7NAD: RRP17 isoform 1
State E2 nucleolar 60S ribosomal biogenesis intermediate - Spb4 local refinement 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
- 26
- Atoms
- 43,123
- Mol. weight
- 1068.09 kDa
- Ligands
- ZN
- Released
- 9 Nov 2022
Explore 7NAD in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
7NAD contains 141 α-helices and 140 β-strands across 23 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: 4 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 33-41 | 9 | |
| α-helix | 45-92 | 48 | |
| β-strand | 145-148 | 4 | 1 |
| β-strand | 154-159 | 6 | 1 |
| α-helix | 165-179 | 15 | |
| α-helix | 218-229 | 12 | |
Chain 8: 4 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 6-14 | 9 | |
| α-helix | 16-34 | 19 | |
| α-helix | 42-49 | 8 | |
| α-helix | 52-59 | 8 | |
Chain b: 2 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 490-510 | 21 | |
| β-strand | 518 | 1 | 4 |
| β-strand | 526 | 1 | 7 |
| α-helix | 528-538 | 11 | |
Chain c: 4 helices, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 11-20 | 10 | |
| β-strand | 22-25 | 4 | 12 |
| α-helix | 27-36 | 10 | |
| β-strand | 41-44 | 4 | 12 |
| α-helix | 50-63 | 14 | |
| β-strand | 66-69 | 4 | 12 |
| α-helix | 74-81 | 8 | |
| β-strand | 89-94 | 6 | 12 |
Chain d: 4 helices, 6 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 12-15 | 4 | 13 |
| α-helix | 16-19 | 4 | |
| α-helix | 25-27 | 3 | |
| α-helix | 28-43 | 16 | |
| β-strand | 51 | 1 | 13 |
| α-helix | 53-59 | 7 | |
| β-strand | 62 | 1 | 14 |
| β-strand | 66 | 1 | 14 |
| β-strand | 70-75 | 6 | 13 |
| β-strand | 93-95 | 3 | 13 |
Chain g: 6 helices, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 20-24 | 5 | 15 |
| β-strand | 30-34 | 5 | 15 |
| α-helix | 35-39 | 5 | |
| β-strand | 43 | 1 | 16 |
| α-helix | 49 | 1 | |
| β-strand | 50 | 1 | 16 |
| α-helix | 51 | 1 | |
| α-helix | 59-64 | 6 | |
| α-helix | 67-69 | 3 | |
| α-helix | 82-109 | 28 | |
Chain G: 2 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 48-51 | 4 | |
| α-helix | 54-61 | 8 | |
Chain I: 19 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 131-149 | 19 | |
| α-helix | 156-166 | 11 | |
| α-helix | 171-188 | 18 | |
| α-helix | 199-202 | 4 | |
| α-helix | 211-235 | 25 | |
| α-helix | 243-259 | 17 | |
| α-helix | 263-265 | 3 | |
| α-helix | 269-280 | 12 | |
| α-helix | 291-304 | 14 | |
| α-helix | 309-324 | 16 | |
| α-helix | 331-334 | 4 | |
| α-helix | 335-339 | 5 | |
| α-helix | 363-365 | 3 | |
| α-helix | 366-368 | 3 | |
| α-helix | 371-420 | 50 | |
| α-helix | 426-436 | 11 | |
| α-helix | 437-439 | 3 | |
| α-helix | 520-522 | 3 | |
| α-helix | 526-527 | 2 | |
15 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 | 697 | Saccharomyces cerevisiae BY4741 | |
| 5.8S rRNA | 2 | RNA | 72 | Saccharomyces cerevisiae BY4741 | |
| RRP17 isoform 1 | 5 | protein | 235 | Saccharomyces cerevisiae BY4741 | Q04031 (AlphaFold model) |
| NOC2 isoform 1 | 8 | protein | 710 | Saccharomyces cerevisiae BY4741 | P39744 (AlphaFold model) |
| 60S ribosomal protein L3 | B | protein | 387 | Saccharomyces cerevisiae BY4741 | P14126 (AlphaFold model) |
| RPL8A isoform 1 | G | protein | 256 | Saccharomyces cerevisiae BY4741 | P17076 (AlphaFold model) |
| NOC3 isoform 1 | I | protein | 663 | Saccharomyces cerevisiae BY4741 | Q07896 |
| 60S ribosomal protein L17-A | P | protein | 184 | Saccharomyces cerevisiae BY4741 | P05740 |
| 60S ribosomal protein L19-A | R | protein | 189 | Saccharomyces cerevisiae BY4741 | P0CX82 |
| 60S ribosomal protein L22-A | U | protein | 121 | Saccharomyces cerevisiae BY4741 | P05749 |
| 60S ribosomal protein L23-A | V | protein | 36 | Saccharomyces cerevisiae BY4741 | P0CX41 |
| 60S ribosomal protein L25 | X | protein | 142 | Saccharomyces cerevisiae BY4741 | P04456 |
14 more molecules are not listed.
Sequence of entity 1 (1), FASTA
>7NAD_1 25S rRNA (chains 1)
AUGCCUGAAUAGGGUGAAGCCAGAGGAAACUCUGGUGGAGGCUCGCGAAUUUGGGUAUAG
UAGCAAAUAUUCAAAUGAGAACUUUGAAGACUGAAGUGGGGAAAGGUUCCACGUCAACAG
CAGUUGGACGUGGGUUAGUCGAUCCUAAGAGAUGGUUUCAAAGGCCUGACAGGCCACCAU
CGAAAGGGAAUCCGGUUAAGAUUCCGGAACCUGGAUAUGGAUUCUUCACGGUAACGUAAC
UGAAUGUGGAGACGUCGGCGCGAGCCCUGGGAGGAGUUAUCUUUUCUUCUUAACAGCUUA
UCACCCCGGAAUUGGUUUAUCCGGAGAUGGGGUCUUAUGGCUGGAAGAGGCCAGCACCUU
UGCUGGCUCCGGUGCGCUUGUGACGGCCCGUGAAAAUCCACAGGAAGGAAUAGUUUUCAU
GCCAGGUCGUACUGUCUCCAAGGUGAACAGCCUCUAGUUGAUAGAAGAUAAGGGAAGUCG
GUCCGUAACUUCGGGAUAAGGAUUGGCUCUAAGGGUCGGGUAGUGAGGGCCUUGGUCACG
GCCUUGGCUUGCUACAAUUAACGAUCAACUUAGAACUGGUACGGACAAGGGGAAUCUGAC
UGUUAACGAGAUUCCCACUGUCCCUAUCUACUAUCUAGCGAGGCUGUCUGAUCAGGCAUU
GCGUAAGCAGUAGAGUAGCCGUUACGAUCUGCUGAGA
Sequence of entity 2 (2), FASTA
>7NAD_2 5.8S rRNA (chains 2)
GAACGCGCGAUACUCUUUGAACGCACAUUGCGCCCCUUGGUAUUCCAGGGGGCAUCUUUG
AAAGCGUAUUGC
Sequence of entity 3 (5), FASTA
>7NAD_3 RRP17 isoform 1 (chains 5)
MAVHTNRQILTRGKNYATKQSKKFGTDEVTFDKDSRLDYLTGFHKRKLQRQKKAQEFIKE
QERLRKIEERQKIRQERKEVMEEQLKTFKESLNLEAEIEDAKNDKTEDLQVESDESWHGF
DSDKDDGDNDNNESSVKPILKKGAITEIYDDSTTVELETLEPNDNFEYLAQLNNVKLEKA
EKVLKQSINRATKYAKFLGVDEKQKKKPRVKKFRYLTKNERRINQRKANDNKRRR
Sequence of entity 4 (8), FASTA
>7NAD_4 NOC2 isoform 1 (chains 8)
MGKVSKSTKKFQSKHLKHTLDQRRKEKIQKKRIQGRRGNKTDQEKADAAGTREQQQLKKS
AKEEVFKDMSVETFFEKGIEIPKENKKLKKKTTKEQSDEDSSSSEEEEDMGQSMAKLAEK
DPEFYKYLEENDKDLLDFAGTNPLDGIDSQDEGEDAERNSNIEEKSEQMELEKEKIELSL
KLVRKWKKQLHDSPSLKLLRNIISAFKVAVNLNKEENIEDYKYAITDEKAFHELMFMVLK
DVPQAIQKMAPYKIVKGARTLPNGGNVSRVSSIVKSHAGSLLILLNDITNTETAALVLHS
VNELMPYLLSYRRILKELIKSIVGVWSTTRELETQIASFAFLINTTKEFKKSMLETTLKT
TYSTFIKSCRKTNMRSMPLINFQKNSAAELFGIDEVLGYQVGFEYIRQLAIHLRNTMNAT
TKKSSKINSAEAYKIVYNWQFCHSLDFWSRVLSFACQPEKENGSESPLRQLIYPLVQVTL
GVIRLIPTPQFFPLRFYLIKSLIRLSQNSGVFIPIYPLLSEILTSTAFTKAPKKSPNLAA
FDFEHNIKCTQAYLNTKIYQEGLSEQFVDLLGDYFALYCKNIAFPELVTPVIISLRRYIK
TSTNVKLNKRLSTVVEKLNQNSTFIQEKRSDVEFGPTNKSEVSRFLNDVAWNKTPLGSYV
AVQREVKEEKARLMRESMEEQDKERETEEAKLLNSLESDDDNEDVEMSDA
Sequence of entity 5 (B), FASTA
>7NAD_5 60S ribosomal protein L3 (chains B)
MSHRKYEAPRHGHLGFLPRKRAASIRARVKAFPKDDRSKPVALTSFLGYKAGMTTIVRDL
DRPGSKFHKREVVEAVTVVDTPPVVVVGVVGYVETPRGLRSLTTVWAEHLSDEVKRRFYK
NWYKSKKKAFTKYSAKYAQDGAGIERELARIKKYASVVRVLVHTQIRKTPLAQKKAHLAE
IQLNGGSISEKVDWAREHFEKTVAVDSVFEQNEMIDAIAVTKGHGFEGVTHRWGTKKLPR
KTHRGLRKVACIGAWHPAHVMWSVARAGQRGYHSRTSINHKIYRVGKGDDEANGATSFDR
TKKTITPMGGFVHYGEIKNDFIMVKGCIPGNRKRIVTLRKSLYTNTSRKALEEVSLKWID
TASKFGKGRFQTPAEKHAFMGTLKKDL
Sequence of entity 6 (G), FASTA
>7NAD_6 RPL8A isoform 1 (chains G)
MAPGKKVAPAPFGAKSTKSNKTRNPLTHSTPKNFGIGQAVQPKRNLSRYVKWPEYVRVQR
QKKILSIRLKVPPTIAQFQYTLDRNTAAETFKLFNKYRPETAAEKKERLTKEAAAVAEGK
SKQDASPKPYAVKYGLNHVVALIENKKAKLVLIANDVDPIELVVFLPALCKKMGVPYAIV
KGKARLGTLVNQKTSAVAALTEVRAEDEAALAKLVSTIDANFADKYDEVKKHWGGGILGN
KAQAKMDKRAKNSDSA
Sequence of entity 7 (I), FASTA
>7NAD_7 NOC3 isoform 1 (chains I)
MAKRNRSQFRIQERTAKKRKHEDSLLEGNVFQNAPEDMDENTIYSAKGSSWDEEEQDYEM
VPRKNRSDTSNLVEGLPIKVNGKVERKLHKAQEKPKDDDEEDEDSNDSSEDDEGPNEEQE
AEAKEDEPDTEEKILQLKEDIADLVTKVMEEPEENTAALGRLCKMVESKNPNTCKFSMLA
LVPVFKSIIPGYRIRPLTETEKKEKVSKEVSKLRNFEQALVYNYKNYVGRLQSLSKTPSN
AAPIQVSLGILATQAAKELISTASHFNFRTDIFTLLLRRICKPRISTDPTSIQIIQTFET
LLNEDEEGSISFEILRIFNKILKTRNFNIEESVLNMLLSLDVLHDYDPNTKLKGNVSAPK
LKKKDRVHLSKKQRKARKEMQQIEEEMRNAEQAVSAEERERNQSEILKIVFTIYLNILKN
NAKTLIGSVLEGLTKFGNMANFDLLGDFLEVMKELISDTEFDNLSSAEVRKALLCIVSAF
SLISNTQYMKVNVDLSKFVDGLYALLPYICLDADIELSYRSLRLADPLNNEIIKPSVNVS
TKAELLLKALDHVFFRSKSGTKERATAFTKRLYMCISHTPEKTSIAILKFIDKLMNRYPE
ISGLYSSEDRIGNGHFIMEADNPSRSNPEAATLWDNALLEKHYCPVVTKGLRSLSSRSKE
CSK
Sequence of entity 8 (P), FASTA
>7NAD_8 60S ribosomal protein L17-A (chains P)
MARYGATSTNPAKSASARGSYLRVSFKNTRETAQAINGWELTKAQKYLEQVLDHQRAIPF
RRFNSSIGRTAQGKEFGVTKARWPAKSVKFVQGLLQNAAANAEAKGLDATKLYVSHIQVN
QAPKQRRRTYRAHGRINKYESSPSHIELVVTEKEEAVAKAAEKKVVRLTSRQRGRIAAQK
RIAA
Sequence of entity 9 (R), FASTA
>7NAD_9 60S ribosomal protein L19-A (chains R)
MANLRTQKRLAASVVGVGKRKVWLDPNETSEIAQANSRNAIRKLVKNGTIVKKAVTVHSK
SRTRAHAQSKREGRHSGYGKRKGTREARLPSQVVWIRRLRVLRRLLAKYRDAGKIDKHLY
HVLYKESKGNAFKHKRALVEHIIQAKADAQREKALNEEAEARRLKNRAARDRRAQRVAEK
RDALLKEDA
Sequence of entity 10 (U), FASTA
>7NAD_10 60S ribosomal protein L22-A (chains U)
MAPNTSRKQKIAKTFTVDVSSPTENGVFDPASYAKYLIDHIKVEGAVGNLGNAVTVTEDG
TVVTVVSTAKFSGKYLKYLTKKYLKKNQLRDWIRFVSTKTNEYRLAFYQVTPEEDEEEDE
E
Sequence of entity 11 (V), FASTA
>7NAD_11 60S ribosomal protein L23-A (chains V)
LPVGAIMNCARNLYIIMATVKKGKPELRKKVMEDNA
Sequence of entity 12 (X), FASTA
>7NAD_12 60S ribosomal protein L25 (chains X)
MAPSAKATAAKKAVVKGTNGKKALKVRTSATFRLPKTLKLARAPKYASKAVPHYNRLDSY
KVIEQPITSETAMKKVEDGNILVFQVSMKANKYQIKKAVKELYEVDVLKVNTLVRPNGTK
KAYVRLTADYDALDIANRIGYI
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| ZN | Zinc ion | Zn | 1 |
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 Q04031 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 7NAC 3.04 Å, State E2 nucleolar 60S ribosomal biogenesis intermediate - Composite model
- 7NAF 3.13 Å, State E2 nucleolar 60S ribosomal biogenesis intermediate - Spb1-MTD local model
- 7R6K 3.17 Å, State E2 nucleolar 60S ribosomal intermediate - Model for Noc2/Noc3 region
Browse structure collections
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