9G28 | pdb_00009g28

snR30 snoRNP - State 2 - Utp23-Krr1-deltaC3


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.18 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


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Literature

H/ACA snR30 snoRNP guides independent 18S rRNA subdomain formation.

Fischer, P.Thoms, M.Lau, B.Denk, T.Kuvshinova, M.Berninghausen, O.Flemming, D.Hurt, E.Beckmann, R.

(2025) Nat Commun 16: 4720-4720

  • DOI: https://doi.org/10.1038/s41467-025-59656-8
  • Primary Citation of Related Structures:  
    9G25, 9G28, 9G33

  • PubMed Abstract: 

    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.


  • Organizational Affiliation
    • Biochemistry Center, Heidelberg University, Heidelberg, Germany.

Macromolecules

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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
H/ACA ribonucleoprotein complex subunit CBF5C [auth A],
G [auth E]
483Saccharomyces cerevisiaeMutation(s): 0 
EC: 5.4.99
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
H/ACA ribonucleoprotein complex subunit NOP10D [auth B],
H [auth F]
58Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
H/ACA ribonucleoprotein complex subunit GAR1E [auth C]205Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
H/ACA ribonucleoprotein complex subunit NHP2F [auth D],
I [auth G]
156Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
KRR1 small subunit processome componentJ [auth H]316Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Protein KRI1K [auth I]591Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S13L [auth J]151Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S14-AM [auth L]137Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
rRNA-processing protein UTP23N [auth K]254Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 1
MoleculeChains LengthOrganismImage
RDN18-1A [auth 3]1,800Saccharomyces cerevisiae
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Entity ID: 2
MoleculeChains LengthOrganismImage
snR30B [auth 4]609Saccharomyces cerevisiae
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.18 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Research Council (ERC)European Union--

Revision History  (Full details and data files)

  • Version 1.0: 2025-06-18
    Type: Initial release