9G33 image
Deposition Date 2024-07-11
Release Date 2025-06-18
Last Version Date 2025-06-18
Entry Detail
PDB ID:
9G33
Keywords:
Title:
Stalled 90S - Utp23-Krr1-deltaC3
Biological Source:
Source Organism(s):
Method Details:
Experimental Method:
Resolution:
3.05 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:rRNA 2'-O-methyltransferase f
Gene (Uniprot):NOP1
Chain IDs:K (auth: CA), L (auth: CB)
Chain Length:0
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Molecule:Nucleolar protein 56
Gene (Uniprot):NOP56
Chain IDs:TA (auth: CD)
Chain Length:0
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Molecule:Nucleolar protein 58
Gene (Uniprot):NOP58
Chain IDs:SA (auth: CE)
Chain Length:0
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Molecule:13 kDa ribonucleoprotein-asso
Gene (Uniprot):SNU13
Chain IDs:W (auth: CF), X (auth: CG)
Chain Length:0
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Molecule:Ribosomal RNA-processing prot
Gene (Uniprot):RRP9
Chain IDs:PA (auth: CH)
Chain Length:0
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Molecule:U3 small nucleolar ribonucleo
Gene (Uniprot):IMP3
Chain IDs:Y (auth: CI)
Chain Length:0
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Molecule:U3 small nucleolar ribonucleo
Gene (Uniprot):IMP4
Chain IDs:D (auth: CJ)
Chain Length:0
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Molecule:U3 small nucleolar RNA-associ
Gene (Uniprot):MPP10
Chain IDs:E (auth: CK)
Chain Length:0
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Molecule:Ribosome biogenesis protein B
Gene (Uniprot):BMS1
Chain IDs:F (auth: CL)
Chain Length:0
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Molecule:RNA 3'-terminal phosphate cyc
Gene (Uniprot):RCL1
Chain IDs:ZA (auth: CM)
Chain Length:0
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polyribonucleotide
Molecule:5' ETS
Chain IDs:B (auth: D2)
Chain Length:0
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polyribonucleotide
Molecule:18S rRNA
Chain IDs:A (auth: D3)
Chain Length:0
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polyribonucleotide
Molecule:U3 snoRNA
Chain IDs:C (auth: D4)
Chain Length:0
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S4-A
Gene (Uniprot):RPS4A
Chain IDs:KA (auth: DE)
Chain Length:0
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S5
Gene (Uniprot):RPS5
Chain IDs:FA (auth: DF)
Chain Length:0
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S6-A
Gene (Uniprot):RPS6A
Chain IDs:NA (auth: DG)
Chain Length:0
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S7-A
Gene (Uniprot):RPS7A
Chain IDs:JB (auth: DH)
Chain Length:0
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S8-A
Gene (Uniprot):RPS8A
Chain IDs:GA (auth: DI)
Chain Length:0
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S9-A
Gene (Uniprot):RPS9A
Chain IDs:HA (auth: DJ)
Chain Length:0
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S11-A
Gene (Uniprot):RPS11A
Chain IDs:OA (auth: DL)
Chain Length:0
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S16-A
Gene (Uniprot):RPS16A
Chain IDs:RA (auth: DQ)
Chain Length:0
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S18-A
Gene (Uniprot):RPS18A
Chain IDs:IA (auth: DS)
Chain Length:0
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S22-A
Gene (Uniprot):RPS22A
Chain IDs:MA (auth: DW)
Chain Length:0
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S23-A
Gene (Uniprot):RPS23A
Chain IDs:LA (auth: DX)
Chain Length:0
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S24-A
Gene (Uniprot):RPS24A
Chain IDs:G (auth: DY)
Chain Length:0
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S28-A
Gene (Uniprot):RPS28A
Chain IDs:QA (auth: Dc)
Chain Length:0
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Molecule:RNA cytidine acetyltransferas
Gene (Uniprot):KRE33
Chain IDs:LB (auth: JA), MB (auth: JB)
Chain Length:0
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Molecule:Ribosome biogenesis protein E
Gene (Uniprot):ENP2
Chain IDs:JA (auth: JC)
Chain Length:0
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Molecule:U3 small nucleolar ribonucleo
Gene (Uniprot):LCP5
Chain IDs:Z (auth: JE)
Chain Length:0
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Molecule:Ribosomal RNA small subunit m
Gene (Uniprot):EMG1
Chain IDs:I (auth: JG), J (auth: JF)
Chain Length:0
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Molecule:Essential nuclear protein 1
Gene (Uniprot):ENP1
Chain IDs:AA (auth: JH)
Chain Length:0
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Molecule:Pre-rRNA-processing protein P
Gene (Uniprot):PNO1
Chain IDs:BA (auth: JJ)
Chain Length:0
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Molecule:Protein BFR2
Gene (Uniprot):BFR2
Chain IDs:CA (auth: JK)
Chain Length:0
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Molecule:rRNA-processing protein FCF2
Gene (Uniprot):FCF2
Chain IDs:DA (auth: JM)
Chain Length:0
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Molecule:Protein FAF1
Gene (Uniprot):FAF1
Chain IDs:XA (auth: JN)
Chain Length:0
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Molecule:KRR1 small subunit processome
Gene (Uniprot):KRR1
Chain IDs:YA (auth: JO)
Chain Length:0
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Molecule:Protein SOF1
Gene (Uniprot):SOF1
Chain IDs:BB (auth: JP)
Chain Length:0
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Molecule:Regulator of rDNA transcripti
Gene (Uniprot):RRT14
Chain IDs:EA (auth: JQ)
Chain Length:0
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Molecule:Periodic tryptophan protein 2
Gene (Uniprot):PWP2
Chain IDs:GB (auth: UA)
Chain Length:0
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Molecule:Nucleolar complex protein 14
Gene (Uniprot):NOP14
Chain IDs:M (auth: UB)
Chain Length:0
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Molecule:Something about silencing pro
Gene (Uniprot):SAS10
Chain IDs:N (auth: UC)
Chain Length:0
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Molecule:U3 small nucleolar RNA-associ
Gene (Uniprot):UTP4
Chain IDs:EB (auth: UD)
Chain Length:0
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Molecule:U3 small nucleolar RNA-associ
Gene (Uniprot):UTP5
Chain IDs:O (auth: UE)
Chain Length:0
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Molecule:U3 small nucleolar RNA-associ
Gene (Uniprot):UTP6
Chain IDs:VA (auth: UF)
Chain Length:0
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Molecule:U3 small nucleolar RNA-associ
Gene (Uniprot):UTP7
Chain IDs:WA (auth: UG)
Chain Length:0
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Molecule:U3 small nucleolar RNA-associ
Gene (Uniprot):UTP8
Chain IDs:P (auth: UH)
Chain Length:0
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Molecule:U3 small nucleolar RNA-associ
Gene (Uniprot):UTP9
Chain IDs:HB (auth: UI)
Chain Length:0
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Molecule:U3 small nucleolar RNA-associ
Gene (Uniprot):UTP10
Chain IDs:IB (auth: UJ)
Chain Length:0
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Molecule:U3 small nucleolar RNA-associ
Gene (Uniprot):UTP11
Chain IDs:Q (auth: UK)
Chain Length:0
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Molecule:U3 small nucleolar RNA-associ
Gene (Uniprot):DIP2
Chain IDs:R (auth: UL)
Chain Length:0
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Molecule:U3 small nucleolar RNA-associ
Gene (Uniprot):UTP13
Chain IDs:S (auth: UM)
Chain Length:0
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Molecule:U3 small nucleolar RNA-associ
Gene (Uniprot):UTP14
Chain IDs:UA (auth: UN)
Chain Length:0
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Molecule:U3 small nucleolar RNA-associ
Gene (Uniprot):UTP15
Chain IDs:T (auth: UO)
Chain Length:0
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Molecule:U3 small nucleolar RNA-associ
Gene (Uniprot):BUD21
Chain IDs:U (auth: UP)
Chain Length:0
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Molecule:NET1-associated nuclear prote
Gene (Uniprot):NAN1
Chain IDs:FB (auth: UQ)
Chain Length:0
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Molecule:U3 small nucleolar RNA-associ
Gene (Uniprot):UTP18
Chain IDs:CB (auth: UR)
Chain Length:0
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Molecule:Nucleolar complex protein 4
Gene (Uniprot):NOC4
Chain IDs:V (auth: US)
Chain Length:0
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Molecule:U3 small nucleolar RNA-associ
Gene (Uniprot):UTP20
Chain IDs:KB (auth: UT)
Chain Length:0
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Molecule:U3 small nucleolar RNA-associ
Gene (Uniprot):UTP21
Chain IDs:DB (auth: UU)
Chain Length:0
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Molecule:rRNA-processing protein FCF1
Gene (Uniprot):FCF1
Chain IDs:H (auth: UX)
Chain Length:0
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Molecule:Ribosome biogenesis protein U
Gene (Uniprot):UTP30
Chain IDs:AB (auth: UZ)
Chain Length:0
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
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
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