8V87: 60S ribosome biogenesis intermediate

60S ribosome biogenesis intermediate (Dbp10 post-catalytic structure - Overall map). Determined by electron microscopy at 2.66 Å resolution. Released 1 May 2024.

Method
Electron microscopy
Resolution
2.66 Å
Organism
Saccharomyces cerevisiae BY4741
Chains
56
Atoms
150,186
Mol. weight
2997.72 kDa
Ligands
ADP, GDP, ZN, MG
Released
1 May 2024

Explore 8V87 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8V87 contains 594 α-helices and 468 β-strands across 53 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 3: 36 helices, 21 β-strands

ElementResiduesLengthSheet
α-helix146-1549
α-helix162-17211
β-strand177-179313
α-helix189-19810
β-strand210-213413
α-helix217-23115
β-strand238-241413
α-helix247-2559
β-strand260-263413
α-helix265-27511
α-helix279-2813
β-strand284-288513
α-helix290-2967
α-helix299-30810
β-strand314-318513
α-helix324-33310
β-strand338-340313
α-helix343-3464
α-helix348-3492
β-strand353114
β-strand356-358314
α-helix364-3707
α-helix371-3755
α-helix378-3825
α-helix383-39210
β-strand435-438414
α-helix441-45515
β-strand459-462414
α-helix468-48013
β-strand485-488414
α-helix490-4945
β-strand503-506414
α-helix513-5208
β-strand531-536614
α-helix541-55111
β-strand555-556215
α-helix558-57518
α-helix584-5885
β-strand593-594215
β-strand595-596214
β-strand597116
α-helix600-61617
α-helix619-63618
α-helix643-65412
β-strand660116
α-helix6611
α-helix662-6643
α-helix6671
α-helix670-67910
α-helix688-6914
α-helix697-72832
α-helix810-8156
β-strand858117
β-strand864117
α-helix873-8819
α-helix925-9284
α-helix936-94510
Chain 7: 8 helices, 5 β-strands
ElementResiduesLengthSheet
β-strand12-15430
β-strand20-21231
α-helix24-296
β-strand30132
α-helix38-403
α-helix43-464
α-helix47-6014
β-strand89-90233
α-helix981
β-strand99134
α-helix100-1012
α-helix106-11510
α-helix126-14722
Chain 8: 30 helices, 1 β-strand
ElementResiduesLengthSheet
α-helix6-149
α-helix16-3217
α-helix42-498
α-helix52-6110
α-helix71-766
α-helix79-824
α-helix266-28621
α-helix291-30313
α-helix305-3084
α-helix312-32817
α-helix332-34817
α-helix354-36916
α-helix377-39317
α-helix395-42026
α-helix431-4377
α-helix439-45517
α-helix458-4614
α-helix467-4715
α-helix472-48514
α-helix489-4913
α-helix492-50918
β-strand512136
α-helix516-5249
α-helix543-5453
α-helix549-5502
α-helix557-57721
α-helix584-60118
α-helix605-62925
α-helix639-6446
α-helix651-6533
α-helix655-67723
Chain a: 13 helices, 10 β-strands
ElementResiduesLengthSheet
α-helix6-1813
α-helix19-235
β-strand31-38837
β-strand52-53238
β-strand65-67339
α-helix71-799
β-strand84139
α-helix87-915
α-helix97-10610
β-strand109-111339
α-helix114-1174
α-helix120-1245
α-helix127-1315
α-helix1351
β-strand136139
α-helix1371
α-helix144-1529
β-strand155-156238
β-strand164-171837
α-helix176-19318
β-strand201-208837
α-helix212-2132
β-strand214-215237
Chain A: 8 helices, 15 β-strands
ElementResiduesLengthSheet
β-strand33-37540
α-helix43-5513
β-strand59-61340
α-helix72-8110
β-strand85-92840
β-strand96-102740
β-strand109-1181040
β-strand130141
β-strand133142
α-helix134-1352
β-strand136-139440
α-helix141-1444
α-helix147-16014
α-helix162-1632
β-strand170142
β-strand175-182840
β-strand185-1951140
β-strand196-197233
α-helix200-2034
β-strand210-214540
β-strand218-2291240
β-strand232-238740
α-helix245-27127
Chain b: 25 helices, 9 β-strands
ElementResiduesLengthSheet
α-helix8-136
α-helix14-2815
α-helix39-6729
α-helix76-8510
α-helix88-11528
α-helix116-1183
α-helix122-14120
α-helix144-15714
β-strand169-174643
α-helix180-1878
β-strand205-211743
β-strand214-220743
α-helix229-2313
α-helix234-24512
β-strand249-255743
α-helix264-27310
α-helix276-2783
β-strand282-288743
α-helix300-31112
β-strand315-319543
α-helix327-34317
α-helix344-3485
α-helix353-3619
β-strand363-364225
α-helix380-3845
α-helix385-3895
α-helix395-3973
α-helix399-4057
α-helix425-4284
α-helix430-4334
β-strand435-436244
β-strand439-440244
α-helix441-4444
α-helix449-46517
Chain B: 15 helices, 17 β-strands
ElementResiduesLengthSheet
α-helix14-163
α-helix33-353
α-helix40-412
β-strand42-43245
β-strand45-601646
β-strand70-801146
α-helix82-832
β-strand84-951247
β-strand98-106947
α-helix112-1154
α-helix116-1183
α-helix133-1375
α-helix142-15413
β-strand157-163747
α-helix166-1683
β-strand178-182547
β-strand183-184245
α-helix188-19811
β-strand202-203247
α-helix205-2073
β-strand214-220746
α-helix221-2222
β-strand223148
β-strand271148
β-strand274-2861346
β-strand299144
α-helix3071
β-strand321-325546
β-strand335-340646
α-helix348-3514
β-strand356-359446
α-helix373-3808
Chain c: 5 helices, 4 β-strands
ElementResiduesLengthSheet
α-helix10-2011
β-strand22-25449
α-helix27-3610
β-strand41-45549
α-helix50-6314
β-strand66-70549
α-helix74-818
β-strand89-94649
α-helix100-1034

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

Molecules and chains

MoleculeChainsTypeLengthOrganismUniProt
25S ribosomal RNA1RNA3396Saccharomyces cerevisiae BY4741
5.8S ribosomal RNA2RNA158Saccharomyces cerevisiae BY4741
ATP-dependent RNA helicase DBP103protein995Saccharomyces cerevisiae BY4741Q12389 (AlphaFold model)
ITS2 RNA6RNA232Saccharomyces cerevisiae BY4741
60S ribosomal subunit assembly/export protein LOC17protein204Saccharomyces cerevisiae BY4741P43586 (AlphaFold model)
Nucleolar complex protein 28protein710Saccharomyces cerevisiae BY4741P39744 (AlphaFold model)
Ribosome biogenesis protein BRX1Aprotein291Saccharomyces cerevisiae BY4741Q08235 (AlphaFold model)
60S ribosomal protein L3Bprotein387Saccharomyces cerevisiae BY4741P14126
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

44 more molecules are not listed.

Sequence of entity 1 (1), FASTA
>8V87_1 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
>8V87_2 5.8S ribosomal RNA (chains 2)
AAACUUUCAACAACGGAUCUCUUGGUUCUCGCAUCGAUGAAGAACGCAGCGAAAUGCGAU
ACGUAAUGUGAAUUGCAGAAUUCCGUGAAUCAUCGAAUCUUUGAACGCACAUUGCGCCCC
UUGGUAUUCCAGGGGGCAUGCCUGUUUGAGCGUCAUUU
Sequence of entity 3 (3), FASTA
>8V87_3 ATP-dependent RNA helicase DBP10 (chains 3)
MAGVQKRKRDLEDQDDNGSEEDDIAFDIANEIALNDSESDANDSDSEVEADYGPNDVQDV
IEYSSDEEEGVNNKKKAENKDIKKKKNSKKEIAAFPMLEMSDDENNASGKTQTGDDEDDV
NEYFSTNNLEKTKHKKGSFPSFGLSKIVLNNIKRKGFRQPTPIQRKTIPLILQSRDIVGM
ARTGSGKTAAFILPMVEKLKSHSGKIGARAVILSPSRELAMQTFNVFKDFARGTELRSVL
LTGGDSLEEQFGMMMTNPDVIIATPGRFLHLKVEMNLDLKSVEYVVFDEADRLFEMGFQE
QLNELLASLPTTRQTLLFSATLPNSLVDFVKAGLVNPVLVRLDAETKVSENLEMLFLSSK
NADREANLLYILQEIIKIPLATSEQLQKLQNSNNEADSDSDDENDRQKKRRNFKKEKFRK
QKMPAANELPSEKATILFVPTRHHVEYISQLLRDCGYLISYIYGTLDQHARKRQLYNFRA
GLTSILVVTDVAARGVDIPMLANVINYTLPGSSKIFVHRVGRTARAGNKGWAYSIVAENE
LPYLLDLELFLGKKILLTPMYDSLVDVMKKRWIDEGKPEYQFQPPKLSYTKRLVLGSCPR
LDVEGLGDLYKNLMSSNFDLQLAKKTAMKAEKLYYRTRTSASPESLKRSKEIISSGWDAQ
NAFFGKNEEKEKLDFLAKLQNRRNKETVFEFTRNPDDEMAVFMKRRRKQLAPIQRKATER
RELLEKERMAGLSHSIEDEILKGDDGETGYTVSEDALKEFEDADQLLEAQENENKKKKKP
KSFKDPTFFLSHYAPAGDIQDKQLQITNGFANDAAQAAYDLNSDDKVQVHKQTATVKWDK
KRKKYVNTQGIDNKKYIIGESGQKIAASFRSGRFDDWSKARNLKPLKVGSRETSIPSNLL
EDPSQGPAANGRTVRGKFKHKQMKAPKMPDKHRDNYYSQKKKVEKALQSGISVKGYNNAP
GLRSELKSTEQIRKDRIIAEKKRAKNARPSKKRKF
Sequence of entity 4 (6), FASTA
>8V87_4 ITS2 RNA (chains 6)
CCUUCUCAAACAUUCUGUUUGGUAGUGAGUGAUACUCUUUGGAGUUAACUUGAAAUUGCU
GGCCUUUUCAUUGGAUGUUUUUUUUCCAAAGAGAGGUUUCUCUGCGUGCUUGAGGUAUAA
UGCAAGUACGGUCGUUUUAGGUUUUACCAACUGCGGCUAAUCUUUUUUUAUACUGAGCGU
AUUGGAACGUUAUCGAUAAGAAGAGAGCGUCUAGGCGAACAAUGUUCUUAAA
Sequence of entity 5 (7), FASTA
>8V87_5 60S ribosomal subunit assembly/export protein LOC1 (chains 7)
MAPKKPSKRQNLRREVAPEVFQDSQARNQLANVPHLTEKSAQRKPSKTKVKKEQSLARLY
GAKKDKKGKYSEKDLNIPTLNRAIVPGVKIRRGKKGKKFIADNDTLTLNRLITTIGDKYD
DIAESKLEKARRLEEIRELKRKEIERKEALKQDKLEEKKDEIKKKSSVARTIRRKNKRDM
LKSEAKASESKTEGRKVKKVSFAQ
Sequence of entity 6 (8), FASTA
>8V87_6 Nucleolar complex protein 2 (chains 8)
MGKVSKSTKKFQSKHLKHTLDQRRKEKIQKKRIQGRRGNKTDQEKADAAGTREQQQLKKS
AKEEVFKDMSVETFFEKGIEIPKENKKLKKKTTKEQSDEDSSSSEEEEDMGQSMAKLAEK
DPEFYKYLEENDKDLLDFAGTNPLDGIDSQDEGEDAERNSNIEEKSEQMELEKEKIELSL
KLVRKWKKQLHDSPSLKLLRNIISAFKVAVNLNKEENIEDYKYAITDEKAFHELMFMVLK
DVPQAIQKMAPYKIVKGARTLPNGGNVSRVSSIVKSHAGSLLILLNDITNTETAALVLHS
VNELMPYLLSYRRILKELIKSIVGVWSTTRELETQIASFAFLINTTKEFKKSMLETTLKT
TYSTFIKSCRKTNMRSMPLINFQKNSAAELFGIDEVLGYQVGFEYIRQLAIHLRNTMNAT
TKKSSKINSAEAYKIVYNWQFCHSLDFWSRVLSFACQPEKENGSESPLRQLIYPLVQVTL
GVIRLIPTPQFFPLRFYLIKSLIRLSQNSGVFIPIYPLLSEILTSTAFTKAPKKSPNLAA
FDFEHNIKCTQAYLNTKIYQEGLSEQFVDLLGDYFALYCKNIAFPELVTPVIISLRRYIK
TSTNVKLNKRLSTVVEKLNQNSTFIQEKRSDVEFGPTNKSEVSRFLNDVAWNKTPLGSYV
AVQREVKEEKARLMRESMEEQDKERETEEAKLLNSLESDDDNEDVEMSDA
Sequence of entity 7 (A), FASTA
>8V87_7 Ribosome biogenesis protein BRX1 (chains A)
MSSIYKALAGKSKDNKSEKKQGNVKQFMNKQRTLLISSRGVNYRHRHLIQDLSGLLPHSR
KEPKLDTKKDLQQLNEIAELYNCNNVLFFEARKHQDLYLWLSKPPNGPTIKFYIQNLHTM
DELNFTGNCLKGSRPVLSFDQRFESSPHYQLIKELLVHNFGVPPNARKSKPFIDHVMSFS
IVDDKIWVRTYEISHSTKNKEEYEDGEEDISLVEIGPRFVMTVILILEGSFGGPKIYENK
QYVSPNVVRAQIKQQAAEEAKSRAEAAVERKIKRRENVLAADPLSNDALFK
Sequence of entity 8 (B), FASTA
>8V87_8 60S ribosomal protein L3 (chains B)
MSHRKYEAPRHGHLGFLPRKRAASIRARVKAFPKDDRSKPVALTSFLGYKAGMTTIVRDL
DRPGSKFHKREVVEAVTVVDTPPVVVVGVVGYVETPRGLRSLTTVWAEHLSDEVKRRFYK
NWYKSKKKAFTKYSAKYAQDGAGIERELARIKKYASVVRVLVHTQIRKTPLAQKKAHLAE
IQLNGGSISEKVDWAREHFEKTVAVDSVFEQNEMIDAIAVTKGHGFEGVTHRWGTKKLPR
KTHRGLRKVACIGAWHPAHVMWSVARAGQRGYHSRTSINHKIYRVGKGDDEANGATSFDR
TKKTITPMGGFVHYGEIKNDFIMVKGCIPGNRKRIVTLRKSLYTNTSRKALEEVSLKWID
TASKFGKGRFQTPAEKHAFMGTLKKDL
Sequence of entity 9 (C), FASTA
>8V87_9 60S ribosomal protein L4-A (chains C)
MSRPQVTVHSLTGEATANALPLPAVFSAPIRPDIVHTVFTSVNKNKRQAYAVSEKAGHQT
SAESWGTGRAVARIPRVGGGGTGRSGQGAFGNMCRGGRMFAPTKTWRKWNVKVNHNEKRY
ATASAIAATAVASLVLARGHRVEKIPEIPLVVSTDLESIQKTKEAVAALKAVGAHSDLLK
VLKSKKLRAGKGKYRNRRWTQRRGPLVVYAEDNGIVKALRNVPGVETANVASLNLLQLAP
GAHLGRFVIWTEAAFTKLDQVWGSETVASSKVGYTLPSHIISTSDVTRIINSSEIQSAIR
PAGQATQKRTHVLKKNPLKNKQVLLRLNPYAKVFAAEKLGSKKAEKTGTKPAAVFTETLK
HD
Sequence of entity 10 (D), FASTA
>8V87_10 ATP-dependent RNA helicase HAS1 (chains D)
MATPSNKRSRDSESTEEPVVDEKSTSKQNNAAPEGEQTTCVEKFEELKLSQPTLKAIEKM
GFTTMTSVQARTIPPLLAGRDVLGAAKTGSGKTLAFLIPAIELLHSLKFKPRNGTGIIVI
TPTRELALQIFGVARELMEFHSQTFGIVIGGANRRQEAEKLMKGVNMLIATPGRLLDHLQ
NTKGFVFKNLKALIIDEADRILEIGFEDEMRQIIKILPNEDRQSMLFSATQTTKVEDLAR
ISLRPGPLFINVVPETDNSTADGLEQGYVVCDSDKRFLLLFSFLKRNQKKKIIVFLSSCN
SVKYYAELLNYIDLPVLELHGKQKQQKRTNTFFEFCNAERGILICTDVAARGLDIPAVDW
IIQFDPPDDPRDYIHRVGRTARGTKGKGKSLMFLTPNELGFLRYLKASKVPLNEYEFPEN
KIANVQSQLEKLIKSNYYLHQTAKDGYRSYLQAYASHSLKTVYQIDKLDLAKVAKSYGFP
VPPKVNITIGASGKTPNTKRRKTHK
Sequence of entity 11 (E), FASTA
>8V87_11 60S ribosomal protein L6-A (chains E)
MSAQKAPKWYPSEDVAALKKTRKAARPQKLRASLVPGTVLILLAGRFRGKRVVYLKHLED
NTLLISGPFKVNGVPLRRVNARYVIATSTKVSVEGVNVEKFNVEYFAKEKLTKKEKKEAN
LFPEQQNKEIKAERVEDQKVVDKALIAEIKKTPLLKQYLSASFSLKNGDKPHMLKF
Sequence of entity 12 (F), FASTA
>8V87_12 60S ribosomal protein L7-A (chains F)
MAAEKILTPESQLKKSKAQQKTAEQVAAERAARKAANKEKRAIILERNAAYQKEYETAER
NIIQAKRDAKAAGSYYVEAQHKLVFVVRIKGINKIPPKPRKVLQLLRLTRINSGTFVKVT
KATLELLKLIEPYVAYGYPSYSTIRQLVYKRGFGKINKQRVPLSDNAIIEANLGKYGILS
IDDLIHEIITVGPHFKQANNFLWPFKLSNPSGGWGVPRKFKHFIQGGSFGNREEFINKLV
KSMN

Ligands and cofactors

IDNameFormulaCopies
ADPAdenosine-5'-diphosphateC10 H15 N5 O10 P21
GDPGuanosine-5'-diphosphateC10 H15 N5 O11 P21
ZNZinc ionZn2
MGMagnesium ionMg2

Water and common crystallization additives (K) are not listed.

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 Q12389 (AlphaFold model), which also has an AlphaFold model), best resolution first:

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