7R6K: PDB entry 7R6K
State E2 nucleolar 60S ribosomal intermediate - Model for Noc2/Noc3 region. Determined by electron microscopy at 3.17 Å resolution. Released 9 Nov 2022.
- Method
- Electron microscopy
- Resolution
- 3.17 Å
- Organism
- Saccharomyces cerevisiae BY4741
- Chains
- 16
- Atoms
- 20,543
- Mol. weight
- 700.94 kDa
- Released
- 9 Nov 2022
Explore 7R6K in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
7R6K contains 120 α-helices and 56 β-strands across 15 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 5: 1 helix, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 218-221 | 4 | |
Chain 7: 8 helices, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 12-15 | 4 | 1 |
| β-strand | 20-21 | 2 | 2 |
| α-helix | 24-28 | 5 | |
| β-strand | 30 | 1 | 3 |
| α-helix | 37-39 | 3 | |
| α-helix | 44-46 | 3 | |
| β-strand | 89-90 | 2 | 4 |
| α-helix | 91 | 1 | |
| α-helix | 97-98 | 2 | |
| β-strand | 99 | 1 | 5 |
| α-helix | 100-101 | 2 | |
| α-helix | 107-115 | 9 | |
| α-helix | 126-146 | 21 | |
Chain 8: 23 helices, 1 β-strand
| Element | Residues | Length | Sheet |
|---|
| α-helix | 26-34 | 9 | |
| α-helix | 42-49 | 8 | |
| α-helix | 52-63 | 12 | |
| α-helix | 71-74 | 4 | |
| α-helix | 79-82 | 4 | |
| α-helix | 268-284 | 17 | |
| α-helix | 292-302 | 11 | |
| α-helix | 314-328 | 15 | |
| α-helix | 336-348 | 13 | |
| α-helix | 354-366 | 13 | |
| α-helix | 377-390 | 14 | |
| α-helix | 397-418 | 22 | |
| α-helix | 428-434 | 7 | |
| α-helix | 439-452 | 14 | |
| α-helix | 472-483 | 12 | |
| α-helix | 492-507 | 16 | |
| β-strand | 512 | 1 | 6 |
| α-helix | 516-520 | 5 | |
| α-helix | 557-574 | 18 | |
| α-helix | 576-578 | 3 | |
| α-helix | 584-601 | 18 | |
| α-helix | 606-628 | 23 | |
| α-helix | 641-644 | 4 | |
| α-helix | 655-677 | 23 | |
Chain A: 4 helices, 11 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 33-35 | 3 | 7 |
| α-helix | 51-55 | 5 | |
| β-strand | 59-61 | 3 | 7 |
| α-helix | 75-80 | 6 | |
| β-strand | 85-87 | 3 | 7 |
| β-strand | 130 | 1 | 8 |
| β-strand | 133 | 1 | 9 |
| β-strand | 136 | 1 | 10 |
| α-helix | 162-163 | 2 | |
| β-strand | 170 | 1 | 9 |
| β-strand | 175-176 | 2 | 10 |
| β-strand | 191-195 | 5 | 10 |
| β-strand | 196-197 | 2 | 4 |
| α-helix | 200-205 | 6 | |
| β-strand | 210-214 | 5 | 10 |
Chain g: 1 helix, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 98-110 | 13 | |
Chain G: 5 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 49-51 | 3 | |
| α-helix | 54-68 | 15 | |
| β-strand | 70-71 | 2 | 11 |
| α-helix | 73-76 | 4 | |
| β-strand | 234-235 | 2 | 11 |
| α-helix | 237-239 | 3 | |
| α-helix | 240-247 | 8 | |
Chain i: 4 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 45-48 | 4 | |
| α-helix | 52-62 | 11 | |
| α-helix | 66-77 | 12 | |
| α-helix | 80-94 | 15 | |
Chain I: 31 helices, 1 β-strand
| Element | Residues | Length | Sheet |
|---|
| α-helix | 131-150 | 20 | |
| α-helix | 156-166 | 11 | |
| α-helix | 171-188 | 18 | |
| α-helix | 199-202 | 4 | |
| α-helix | 210-235 | 26 | |
| α-helix | 243-259 | 17 | |
| α-helix | 269-280 | 12 | |
| α-helix | 291-303 | 13 | |
| α-helix | 309-324 | 16 | |
| α-helix | 331-334 | 4 | |
| α-helix | 335-339 | 5 | |
| α-helix | 341-343 | 3 | |
| α-helix | 381-420 | 40 | |
| α-helix | 426-435 | 10 | |
| α-helix | 437-439 | 3 | |
| α-helix | 445-462 | 18 | |
| α-helix | 468-485 | 18 | |
| α-helix | 496-502 | 7 | |
| α-helix | 503-505 | 3 | |
| α-helix | 506-510 | 5 | |
| α-helix | 526-527 | 2 | |
| α-helix | 542-551 | 10 | |
| α-helix | 552-556 | 5 | |
| α-helix | 562-576 | 15 | |
| α-helix | 581-597 | 17 | |
| α-helix | 599-602 | 4 | |
| α-helix | 603-606 | 4 | |
| α-helix | 628-630 | 3 | |
| α-helix | 634-637 | 4 | |
| α-helix | 639-641 | 3 | |
| β-strand | 642 | 1 | 6 |
| α-helix | 645-661 | 17 | |
7 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| 25S rRNA | 1 | RNA | 152 | Saccharomyces cerevisiae BY4741 | |
| 60S ribosomal subunit assembly/export protein LOC1 | 7 | protein | 204 | Saccharomyces cerevisiae BY4741 | P43586 (AlphaFold model) |
| Nucleolar complex protein 2 | 8 | protein | 710 | Saccharomyces cerevisiae BY4741 | P39744 (AlphaFold model) |
| Ribosome biogenesis protein BRX1 | A | protein | 291 | Saccharomyces cerevisiae BY4741 | Q08235 (AlphaFold model) |
| 60S ribosomal protein L8-A | G | protein | 256 | Saccharomyces cerevisiae BY4741 | P17076 (AlphaFold model) |
| Nucleolar complex-associated protein 3 | I | protein | 663 | Saccharomyces cerevisiae BY4741 | Q07896 |
| rRNA-processing protein EBP2 | J | protein | 427 | Saccharomyces cerevisiae BY4741 | P36049 |
| 60S ribosomal protein L15-A | N | protein | 204 | Saccharomyces cerevisiae BY4741 | P05748 |
| 60S ribosomal protein L34-A | g | protein | 121 | Saccharomyces cerevisiae BY4741 | P87262 |
| 60S ribosomal protein L36-A | i | protein | 100 | Saccharomyces cerevisiae BY4741 | P05745 |
| 60S ribosome subunit biogenesis protein NIP7 | l | protein | 181 | Saccharomyces cerevisiae BY4741 | Q08962 |
| Ribosome biogenesis protein ERB1 | m | protein | 807 | Saccharomyces cerevisiae BY4741 | Q04660 |
4 more molecules are not listed.
Sequence of entity 1 (1), FASTA
>7R6K_1 25S rRNA (chains 1)
GCUGAACUUAAGCAUAAAGCGGAGUCGAGUUGUUUGCAGCUCUAAGCUACGGUGAUCGUC
GAAGGGGCGAAAGACAAGAUGGGGAAGCUCCGUUUCAAUGUUGAGCUUGACUCUAGUUGU
GGGGAGUAAAGUUACCACAUCGUGAGACAGGU
Sequence of entity 2 (7), FASTA
>7R6K_2 60S ribosomal subunit assembly/export protein LOC1 (chains 7)
MAPKKPSKRQNLRREVAPEVFQDSQARNQLANVPHLTEKSAQRKPSKTKVKKEQSLARLY
GAKKDKKGKYSEKDLNIPTLNRAIVPGVKIRRGKKGKKFIADNDTLTLNRLITTIGDKYD
DIAESKLEKARRLEEIRELKRKEIERKEALKQDKLEEKKDEIKKKSSVARTIRRKNKRDM
LKSEAKASESKTEGRKVKKVSFAQ
Sequence of entity 3 (8), FASTA
>7R6K_3 Nucleolar complex protein 2 (chains 8)
MGKVSKSTKKFQSKHLKHTLDQRRKEKIQKKRIQGRRGNKTDQEKADAAGTREQQQLKKS
AKEEVFKDMSVETFFEKGIEIPKENKKLKKKTTKEQSDEDSSSSEEEEDMGQSMAKLAEK
DPEFYKYLEENDKDLLDFAGTNPLDGIDSQDEGEDAERNSNIEEKSEQMELEKEKIELSL
KLVRKWKKQLHDSPSLKLLRNIISAFKVAVNLNKEENIEDYKYAITDEKAFHELMFMVLK
DVPQAIQKMAPYKIVKGARTLPNGGNVSRVSSIVKSHAGSLLILLNDITNTETAALVLHS
VNELMPYLLSYRRILKELIKSIVGVWSTTRELETQIASFAFLINTTKEFKKSMLETTLKT
TYSTFIKSCRKTNMRSMPLINFQKNSAAELFGIDEVLGYQVGFEYIRQLAIHLRNTMNAT
TKKSSKINSAEAYKIVYNWQFCHSLDFWSRVLSFACQPEKENGSESPLRQLIYPLVQVTL
GVIRLIPTPQFFPLRFYLIKSLIRLSQNSGVFIPIYPLLSEILTSTAFTKAPKKSPNLAA
FDFEHNIKCTQAYLNTKIYQEGLSEQFVDLLGDYFALYCKNIAFPELVTPVIISLRRYIK
TSTNVKLNKRLSTVVEKLNQNSTFIQEKRSDVEFGPTNKSEVSRFLNDVAWNKTPLGSYV
AVQREVKEEKARLMRESMEEQDKERETEEAKLLNSLESDDDNEDVEMSDA
Sequence of entity 4 (A), FASTA
>7R6K_4 Ribosome biogenesis protein BRX1 (chains A)
MSSIYKALAGKSKDNKSEKKQGNVKQFMNKQRTLLISSRGVNYRHRHLIQDLSGLLPHSR
KEPKLDTKKDLQQLNEIAELYNCNNVLFFEARKHQDLYLWLSKPPNGPTIKFYIQNLHTM
DELNFTGNCLKGSRPVLSFDQRFESSPHYQLIKELLVHNFGVPPNARKSKPFIDHVMSFS
IVDDKIWVRTYEISHSTKNKEEYEDGEEDISLVEIGPRFVMTVILILEGSFGGPKIYENK
QYVSPNVVRAQIKQQAAEEAKSRAEAAVERKIKRRENVLAADPLSNDALFK
Sequence of entity 5 (G), FASTA
>7R6K_5 60S ribosomal protein L8-A (chains G)
MAPGKKVAPAPFGAKSTKSNKTRNPLTHSTPKNFGIGQAVQPKRNLSRYVKWPEYVRVQR
QKKILSIRLKVPPTIAQFQYTLDRNTAAETFKLFNKYRPETAAEKKERLTKEAAAVAEGK
SKQDASPKPYAVKYGLNHVVALIENKKAKLVLIANDVDPIELVVFLPALCKKMGVPYAIV
KGKARLGTLVNQKTSAVAALTEVRAEDEAALAKLVSTIDANFADKYDEVKKHWGGGILGN
KAQAKMDKRAKNSDSA
Sequence of entity 6 (I), FASTA
>7R6K_6 Nucleolar complex-associated protein 3 (chains I)
MAKRNRSQFRIQERTAKKRKHEDSLLEGNVFQNAPEDMDENTIYSAKGSSWDEEEQDYEM
VPRKNRSDTSNLVEGLPIKVNGKVERKLHKAQEKPKDDDEEDEDSNDSSEDDEGPNEEQE
AEAKEDEPDTEEKILQLKEDIADLVTKVMEEPEENTAALGRLCKMVESKNPNTCKFSMLA
LVPVFKSIIPGYRIRPLTETEKKEKVSKEVSKLRNFEQALVYNYKNYVGRLQSLSKTPSN
AAPIQVSLGILATQAAKELISTASHFNFRTDIFTLLLRRICKPRISTDPTSIQIIQTFET
LLNEDEEGSISFEILRIFNKILKTRNFNIEESVLNMLLSLDVLHDYDPNTKLKGNVSAPK
LKKKDRVHLSKKQRKARKEMQQIEEEMRNAEQAVSAEERERNQSEILKIVFTIYLNILKN
NAKTLIGSVLEGLTKFGNMANFDLLGDFLEVMKELISDTEFDNLSSAEVRKALLCIVSAF
SLISNTQYMKVNVDLSKFVDGLYALLPYICLDADIELSYRSLRLADPLNNEIIKPSVNVS
TKAELLLKALDHVFFRSKSGTKERATAFTKRLYMCISHTPEKTSIAILKFIDKLMNRYPE
ISGLYSSEDRIGNGHFIMEADNPSRSNPEAATLWDNALLEKHYCPVVTKGLRSLSSRSKE
CSK
Sequence of entity 7 (J), FASTA
>7R6K_7 rRNA-processing protein EBP2 (chains J)
MAKGFKLKELLSHQKEIEKAEKLENDLKKKKSQELKKEEPTIVTASNLKKLEKKEKKADV
KKEVAADTEEYQSQALSKKEKRKLKKELKKMQEQDATEAQKHMSGDEDESGDDREEEEEE
EEEEEGRLDLEKLAKSDSESEDDSESENDSEEDEDVVAKEESEEKEEQEEEQDVPLSDVE
FDSDADVVPHHKLTVNNTKAMKHALERVQLPWKKHSFQEHQSVTSETNTDEHIKDIYDDT
ERELAFYKQSLDAVLVARDELKRLKVPFKRPLDYFAEMVKSDEHMDKIKGKLIEEASDKK
AREEARRQRQLKKFGKQVQNATLQKRQLEKRETLEKIKSLKNKRKHNEIDHSEFNVGVEE
EVEGKRFDRGRPNGKRAAKNAKYGQGGMKRFKRKNDATSSADVSGFSSRKMKGKTNRPGK
SRRARRF
Sequence of entity 8 (N), FASTA
>7R6K_8 60S ribosomal protein L15-A (chains N)
MGAYKYLEELQRKKQSDVLRFLQRVRVWEYRQKNVIHRAARPTRPDKARRLGYKAKQGFV
IYRVRVRRGNRKRPVPKGATYGKPTNQGVNELKYQRSLRATAEERVGRRAANLRVLNSYW
VNQDSTYKYFEVILVDPQHKAIRRDARYNWICDPVHKHREARGLTATGKKSRGINKGHKF
NNTKAGRRKTWKRQNTLSLWRYRK
Sequence of entity 9 (g), FASTA
>7R6K_9 60S ribosomal protein L34-A (chains g)
MAQRVTFRRRNPYNTRSNKIKVVKTPGGILRAQHVKKLATRPKCGDCGSALQGISTLRPR
QYATVSKTHKTVSRAYGGSRCANCVKERIIRAFLIEEQKIVKKVVKEQTEAAKKSEKKAK
K
Sequence of entity 10 (i), FASTA
>7R6K_10 60S ribosomal protein L36-A (chains i)
MTVKTGIAIGLNKGKKVTSMTPAPKISYKKGAASNRTKFVRSLVREIAGLSPYERRLIDL
IRNSGEKRARKVAKKRLGSFTRAKAKVEEMNNIIAASRRH
Sequence of entity 11 (l), FASTA
>7R6K_11 60S ribosome subunit biogenesis protein NIP7 (chains l)
MRQLTEEETKVVFEKLAGYIGRNISFLVDNKELPHVFRLQKDRVYYVPDHVAKLATSVAR
PNLMSLGICLGKFTKTGKFRLHITSLTVLAKHAKYKIWIKPNGEMPFLYGNHVLKAHVGK
MSDDIPEHAGVIVFAMNDVPLGFGVSAKSTSESRNMQPTGIVAFRQADIGEYLRDEDTLF
T
Sequence of entity 12 (m), FASTA
>7R6K_12 Ribosome biogenesis protein ERB1 (chains m)
MMAKNNKTTEAKMSKKRAASEESDVEEDEDKLLSVDGLIDAEASESDEDDDEYESAVEEK
ESSSDKEAQDDSDDDSDAELNKLLAEEEGDGEEDYDSSEFSDDTTSLTDRLSGVKLQTIV
DPNIYSKYADGSDRIIKPEINPVYDSDDSDAETQNTIGNIPLSAYDEMPHIGYDINGKRI
MRPAKGSALDQLLDSIELPEGWTGLLDKNSGSSLNLTKEELELISKIQRNEQTDDSINPY
EPLIDWFTRHEEVMPLTAVPEPKRRFVPSKNEAKRVMKIVRAIREGRIIPPKKLKEMKEK
EKIENYQYDLWGDSTETNDHVMHLRAPKLPPPTNEESYNPPEEYLLSPEEKEAWENTEYS
ERERNFIPQKYSALRKVPGYGESIRERFERSLDLYLAPRVRKNKLNIDPNSLIPELPSPK
DLRPFPIRCSTIYAGHKGKVRTLSIDPSGLWLATGSDDGTVRVWEILTGREVYRTTLIDD
EENPDYHIECIEWNPDANNGILAVAVGENIHLIVPPIFGYDIENNGKTKIEDGFGYDTFG
TVKKSNLEVNENGDGDEDGENESAKNAVKKQVAQWNKPSQKQLEKDICITISCKKTVKKL
SWHRKGDYFVTVQPDSGNTSVLIHQVSKHLTQSPFKKSKGIIMDAKFHPFKPQLFVCSQR
YVRIYDLSQQILVKKLLPGARWLSKIDIHPRGDNLIASSFDKRVLWHDLDLASTPYKTLR
YHEKAVRSVNFHKKLPLFSSAADDGTIHVFHATVYDDMMKNPMIVPLKKLTGHKVINSLG
VLDAIWHPREAWLFSAGADNTARLWTT
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:
- 8V83 2.53 Å, 60S ribosome biogenesis intermediate (Dbp10 pre-catalytic structure - Overall map)
- 8V87 2.66 Å, 60S ribosome biogenesis intermediate (Dbp10 post-catalytic structure - Overall map)
- 8V84 2.7 Å, 60S ribosome biogenesis intermediate (Dbp10 catalytic structure - Overall map)
- 7NAC 3.04 Å, State E2 nucleolar 60S ribosomal biogenesis intermediate - Composite model
- 7R7A 3.04 Å, State E1 nucleolar 60S ribosome biogenesis intermediate - Composite model
- 7R7C 3.71 Å, State E2 nucleolar 60S ribosomal biogenesis intermediate - L1 stalk local model
Browse structure collections
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