7NAC image
Entry Detail
PDB ID:
7NAC
EMDB ID:
Keywords:
Title:
State E2 nucleolar 60S ribosomal biogenesis intermediate - Composite model
Biological Source:
PDB Version:
Deposition Date:
2021-06-21
Release Date:
2022-11-09
Method Details:
Experimental Method:
Resolution:
3.04 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
Macromolecular Entities
Polymer Type:polyribonucleotide
Description:25S rRNA
Chain IDs:A (auth: 1)
Chain Length:3396
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
Polymer Type:polyribonucleotide
Description:5.8S rRNA
Chain IDs:B (auth: 2)
Chain Length:158
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
Polymer Type:polypeptide(L)
Description:RRP17 isoform 1
Chain IDs:EB (auth: 5)
Chain Length:235
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
Polymer Type:polyribonucleotide
Description:5.8S ribosomal RNA gene and internal transcribed spacer 2
Chain IDs:ZA (auth: 6)
Chain Length:87
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
Polymer Type:polypeptide(L)
Description:60S ribosomal subunit assembly/export protein LOC1
Chain IDs:C (auth: 7)
Chain Length:204
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
Polymer Type:polypeptide(L)
Description:NOC2 isoform 1
Chain IDs:LA (auth: 8)
Chain Length:710
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
Polymer Type:polypeptide(L)
Description:Ribosome biogenesis protein BRX1
Chain IDs:D (auth: A)
Chain Length:217
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L3
Chain IDs:E (auth: B)
Chain Length:387
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L4-A
Chain IDs:F (auth: C)
Chain Length:362
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
Polymer Type:polypeptide(L)
Description:ATP-dependent RNA helicase HAS1
Chain IDs:AB (auth: D)
Chain Length:505
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L6-A
Chain IDs:G (auth: E)
Chain Length:130
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L7-A
Chain IDs:H (auth: F)
Chain Length:244
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L8-A
Chain IDs:QA (auth: G)
Chain Length:121
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L9-A
Chain IDs:I (auth: H)
Chain Length:191
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
Polymer Type:polypeptide(L)
Description:Nucleolar complex-associated protein 3
Chain IDs:MA (auth: I)
Chain Length:663
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
Polymer Type:polypeptide(L)
Description:rRNA-processing protein EBP2
Chain IDs:J
Chain Length:427
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
Polymer Type:polypeptide(L)
Description:Proteasome-interacting protein CIC1
Chain IDs:NA (auth: K)
Chain Length:376
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L13-A
Chain IDs:K (auth: L)
Chain Length:181
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L14-A
Chain IDs:L (auth: M)
Chain Length:138
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L15-A
Chain IDs:M (auth: N)
Chain Length:605
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L16-A
Chain IDs:N (auth: O)
Chain Length:199
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L17-A
Chain IDs:O (auth: P)
Chain Length:184
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L18-A
Chain IDs:P (auth: Q)
Chain Length:618
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L19-A
Chain IDs:PA (auth: R)
Chain Length:261
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L20-A
Chain IDs:Q (auth: S)
Chain Length:172
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L21-A
Chain IDs:R (auth: T)
Chain Length:322
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L22-A
Chain IDs:SA (auth: U)
Chain Length:121
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L23-A
Chain IDs:OA (auth: V)
Chain Length:231
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
Polymer Type:polypeptide(L)
Description:Ribosome assembly factor MRT4
Chain IDs:S (auth: W)
Chain Length:236
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L25
Chain IDs:T (auth: X)
Chain Length:142
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L26-A
Chain IDs:U (auth: Y)
Chain Length:127
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L27-A
Chain IDs:RA (auth: Z)
Chain Length:106
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
Polymer Type:polypeptide(L)
Description:Ribosomal protein
Chain IDs:DB (auth: a)
Chain Length:217
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
Polymer Type:polypeptide(L)
Description:Nucleolar GTP-binding protein 1
Chain IDs:V (auth: b)
Chain Length:387
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L30
Chain IDs:TA (auth: c)
Chain Length:362
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L31-A
Chain IDs:W (auth: d)
Chain Length:505
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L32
Chain IDs:X (auth: e)
Chain Length:130
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L33-A
Chain IDs:Y (auth: f)
Chain Length:244
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L34-A
Chain IDs:UA (auth: g)
Chain Length:121
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L35-A
Chain IDs:Z (auth: h)
Chain Length:191
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L36-A
Chain IDs:AA (auth: i)
Chain Length:663
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L37-A
Chain IDs:BA (auth: j)
Chain Length:427
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L38
Chain IDs:VA (auth: k)
Chain Length:376
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
Polymer Type:polypeptide(L)
Description:60S ribosome subunit biogenesis protein NIP7
Chain IDs:CA (auth: l)
Chain Length:181
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
Polymer Type:polypeptide(L)
Description:Ribosome biogenesis protein ERB1
Chain IDs:DA (auth: m)
Chain Length:138
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
Polymer Type:polypeptide(L)
Description:Pescadillo homolog
Chain IDs:WA (auth: n)
Chain Length:605
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
Polymer Type:polypeptide(L)
Description:Ribosome biogenesis protein 15
Chain IDs:BB (auth: o)
Chain Length:199
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
Polymer Type:polypeptide(L)
Description:YTM1 isoform 1
Chain IDs:XA (auth: p)
Chain Length:184
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
Polymer Type:polypeptide(L)
Description:25S rRNA (cytosine(2870)-C(5))-methyltransferase
Chain IDs:EA (auth: q)
Chain Length:618
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
Polymer Type:polypeptide(L)
Description:Ribosome biogenesis protein NSA2
Chain IDs:FA (auth: r)
Chain Length:261
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
Polymer Type:polypeptide(L)
Description:Nuclear GTP-binding protein NUG1
Chain IDs:GA (auth: s)
Chain Length:172
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
Polymer Type:polypeptide(L)
Description:Ribosome biogenesis protein RLP7
Chain IDs:YA (auth: t)
Chain Length:322
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
Polymer Type:polypeptide(L)
Description:Ribosome biogenesis protein RLP24
Chain IDs:HA (auth: u)
Chain Length:121
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
Polymer Type:polypeptide(L)
Description:Nucleolar protein 16
Chain IDs:IA (auth: v)
Chain Length:231
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
Polymer Type:polypeptide(L)
Description:27S pre-rRNA (guanosine(2922)-2'-O)-methyltransferase
Chain IDs:CB (auth: w)
Chain Length:236
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
Polymer Type:polypeptide(L)
Description:ATP-dependent rRNA helicase SPB4
Chain IDs:FB (auth: x)
Chain Length:142
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
Polymer Type:polypeptide(L)
Description:Eukaryotic translation initiation factor 6
Chain IDs:JA (auth: y)
Chain Length:127
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
Polymer Type:polypeptide(L)
Description:UPF0642 protein YBL028C
Chain IDs:KA (auth: z)
Chain Length:106
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
Primary Citation
Sequence-specific remodeling of a topologically complex RNP substrate by Spb4.
Nat.Struct.Mol.Biol. 29 1228 1238 (2022)
PMID: 36482249 DOI: 10.1038/s41594-022-00874-9

Abstact

DEAD-box ATPases are ubiquitous enzymes essential in all aspects of RNA biology. However, the limited in vitro catalytic activities described for these enzymes are at odds with their complex cellular roles, most notably in driving large-scale RNA remodeling steps during the assembly of ribonucleoproteins (RNPs). We describe cryo-EM structures of 60S ribosomal biogenesis intermediates that reveal how context-specific RNA unwinding by the DEAD-box ATPase Spb4 results in extensive, sequence-specific remodeling of rRNA secondary structure. Multiple cis and trans interactions stabilize Spb4 in a post-catalytic, high-energy intermediate that drives the organization of the three-way junction at the base of rRNA domain IV. This mechanism explains how limited strand separation by DEAD-box ATPases is leveraged to provide non-equilibrium directionality and ensure efficient and accurate RNP assembly.

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Primary Citation of related structures