7R7A: PDB entry 7R7A

State E1 nucleolar 60S ribosome biogenesis intermediate - Composite model. Determined by electron microscopy at 3.04 Å resolution. Released 9 Nov 2022.

Method
Electron microscopy
Resolution
3.04 Å
Organism
Saccharomyces cerevisiae BY4741
Chains
57
Atoms
153,087
Mol. weight
2924.75 kDa
Ligands
ZN
Released
9 Nov 2022

Explore 7R7A in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7R7A contains 568 α-helices and 492 β-strands across 54 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: 9 helices, 5 β-strands

ElementResiduesLengthSheet
β-strand12-1546
β-strand20-2127
α-helix24-274
β-strand3018
α-helix37-393
α-helix47-5913
α-helix78-803
β-strand89-9029
α-helix911
α-helix981
β-strand99110
α-helix100-1012
α-helix105-11511
α-helix126-14520
Chain 8: 25 helices, 1 β-strand
ElementResiduesLengthSheet
α-helix6-149
α-helix16-3419
α-helix42-498
α-helix52-6110
α-helix71-744
α-helix79-824
α-helix268-28619
α-helix292-30211
α-helix314-32815
α-helix336-34813
α-helix355-36612
α-helix377-39115
α-helix397-41923
α-helix432-4365
α-helix439-45517
α-helix469-4713
α-helix472-48514
α-helix492-50918
β-strand512181
α-helix516-5249
α-helix526-5283
α-helix557-57620
α-helix584-59916
α-helix605-62824
α-helix641-6444
α-helix655-67723
Chain a: 9 helices, 9 β-strands
ElementResiduesLengthSheet
α-helix6-1611
β-strand31-36632
β-strand52-53233
β-strand66-68334
α-helix71-8010
β-strand84134
α-helix87-915
α-helix97-10610
β-strand110-112334
α-helix120-1234
α-helix127-1315
α-helix145-1528
β-strand155-156233
β-strand165-171732
α-helix176-19217
β-strand204-208532
α-helix212-2132
β-strand214-215232
Chain A: 8 helices, 15 β-strands
ElementResiduesLengthSheet
β-strand33-37516
α-helix43-5513
β-strand59-61316
α-helix73-808
β-strand85-92816
β-strand96-102716
β-strand109-1181016
β-strand130117
β-strand133118
β-strand136-139416
α-helix141-1444
α-helix147-16014
β-strand170118
β-strand175-181716
β-strand186-1951016
β-strand196-19729
α-helix203-2053
β-strand210-214516
β-strand218-2291216
β-strand232-238716
α-helix245-27733
α-helix280-2823
α-helix287-2893
Chain b: 24 helices, 12 β-strands
ElementResiduesLengthSheet
α-helix14-2714
α-helix39-6729
α-helix76-8510
α-helix88-11629
α-helix122-14120
α-helix144-15815
β-strand169-1724128
α-helix180-1878
β-strand205-2106128
β-strand215-2206128
α-helix2281
α-helix236-24510
β-strand2481128
β-strand251-2544129
α-helix259-2613
α-helix264-27310
α-helix275-2784
β-strand283-2875129
α-helix304-3074
β-strand315-3195129
α-helix327-34014
β-strand364172
α-helix380-3834
α-helix399-4057
α-helix416-4183
α-helix425-4295
α-helix430-4334
β-strand435-436240
β-strand439-440240
α-helix441-4444
α-helix449-46517
α-helix483-51028
β-strand5181130
α-helix521-5233
β-strand526-5272131
α-helix528-53811
Chain B: 10 helices, 20 β-strands
ElementResiduesLengthSheet
α-helix14-163
α-helix27-293
α-helix33-353
β-strand42-43235
β-strand45-601636
β-strand70-801136
β-strand84-931037
β-strand100-106737
α-helix112-1154
α-helix116-1183
α-helix142-15413
β-strand157-163737
α-helix166-1683
β-strand178-182537
β-strand183-184235
α-helix188-19710
β-strand202-203237
β-strand214-215238
β-strand216-220536
β-strand223139
β-strand271139
β-strand274-276336
β-strand280-281238
β-strand282-285436
β-strand299140
β-strand321-325536
β-strand335-339536
α-helix348-3514
β-strand356-359436
α-helix373-3808
Chain c: 4 helices, 4 β-strands
ElementResiduesLengthSheet
α-helix10-2011
β-strand22-254119
α-helix27-359
β-strand41-444119
α-helix50-6314
β-strand66-694119
α-helix74-818
β-strand89-946119
Chain C: 20 helices, 12 β-strands
ElementResiduesLengthSheet
α-helix3-42
β-strand5-9548
β-strand15-21748
α-helix32-4211
β-strand62-63249
β-strand76-77249
β-strand88149
α-helix115-12713
α-helix132-1387
β-strand150-152348
α-helix154-1563
α-helix162-17110
α-helix175-1828
β-strand186-187250
α-helix1881
β-strand199-200250
β-strand206-209448
α-helix215-2195
β-strand226-229448
β-strand232148
α-helix235-2384
α-helix240-2423
β-strand248-251448
α-helix252-26211
α-helix276-2794
α-helix286-2905
α-helix295-2984
α-helix300-3023
α-helix307-3093
α-helix321-3277
α-helix330-3378
α-helix353-3597

46 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 rRNA1RNA3396Saccharomyces cerevisiae BY4741
5.8S rRNA2RNA158Saccharomyces cerevisiae BY4741
60S ribosomal subunit assembly/export protein LOC17protein204Saccharomyces cerevisiae BY4741P43586 (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 (AlphaFold model)
60S ribosomal protein L6-AEprotein175Saccharomyces cerevisiae BY4741Q02326
60S ribosomal protein L7-AFprotein244Saccharomyces cerevisiae BY4741P05737
60S ribosomal protein L9-AHprotein191Saccharomyces cerevisiae BY4741P05738
rRNA-processing protein EBP2Jprotein427Saccharomyces cerevisiae BY4741P36049
60S ribosomal protein L13-ALprotein199Saccharomyces cerevisiae BY4741Q12690
60S ribosomal protein L14-AMprotein138Saccharomyces cerevisiae BY4741P36105

45 more molecules are not listed.

Sequence of entity 1 (1), FASTA
>7R7A_1 25S rRNA (chains 1)
GUUUGACCUCAAAUCAGGUAGGAGUACCCGCUGAACUUAAGCAUAUCAAUAAGCGGAGGA
AAAGAAACCAACCGGGAUUGCCUUAGUAACGGCGAGUGAAGCGGCAAAAGCUCAAAUUUG
AAAUCUGGUACCUUCGGUGCCCGAGUUGUAAUUUGGAGAGGGCAACUUUGGGGCCGUUCC
UUGUCUAUGUUCCUUGGAACAGGACGUCAUAGAGGGUGAGAAUCCCGUGUGGCGAGGAGU
GCGGUUCUUUGUAAAGUGCCUUCGAAGAGUCGAGUUGUUUGGGAAUGCAGCUCUAAGUGG
GUGGUAAAUUCCAUCUAAAGCUAAAUAUUGGCGAGAGACCGAUAGCGAACAAGUACAGUG
AUGGAAAGAUGAAAAGAACUUUGAAAAGAGAGUGAAAAAGUACGUGAAAUUGUUGAAAGG
GAAGGGCAUUUGAUCAGACAUGGUGUUUUGUGCCCUCUGCUCCUUGUGGGUAGGGGAAUC
UCGCAUUUCACUGGGCCAGCAUCAGUUUUGGUGGCAGGAUAAAUCCAUAGGAAUGUAGCU
UGCCUCGGUAAGUAUUAUAGCCUGUGGGAAUACUGCCAGCUGGGACUGAGGACUGCGACG
UAAGUCAAGGAUGCUGGCAUAAUGGUUAUAUGCCGCCCGUCUUGAAACACGGACCAAGGA
GUCUAACGUCUAUGCGAGUGUUUGGGUGUAAAACCCAUACGCGUAAUGAAAGUGAACGUA
GGUUGGGGCCUCGCAAGAGGUGCACAAUCGACCGAUCCUGAUGUCUUCGGAUGGAUUUGA
GUAAGAGCAUAGCUGUUGGGACCCGAAAGAUGGUGAACUAUGCCUGAAUAGGGUGAAGCC
AGAGGAAACUCUGGUGGAGGCUCGUAGCGCGGUUGACGUGCAAAUCGAUCGUCGAAUUUG
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
>7R7A_2 5.8S rRNA (chains 2)
AAACUUUCAACAACGGAUCUCUUGGUUCUCGCAUCGAUGAAGAACGCAGCGAAAUGCGAU
ACGUAAUGUGAAUUGCAGAAUUCCGUGAAUCAUCGAAUCUUUGAACGCACAUUGCGCCCC
UUGGUAUUCCAGGGGGCAUGCCUGUUUGAGCGUCAUUU
Sequence of entity 3 (7), FASTA
>7R7A_3 60S ribosomal subunit assembly/export protein LOC1 (chains 7)
MAPKKPSKRQNLRREVAPEVFQDSQARNQLANVPHLTEKSAQRKPSKTKVKKEQSLARLY
GAKKDKKGKYSEKDLNIPTLNRAIVPGVKIRRGKKGKKFIADNDTLTLNRLITTIGDKYD
DIAESKLEKARRLEEIRELKRKEIERKEALKQDKLEEKKDEIKKKSSVARTIRRKNKRDM
LKSEAKASESKTEGRKVKKVSFAQ
Sequence of entity 4 (A), FASTA
>7R7A_4 Ribosome biogenesis protein BRX1 (chains A)
MSSIYKALAGKSKDNKSEKKQGNVKQFMNKQRTLLISSRGVNYRHRHLIQDLSGLLPHSR
KEPKLDTKKDLQQLNEIAELYNCNNVLFFEARKHQDLYLWLSKPPNGPTIKFYIQNLHTM
DELNFTGNCLKGSRPVLSFDQRFESSPHYQLIKELLVHNFGVPPNARKSKPFIDHVMSFS
IVDDKIWVRTYEISHSTKNKEEYEDGEEDISLVEIGPRFVMTVILILEGSFGGPKIYENK
QYVSPNVVRAQIKQQAAEEAKSRAEAAVERKIKRRENVLAADPLSNDALFK
Sequence of entity 5 (B), FASTA
>7R7A_5 60S ribosomal protein L3 (chains B)
MSHRKYEAPRHGHLGFLPRKRAASIRARVKAFPKDDRSKPVALTSFLGYKAGMTTIVRDL
DRPGSKFHKREVVEAVTVVDTPPVVVVGVVGYVETPRGLRSLTTVWAEHLSDEVKRRFYK
NWYKSKKKAFTKYSAKYAQDGAGIERELARIKKYASVVRVLVHTQIRKTPLAQKKAHLAE
IQLNGGSISEKVDWAREHFEKTVAVDSVFEQNEMIDAIAVTKGHGFEGVTHRWGTKKLPR
KTHRGLRKVACIGAWHPAHVMWSVARAGQRGYHSRTSINHKIYRVGKGDDEANGATSFDR
TKKTITPMGGFVHYGEIKNDFIMVKGCIPGNRKRIVTLRKSLYTNTSRKALEEVSLKWID
TASKFGKGRFQTPAEKHAFMGTLKKDL
Sequence of entity 6 (C), FASTA
>7R7A_6 60S ribosomal protein L4-A (chains C)
MSRPQVTVHSLTGEATANALPLPAVFSAPIRPDIVHTVFTSVNKNKRQAYAVSEKAGHQT
SAESWGTGRAVARIPRVGGGGTGRSGQGAFGNMCRGGRMFAPTKTWRKWNVKVNHNEKRY
ATASAIAATAVASLVLARGHRVEKIPEIPLVVSTDLESIQKTKEAVAALKAVGAHSDLLK
VLKSKKLRAGKGKYRNRRWTQRRGPLVVYAEDNGIVKALRNVPGVETANVASLNLLQLAP
GAHLGRFVIWTEAAFTKLDQVWGSETVASSKVGYTLPSHIISTSDVTRIINSSEIQSAIR
PAGQATQKRTHVLKKNPLKNKQVLLRLNPYAKVFAAEKLGSKKAEKTGTKPAAVFTETLK
HD
Sequence of entity 7 (E), FASTA
>7R7A_7 60S ribosomal protein L6-A (chains E)
MSAQKAPKWYPSEDVAALKKTRKAARPQKLRASLVPGTVLILLAGRFRGKRVVYLKHLED
NTLLISGPFKVNGVPLRRVNARYVIATSTKVSVEGVNVEKFNVEYFAKEKLTKKEKKEAN
FPEQQNKEIKAERVEDQKVVDKALIAEIKKTPLLKQYLSASFSLKNGDKPHMLKF
Sequence of entity 8 (F), FASTA
>7R7A_8 60S ribosomal protein L7-A (chains F)
MAAEKILTPESQLKKSKAQQKTAEQVAAERAARKAANKEKRAIILERNAAYQKEYETAER
NIIQAKRDAKAAGSYYVEAQHKLVFVVRIKGINKIPPKPRKVLQLLRLTRINSGTFVKVT
KATLELLKLIEPYVAYGYPSYSTIRQLVYKRGFGKINKQRVPLSDNAIIEANLGKYGILS
IDDLIHEIITVGPHFKQANNFLWPFKLSNPSGGWGVPRKFKHFIQGGSFGNREEFINKLV
KSMN
Sequence of entity 9 (H), FASTA
>7R7A_9 60S ribosomal protein L9-A (chains H)
MKYIQTEQQIEVPEGVTVSIKSRIVKVVGPRGTLTKNLKHIDVTFTKVNNQLIKVAVHNG
GRKHVAALRTVKSLVDNMITGVTKGYKYKMRYVYAHFPINVNIVEKDGAKFIEVRNFLGD
KKIRNVPVRDGVTIEFSTNVKDEIVLSGNSVEDVSQNAADLQQICRVRNKDIRKFLDGIY
VSHKGFITEDL
Sequence of entity 10 (J), FASTA
>7R7A_10 rRNA-processing protein EBP2 (chains J)
MAKGFKLKELLSHQKEIEKAEKLENDLKKKKSQELKKEEPTIVTASNLKKLEKKEKKADV
KKEVAADTEEYQSQALSKKEKRKLKKELKKMQEQDATEAQKHMSGDEDESGDDREEEEEE
EEEEEGRLDLEKLAKSDSESEDDSESENDSEEDEDVVAKEESEEKEEQEEEQDVPLSDVE
FDSDADVVPHHKLTVNNTKAMKHALERVQLPWKKHSFQEHQSVTSETNTDEHIKDIYDDT
ERELAFYKQSLDAVLVARDELKRLKVPFKRPLDYFAEMVKSDEHMDKIKGKLIEEASDKK
AREEARRQRQLKKFGKQVQNATLQKRQLEKRETLEKIKSLKNKRKHNEIDHSEFNVGVEE
EVEGKRFDRGRPNGKRAAKNAKYGQGGMKRFKRKNDATSSADVSGFSSRKMKGKTNRPGK
SRRARRF
Sequence of entity 11 (L), FASTA
>7R7A_11 60S ribosomal protein L13-A (chains L)
MAISKNLPILKNHFRKHWQERVKVHFDQAGKKVSRRNARATRAAKIAPRPLDLLRPVVRA
PTVKYNRKVRAGRGFTLAEVKAAGLTAAYARTIGIAVDHRRQNRNQEIFDANVQRLKEYQ
SKIIVFPRNGKAPEAEQVLSAAATFPIAQPATDVEARAVQDNGESAFRTLRLARSEKKFR
GIREKRAREKAEAEAEKKK
Sequence of entity 12 (M), FASTA
>7R7A_12 60S ribosomal protein L14-A (chains M)
MSTDSIVKASNWRLVEVGRVVLIKKGQSAGKLAAIVEIIDQKKVLIDGPKAGVPRQAINL
GQVVLTPLTFALPRGARTATVSKKWAAAAVCEKWAASSWAKKIAQRERRAALTDFERFQV
MVLRKQKRYTVKKALAKA

Ligands and cofactors

IDNameFormulaCopies
ZNZinc ionZn2

Primary citation

Sequence-specific remodeling of a topologically complex RNP substrate by Spb4. Cruz, V.E., Sekulski, K., Peddada, N. et al. Nat Struct Mol Biol (2022) 29:1228-1238. DOI 10.1038/s41594-022-00874-9 · PubMed

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

Browse structure collections

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