUUCAACCAAGCGCGGGUAAACGGCGGGAGUAACUAUGACUCUCUUAAGGUAGCCAA
AUGCCUCGUCAUCUAAUUAGUGACGCGCAUGAAUGGAUUAACGAGAUUCCCACUGUCCCU
AUCUACUAUCUAGCGAAACCACAGCCAAGGGAACGGGCUUGGCAGAAUCAGCGGGGAAAG
AAGACCCUGUUGAGCUUGACUCUAGUUUGACAUUGUGAAGAGACAUAGAGGGUGUAGAAU
AAGUGGGAGCUUCGGCGCCAGUGAAAUACCACUACCUUUAUAGUUUCUUUACUUAUUCAA
UGAAGCGGAGCUGGAAUUCAUUUUCCACGUUCUAGCAUUCAAGGUCCCAUUCGGGGCUGA
UCCGGGUUGAAGACAUUGUCAGGUGGGGAGUUUGGCUGGGGCGGCACAUCUGUUAAACGA
UAACGCAGAUGUCCUAAGGGGGGCUCAUGGAGAACAGAAAUCUCCAGUAGAACAAAAGGG
UAAAAGCCCCCUUGAUUUUGAUUUUCAGUGUGAAUACAAACCAUGAAAGUGUGGCCUAUC
GAUCCUUUAGUCCCUCGGAAUUUGAGGCUAGAGGUGCCAGAAAAGUUACCACAGGGAUAA
CUGGCUUGUGGCAGUCAAGCGUUCAUAGCGACAUUGCUUUUUGAUUCUUCGAUGUCGGCU
CUUCCUAUCAUACCGAAGCAGAAUUCGGUAAGCGUUGGAUUGUUCACCCACUAAUAGGGA
ACGUGAGCUGGGUUUAGACCGUCGUGAGACAGGUUAGUUUUACCCUACUGAUGAAUGUUA
CCGCAAUAGUAAUUGAACUUAGUACGAGAGGAACAGUUCAUUCGGAUAAUUGGUUUUUGC
GGCUGUCUGAUCAGGCAUUGCCGCGAAGCUACCAUCCGCUGGAUUAUGGCUGAACGCCUC
UAAGUCAGAAUCCAUGCUAGAACGCGGUGAUUUCUUUGCUCCACACAAUAUAGAUGGAUA
CGAAUAAGGCGUCCUUGUGGCGUCGCUGAACCAUAGCAGGCUAGCAACGGUGCACUUGGC
GGAAAGGCCUUGGGUGCUUGCUGGCGAAUUGCAAUGUCAUUUUGCGUGGGGAUAAAUCAU
UUGUAUACGACUUAGAUGUACAACGGGGUAUUGUAAGCAGUAGAGUAGCCUUGUUGUUAC
GAUCUGCUGAGAUUAAGCCUUUGUUGUCUGAUUUGU
Sequence of entity 2 (2), FASTA
>8V83_2 Saccharomyces cerevisiae S288C 5.8S ribosomal RNA (chains 2)
AAACUUUCAACAACGGAUCUCUUGGUUCUCGCAUCGAUGAAGAACGCAGCGAAAUGCGAU
ACGUAAUGUGAAUUGCAGAAUUCCGUGAAUCAUCGAAUCUUUGAACGCACAUUGCGCCCC
UUGGUAUUCCAGGGGGCAUGCCUGUUUGAGCGUCAUUU
Sequence of entity 3 (6), FASTA
>8V83_3 Saccharomyces cerevisiae ITS-2 (chains 6)
CCUUCUCAAACAUUCUGUUUGGUAGUGAGUGAUACUCUUUGGAGUUAACUUGAAAUUGCU
GGCCUUUUCAUUGGAUGUUUUUUUUCCAAAGAGAGGUUUCUCUGCGUGCUUGAGGUAUAA
UGCAAGUACGGUCGUUUUAGGUUUUACCAACUGCGGCUAAUCUUUUUUUAUACUGAGCGU
AUUGGAACGUUAUCGAUAAGAAGAGAGCGUCUAGGCGAACAAUGUUCUUAAA
Sequence of entity 4 (7), FASTA
>8V83_4 60S ribosomal subunit assembly/export protein LOC1 (chains 7)
MAPKKPSKRQNLRREVAPEVFQDSQARNQLANVPHLTEKSAQRKPSKTKVKKEQSLARLY
GAKKDKKGKYSEKDLNIPTLNRAIVPGVKIRRGKKGKKFIADNDTLTLNRLITTIGDKYD
DIAESKLEKARRLEEIRELKRKEIERKEALKQDKLEEKKDEIKKKSSVARTIRRKNKRDM
LKSEAKASESKTEGRKVKKVSFAQ
Sequence of entity 5 (8), FASTA
>8V83_5 Ribosomal RNA-processing protein 14 (chains 8)
MSNSLEERLRANSSAFDGLLALIPAKYYYDEKSQEQWKAKKKTKEQSKNDKLKKLDPEQR
DDETSSTLEVMKKKEKDAKPVVLPGEKFKHMKMQKQKEATSKVEGDSDLNVEVNDPMIIA
PDEDEEEEEDIKVIFDDEGNEIPLESKKDTTEPDRSVEKKSITEEEKLQRKKNLEALRSK
LQAKISDMKSKRKAPGSREAILAQRKRKEELKKRKRLESEQEQDQDEIASDSDMEDIDSD
LENNSKKRFKKGKKDSEINADGVMFQNIIFDDGARATSDLQRLRKAGRTKGPAKNDVKSH
LKLLEAKKNKMEAKDELEQIKQKEKEKWQKAMLQAEGIKIRDDEKLLRKAIKRKEAQKRK
SAIEWSERKRVVEDTISERQKRREENLRIRKDNKGKKRNKQEKMKRKYVGSAVPKKRAGF
EGRLKTGKKKGGPK
Sequence of entity 6 (A), FASTA
>8V83_6 Ribosome biogenesis protein BRX1 (chains A)
MSSIYKALAGKSKDNKSEKKQGNVKQFMNKQRTLLISSRGVNYRHRHLIQDLSGLLPHSR
KEPKLDTKKDLQQLNEIAELYNCNNVLFFEARKHQDLYLWLSKPPNGPTIKFYIQNLHTM
DELNFTGNCLKGSRPVLSFDQRFESSPHYQLIKELLVHNFGVPPNARKSKPFIDHVMSFS
IVDDKIWVRTYEISHSTKNKEEYEDGEEDISLVEIGPRFVMTVILILEGSFGGPKIYENK
QYVSPNVVRAQIKQQAAEEAKSRAEAAVERKIKRRENVLAADPLSNDALFK
Sequence of entity 7 (B), FASTA
>8V83_7 60S ribosomal protein L3 (chains B)
MSHRKYEAPRHGHLGFLPRKRAASIRARVKAFPKDDRSKPVALTSFLGYKAGMTTIVRDL
DRPGSKFHKREVVEAVTVVDTPPVVVVGVVGYVETPRGLRSLTTVWAEHLSDEVKRRFYK
NWYKSKKKAFTKYSAKYAQDGAGIERELARIKKYASVVRVLVHTQIRKTPLAQKKAHLAE
IQLNGGSISEKVDWAREHFEKTVAVDSVFEQNEMIDAIAVTKGHGFEGVTHRWGTKKLPR
KTHRGLRKVACIGAWHPAHVMWSVARAGQRGYHSRTSINHKIYRVGKGDDEANGATSFDR
TKKTITPMGGFVHYGEIKNDFIMVKGCIPGNRKRIVTLRKSLYTNTSRKALEEVSLKWID
TASKFGKGRFQTPAEKHAFMGTLKKDL
Sequence of entity 8 (C), FASTA
>8V83_8 60S ribosomal protein L4-A (chains C)
MSRPQVTVHSLTGEATANALPLPAVFSAPIRPDIVHTVFTSVNKNKRQAYAVSEKAGHQT
SAESWGTGRAVARIPRVGGGGTGRSGQGAFGNMCRGGRMFAPTKTWRKWNVKVNHNEKRY
ATASAIAATAVASLVLARGHRVEKIPEIPLVVSTDLESIQKTKEAVAALKAVGAHSDLLK
VLKSKKLRAGKGKYRNRRWTQRRGPLVVYAEDNGIVKALRNVPGVETANVASLNLLQLAP
GAHLGRFVIWTEAAFTKLDQVWGSETVASSKVGYTLPSHIISTSDVTRIINSSEIQSAIR
PAGQATQKRTHVLKKNPLKNKQVLLRLNPYAKVFAAEKLGSKKAEKTGTKPAAVFTETLK
HD
Sequence of entity 9 (D), FASTA
>8V83_9 ATP-dependent RNA helicase HAS1 (chains D)
MATPSNKRSRDSESTEEPVVDEKSTSKQNNAAPEGEQTTCVEKFEELKLSQPTLKAIEKM
GFTTMTSVQARTIPPLLAGRDVLGAAKTGSGKTLAFLIPAIELLHSLKFKPRNGTGIIVI
TPTRELALQIFGVARELMEFHSQTFGIVIGGANRRQEAEKLMKGVNMLIATPGRLLDHLQ
NTKGFVFKNLKALIIDEADRILEIGFEDEMRQIIKILPNEDRQSMLFSATQTTKVEDLAR
ISLRPGPLFINVVPETDNSTADGLEQGYVVCDSDKRFLLLFSFLKRNQKKKIIVFLSSCN
SVKYYAELLNYIDLPVLELHGKQKQQKRTNTFFEFCNAERGILICTDVAARGLDIPAVDW
IIQFDPPDDPRDYIHRVGRTARGTKGKGKSLMFLTPNELGFLRYLKASKVPLNEYEFPEN
KIANVQSQLEKLIKSNYYLHQTAKDGYRSYLQAYASHSLKTVYQIDKLDLAKVAKSYGFP
VPPKVNITIGASGKTPNTKRRKTHK
Sequence of entity 10 (E), FASTA
>8V83_10 60S ribosomal protein L6-A (chains E)
MSAQKAPKWYPSEDVAALKKTRKAARPQKLRASLVPGTVLILLAGRFRGKRVVYLKHLED
NTLLISGPFKVNGVPLRRVNARYVIATSTKVSVEGVNVEKFNVEYFAKEKLTKKEKKEAN
LFPEQQNKEIKAERVEDQKVVDKALIAEIKKTPLLKQYLSASFSLKNGDKPHMLKF
Sequence of entity 11 (F), FASTA
>8V83_11 60S ribosomal protein L7-A (chains F)
MAAEKILTPESQLKKSKAQQKTAEQVAAERAARKAANKEKRAIILERNAAYQKEYETAER
NIIQAKRDAKAAGSYYVEAQHKLVFVVRIKGINKIPPKPRKVLQLLRLTRINSGTFVKVT
KATLELLKLIEPYVAYGYPSYSTIRQLVYKRGFGKINKQRVPLSDNAIIEANLGKYGILS
IDDLIHEIITVGPHFKQANNFLWPFKLSNPSGGWGVPRKFKHFIQGGSFGNREEFINKLV
KSMN
Sequence of entity 12 (G), FASTA
>8V83_12 Large ribosomal subunit protein eL8A (chains G)
MAPGKKVAPAPFGAKSTKSNKTRNPLTHSTPKNFGIGQAVQPKRNLSRYVKWPEYVRVQR
QKKILSIRLKVPPTIAQFQYTLDRNTAAETFKLFNKYRPETAAEKKERLTKEAAAVAEGK
SKQDASPKPYAVKYGLNHVVALIENKKAKLVLIANDVDPIELVVFLPALCKKMGVPYAIV
KGKARLGTLVNQKTSAVAALTEVRAEDEAALAKLVSTIDANFADKYDEVKKHWGGGILGN
KAQAKMDKRAKNSDSA

Ligands and cofactors

IDNameFormulaCopies
ZNZinc ionZn2

Primary citation

The DEAD-box ATPase Dbp10/DDX54 initiates peptidyl transferase center formation during 60S ribosome biogenesis. Cruz, V.E., Weirich, C.S., Peddada, N. et al. Nat Commun (2024) 15:3296-3296. DOI 10.1038/s41467-024-47616-7 · PubMed

Other PDB entries of the same protein (UniProt P43586 (AlphaFold model), which also has an AlphaFold model), best resolution first:

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