9G33 | pdb_00009g33

Stalled 90S - Utp23-Krr1-deltaC3


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.05 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


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: 4
MoleculeChains Sequence LengthOrganismDetailsImage
U3 small nucleolar ribonucleoprotein protein IMP4D [auth CJ]290Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
U3 small nucleolar RNA-associated protein MPP10E [auth CK]593Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosome biogenesis protein BMS1F [auth CL]1,183Saccharomyces cerevisiaeMutation(s): 0 
EC: 3.6.5
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S24-AG [auth DY]135Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
rRNA-processing protein FCF1H [auth UX]189Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal RNA small subunit methyltransferase NEP1I [auth JG],
J [auth JF]
252Saccharomyces cerevisiaeMutation(s): 0 
EC: 2.1.1.260
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
rRNA 2'-O-methyltransferase fibrillarinK [auth CA],
L [auth CB]
327Saccharomyces cerevisiaeMutation(s): 0 
EC: 2.1.1
UniProt
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Nucleolar complex protein 14M [auth UB]810Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Something about silencing protein 10N [auth UC]610Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
U3 small nucleolar RNA-associated protein 5O [auth UE]643Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
U3 small nucleolar RNA-associated protein 8P [auth UH]713Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
U3 small nucleolar RNA-associated protein 11Q [auth UK]250Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
U3 small nucleolar RNA-associated protein 12R [auth UL]943Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
U3 small nucleolar RNA-associated protein 13S [auth UM]817Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
U3 small nucleolar RNA-associated protein 15T [auth UO]513Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
U3 small nucleolar RNA-associated protein 16U [auth UP]214Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
Nucleolar complex protein 4V [auth US]552Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
13 kDa ribonucleoprotein-associated proteinW [auth CF],
X [auth CG]
126Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
U3 small nucleolar ribonucleoprotein protein IMP3Y [auth CI]183Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
U3 small nucleolar ribonucleoprotein protein LCP5Z [auth JE]357Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
Essential nuclear protein 1AA [auth JH]483Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-rRNA-processing protein PNO1BA [auth JJ]274Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
Protein BFR2CA [auth JK]534Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
rRNA-processing protein FCF2DA [auth JM]217Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
Regulator of rDNA transcription protein 14EA [auth JQ]206Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S5FA [auth DF]225Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S8-AGA [auth DI]200Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S9-AHA [auth DJ]197Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S18-AIA [auth DS]146Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosome biogenesis protein ENP2JA [auth JC]707Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S4-AKA [auth DE]261Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S23-ALA [auth DX]145Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S22-AMA [auth DW]130Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S6-ANA [auth DG]236Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S11-AOA [auth DL]156Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal RNA-processing protein 9PA [auth CH]573Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S28-AQA [auth Dc]67Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S16-ARA [auth DQ]143Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
Nucleolar protein 58SA [auth CE]511Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
Nucleolar protein 56TA [auth CD]504Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
U3 small nucleolar RNA-associated protein 14UA [auth UN]899Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
U3 small nucleolar RNA-associated protein 6VA [auth UF]440Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
U3 small nucleolar RNA-associated protein 7WA [auth UG]554Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
Protein FAF1XA [auth JN]346Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
KRR1 small subunit processome componentYA [auth JO]316Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P25586 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
RNA 3'-terminal phosphate cyclase-like proteinZA [auth CM]367Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for Q08096 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosome biogenesis protein UTP30AB [auth UZ]274Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P36144 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
Protein SOF1BB [auth JP]489Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P33750 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
U3 small nucleolar RNA-associated protein 18CB [auth UR]594Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P40362 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 53
MoleculeChains Sequence LengthOrganismDetailsImage
U3 small nucleolar RNA-associated protein 21DB [auth UU]939Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for Q06078 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 54
MoleculeChains Sequence LengthOrganismDetailsImage
U3 small nucleolar RNA-associated protein 4EB [auth UD]776Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for Q06679 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 55
MoleculeChains Sequence LengthOrganismDetailsImage
NET1-associated nuclear protein 1FB [auth UQ]896Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for Q02931 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 56
MoleculeChains Sequence LengthOrganismDetailsImage
Periodic tryptophan protein 2GB [auth UA]923Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P25635 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 57
MoleculeChains Sequence LengthOrganismDetailsImage
U3 small nucleolar RNA-associated protein 9HB [auth UI]575Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P38882 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 58
MoleculeChains Sequence LengthOrganismDetailsImage
U3 small nucleolar RNA-associated protein 10IB [auth UJ]1,769Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 59
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S7-AJB [auth DH]190Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 60
MoleculeChains Sequence LengthOrganismDetailsImage
U3 small nucleolar RNA-associated protein 20KB [auth UT]2,493Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P35194 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 61
MoleculeChains Sequence LengthOrganismDetailsImage
RNA cytidine acetyltransferaseLB [auth JA],
MB [auth JB]
1,056Saccharomyces cerevisiaeMutation(s): 0 
EC: 2.3.1
UniProt
Find proteins for P53914 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 1
MoleculeChains LengthOrganismImage
18S rRNAA [auth D3]1,808Saccharomyces cerevisiae
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Entity ID: 2
MoleculeChains LengthOrganismImage
5' ETSB [auth D2]700Saccharomyces cerevisiae
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Entity ID: 3
MoleculeChains LengthOrganismImage
U3 snoRNAC [auth D4]333Saccharomyces cerevisiae
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.05 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.19.2_4158:

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