7NAF: Ribosomal RNA-processing protein 17
State E2 nucleolar 60S ribosomal biogenesis intermediate - Spb1-MTD local model. Determined by electron microscopy at 3.13 Å resolution. Released 9 Nov 2022.
- Method
- Electron microscopy
- Resolution
- 3.13 Å
- Organism
- Saccharomyces cerevisiae BY4741
- Chains
- 16
- Atoms
- 18,868
- Mol. weight
- 311.69 kDa
- Ligands
- SAH
- Released
- 9 Nov 2022
Explore 7NAF in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
7NAF contains 55 α-helices and 74 β-strands across 13 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: 3 helices, 1 β-strand
| Element | Residues | Length | Sheet |
|---|
| β-strand | 26-29 | 4 | 1 |
| α-helix | 33-41 | 9 | |
| α-helix | 45-93 | 49 | |
| α-helix | 218-230 | 13 | |
Chain 8: 2 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 6-14 | 9 | |
| α-helix | 16-32 | 17 | |
Chain b: 3 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 21-27 | 7 | |
| α-helix | 39-55 | 17 | |
| β-strand | 435-436 | 2 | 10 |
| β-strand | 439-440 | 2 | 10 |
| α-helix | 497-510 | 14 | |
| β-strand | 518 | 1 | 11 |
Chain B: 6 helices, 14 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 14-16 | 3 | |
| α-helix | 21-22 | 2 | |
| β-strand | 48-60 | 13 | 14 |
| β-strand | 70-80 | 11 | 14 |
| β-strand | 214-220 | 7 | 15 |
| α-helix | 221-223 | 3 | |
| β-strand | 225-227 | 3 | 16 |
| β-strand | 268-270 | 3 | 16 |
| β-strand | 274-281 | 8 | 15 |
| β-strand | 282-284 | 3 | 14 |
| β-strand | 299 | 1 | 10 |
| β-strand | 311 | 1 | 17 |
| β-strand | 314 | 1 | 17 |
| β-strand | 321-325 | 5 | 14 |
| β-strand | 335-336 | 2 | 14 |
| β-strand | 337-339 | 3 | 15 |
| α-helix | 348-351 | 4 | |
| α-helix | 352-354 | 3 | |
| β-strand | 355-360 | 6 | 14 |
| α-helix | 373-380 | 8 | |
Chain c: 2 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 43-44 | 2 | 13 |
| α-helix | 50-53 | 4 | |
| β-strand | 68-69 | 2 | 13 |
| α-helix | 74-81 | 8 | |
| β-strand | 89-90 | 2 | 13 |
Chain d: 4 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 14-15 | 2 | 12 |
| α-helix | 16-19 | 4 | |
| α-helix | 25-27 | 3 | |
| α-helix | 28-34 | 7 | |
| α-helix | 55-60 | 6 | |
| β-strand | 70-71 | 2 | 12 |
Chain q: 1 helix, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 286-292 | 7 | |
| β-strand | 294-297 | 4 | 26 |
| β-strand | 308-312 | 5 | 26 |
Chain R: 4 helices, 1 β-strand
| Element | Residues | Length | Sheet |
|---|
| β-strand | 54 | 1 | 11 |
| α-helix | 55-56 | 2 | |
| α-helix | 91-109 | 19 | |
| α-helix | 117-128 | 12 | |
| α-helix | 135-144 | 10 | |
5 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 | 378 | Saccharomyces cerevisiae BY4741 | |
| Ribosomal RNA-processing protein 17 | 5 | protein | 105 | Saccharomyces cerevisiae BY4741 | Q04031 (AlphaFold model) |
| Nucleolar complex protein 2 | 8 | protein | 39 | Saccharomyces cerevisiae BY4741 | P39744 (AlphaFold model) |
| 60S ribosomal protein L23-A | V | protein | 134 | Saccharomyces cerevisiae BY4741 | P0CX41 (AlphaFold model) |
| Ribosome biogenesis protein RLP24 | u | protein | 65 | Saccharomyces cerevisiae BY4741 | Q07915 (AlphaFold model) |
| 27S pre-rRNA (guanosine(2922)-2'-O)-methyltransferase | w | protein | 389 | Saccharomyces cerevisiae BY4741 | P25582 |
| 60S ribosome biogenesis factor Nog1 | b | protein | 74 | Saccharomyces cerevisiae BY4741 | Q02892 |
| 60S ribosomal protein L31-A | d | protein | 60 | Saccharomyces cerevisiae BY4741 | P0C2H8 |
| 60S ribosomal protein L22-A | U | protein | 18 | Saccharomyces cerevisiae BY4741 | P05749 |
| 60S ribosome ribosomal protein L19A | R | protein | 62 | Saccharomyces cerevisiae BY4741 | P0CX82 |
| 60S ribosomal protein L30 | c | protein | 41 | Saccharomyces cerevisiae BY4741 | P14120 |
| 60S ribosomal protein L3 | B | protein | 376 | Saccharomyces cerevisiae BY4741 | P14126 |
4 more molecules are not listed.
Sequence of entity 1 (1), FASTA
>7NAF_1 25S rRNA (chains 1)
AUAGGGUGAAGCCAGAGGAAACUCUGGUGGAGGCUCGAAAAUGGAAUUAGACUGAAGGUC
GGCGCCCUGGAGUUAUCUUUUCUUGUUUAUCCCGCUUCGGCCCCAAGGUGAACAGCCUCU
AAUGUAGAUAAGGGAAGUCGGGGGAAUCUGACUGUUAACGAGAUUCCCACUGUCCCUAUC
UACUCGGGGAACUGGCUUGUCGGCUCUUCCUAUCAUACCAUUCGGUAAGCGUUGGAUUGU
UCACCCACUAAUAGGGAACGUGAGCUGAAUUGAACUUAGGAACAGUUCAUUCGGAUAAUU
GGUUUUUGCGGCUGUCUGAUCAGGCAUUGCCGCGAAGCUACCAUCCGAAUCUAUAUAUUG
UAAGCUGAGAUUAAGCCU
Sequence of entity 2 (5), FASTA
>7NAF_2 Ribosomal RNA-processing protein 17 (chains 5)
NRQILTRGKQSKKFGTDEVTFDKDSRLDYLTGFHKRKLQRQKKAQEFIKEQERLRKIEER
QKIRQERKEVMEEQLKTFKESLNLKFRYLTKNERRINQRKANDNK
Sequence of entity 3 (8), FASTA
>7NAF_3 Nucleolar complex protein 2 (chains 8)
KVSKSTKKFQSKHLKHTLDQRRKEKIQKKRIQGRRGNKT
Sequence of entity 4 (V), FASTA
>7NAF_4 60S ribosomal protein L23-A (chains V)
NGAQGTKFRISLGLPVGAIMNCADNSGARNLYIIAVKGSGSRLNRLPAASLGDMVMATVK
KGKPELRKKVMPAIVVRQAKSWRRRDGVFLYFEDNAGVIANPKGEMKGSAITGPVGKECA
DLWPRVASNSGVVV
Sequence of entity 5 (u), FASTA
>7NAF_5 Ribosome biogenesis protein RLP24 (chains u)
MRIYQCHFCSSPCYPGHGIMFVRNDAKEFRFCRSKCHKAFKQRRNPRKLKWTKAFRKAAG
KELAV
Sequence of entity 6 (w), FASTA
>7NAF_6 27S pre-rRNA (guanosine(2922)-2'-O)-methyltransferase (chains w)
MGKTQKKNSKGRLDRYYYLAKEKGYRARSSFKIIQINEKYGHFLEKSKVVIDLCAAPGSW
CQVASKLCPVNSLIIGVDIVPMKPMPNVITFQSDITTEDCRSKLRGYMKTWKADTVLHDG
APNVGLGWVQDAFTQSQLTLQALKLAVENLVVNGTFVTKIFRSKDYNKLIWVFQQLFEKV
EATKPPASRNVSAEIFVVCKGFKAPKRLDPRLLDPKEVFEELPDGQQNMESKIYNPEKKV
RKRQGYEEGDNLLYHETSILDFVRTEDPISMLGEMNKFTIDENDHEWKILKKLKQTTDEF
RSCIEDLKVLGKKDFKMILRWRKIAREILGIEVKDDAKTEIEVVPLTEEEQIEKDLQGLQ
EKQRLNVKRERRRKNEMKQKELQRMQMNM
Sequence of entity 7 (b), FASTA
>7NAF_7 60S ribosome biogenesis factor Nog1 (chains b)
IVLNRTQRKTPTVIRPGFKITRIRAFYMRKVKYTGEGMPEILDGKNVYIRNRQKTMIAEA
RNRKSLKNKAIMPR
Sequence of entity 8 (d), FASTA
>7NAF_8 60S ribosomal protein L31-A (chains d)
TINLHKRLHGVSFKKRAPRAVKEIKKFAKLHMGTDDVRLAPELNQAIWKRGVKGVEYRLR
Sequence of entity 9 (U), FASTA
>7NAF_9 60S ribosomal protein L22-A (chains U)
KYLKYLTKKYLKKNQLRD
Sequence of entity 10 (R), FASTA
>7NAF_10 60S ribosome ribosomal protein L19A (chains R)
KAVTVHSKRLPSQVVWIRRLRVLRRLLAKYRIDKHLYHVLYKESKGNAFKHKRALVEHII
QA
Sequence of entity 11 (c), FASTA
>7NAF_11 60S ribosomal protein L30 (chains c)
LGYIIIAANTPVLRKSVYYFQGGNNELGTAVGKLFRVGVVS
Sequence of entity 12 (B), FASTA
>7NAF_12 60S ribosomal protein L3 (chains B)
GHLGFLPRKRAASIRARVKAFPKDDRSKPVALTSFLGYKAGMTTIVRDLDRPGSKFHKRE
VVEAVTVVDTPPVVVVGVVGYVETPRGLRSLTTVWAEHLSDEVKRRFYKNWYKSKKKAFT
KYSAKYAQDGAGIERELARIKKYASVVRVLVHTQIRKTPLAQKKAHLAEIQLNGGSISEK
VDWAREHFEKTVAVDSVFEQNEMIDAIAVTKGHGFEGVTHRWGTKKLPRKTHRGLRKVAC
IGAWHPAHVMWSVARAGQRGYHSRTSINHKIYRVGKGDDEANGATSFDRTKKTITPMGGF
VHYGEIKNDFIMVKGCIPGNRKRIVTLRKSLYTNTSRKALEEVSLKWIDTASKFGKGRFQ
TPAEKHAFMGTLKKDL
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| SAH | S-adenosyl-L-homocysteine | C14 H20 N6 O5 S | 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
- 7NAD 3.04 Å, State E2 nucleolar 60S ribosomal biogenesis intermediate - Spb4 local refinement model
- 7R6K 3.17 Å, State E2 nucleolar 60S ribosomal intermediate - Model for Noc2/Noc3 region
Browse structure collections
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