9G28 image
Deposition Date 2024-07-10
Release Date 2025-06-18
Last Version Date 2025-06-18
Entry Detail
PDB ID:
9G28
Keywords:
Title:
snR30 snoRNP - State 2 - Utp23-Krr1-deltaC3
Biological Source:
Source Organism:
Method Details:
Experimental Method:
Resolution:
3.18 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
Macromolecular Entities
Polymer Type:polyribonucleotide
Molecule:RDN18-1
Chain IDs:A (auth: 3)
Chain Length:1800
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polyribonucleotide
Molecule:snR30
Chain IDs:B (auth: 4)
Chain Length:609
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Molecule:H/ACA ribonucleoprotein complex subunit CBF5
Gene (Uniprot):CBF5
Chain IDs:C (auth: A), G (auth: E)
Chain Length:483
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Molecule:H/ACA ribonucleoprotein complex subunit NOP10
Gene (Uniprot):NOP10
Chain IDs:D (auth: B), H (auth: F)
Chain Length:58
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Molecule:H/ACA ribonucleoprotein complex subunit GAR1
Gene (Uniprot):GAR1
Chain IDs:E (auth: C)
Chain Length:205
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Molecule:H/ACA ribonucleoprotein complex subunit NHP2
Gene (Uniprot):NHP2
Chain IDs:F (auth: D), I (auth: G)
Chain Length:156
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Molecule:KRR1 small subunit processome component
Gene (Uniprot):KRR1
Chain IDs:J (auth: H)
Chain Length:316
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Molecule:Protein KRI1
Gene (Uniprot):KRI1
Chain IDs:K (auth: I)
Chain Length:591
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S13
Gene (Uniprot):RPS13
Chain IDs:L (auth: J)
Chain Length:151
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Molecule:rRNA-processing protein UTP23
Gene (Uniprot):UTP23
Chain IDs:N (auth: K)
Chain Length:254
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S14-A
Gene (Uniprot):RPS14A
Chain IDs:M (auth: L)
Chain Length:137
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Ligand Molecules
Primary Citation
H/ACA snR30 snoRNP guides independent 18S rRNA subdomain formation.
Nat Commun 16 4720 4720 (2025)
PMID: 40399280 DOI: 10.1038/s41467-025-59656-8

Abstact

Ribosome biogenesis follows a cascade of pre-rRNA folding and processing steps, coordinated with ribosomal protein incorporation. Nucleolar 90S pre-ribosomes are well-described stable intermediates, composed of pre-18S rRNA, ribosomal S-proteins, U3 snoRNA, and ~70 assembly factors. However, how numerous snoRNAs control pre-rRNA modification and folding during early maturation events remains unclear. We identify snR30 (human U17), the only essential H/ACA snoRNA in yeast, which binds with Cbf5-Gar1-Nop10-Nhp2 to a pre-18S rRNA subdomain containing platform helices and ES6 of the 40S central domain. Integration into the 90S is blocked by RNA hybridization with snR30. The snoRNP complex coordinates the recruitment of early assembly factors Krr1-Utp23-Kri1 and ribosomal proteins uS11-uS15, enabling isolated subdomain assembly. Krr1-dependent release of snR30 culminates in integration of the platform into the 90S. Our study reveals the essential role of snR30 in chaperoning central domain formation as a discrete assembly unit externalized from the pre-ribosomal core.

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Primary Citation of related structures