9G33 image
Deposition Date 2024-07-11
Release Date 2025-06-18
Last Version Date 2025-06-18
Entry Detail
PDB ID:
9G33
Keywords:
RIBOSOME
Title:
Stalled 90S - Utp23-Krr1-deltaC3
Biological Source:
Source Organism:
Saccharomyces cerevisiae (Taxon ID: 4932)
Method Details:
Experimental Method:
ELECTRON MICROSCOPY
Resolution:
3.05 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
9G33 validation report
Macromolecular Entities
Protein Blast
Polymer Type:polypeptide(L)
Molecule:rRNA 2'-O-methyltransferase fibrillarin
Gene (Uniprot):NOP1
Chain IDs:K (auth: CA), L (auth: CB)
Chain Length:327
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
UniProt ID:P15646 Pfam ID:PF01269
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Nucleolar protein 56
Gene (Uniprot):NOP56
Chain IDs:TA (auth: CD)
Chain Length:504
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:Q12460 Pfam ID:PF08156, PF01798
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Nucleolar protein 58
Gene (Uniprot):NOP58
Chain IDs:SA (auth: CE)
Chain Length:511
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:Q12499 Pfam ID:PF08156, PF01798
Protein Blast
Polymer Type:polypeptide(L)
Molecule:13 kDa ribonucleoprotein-associated protein
Gene (Uniprot):SNU13
Chain IDs:W (auth: CF), X (auth: CG)
Chain Length:126
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
UniProt ID:P39990 Pfam ID:PF01248
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ribosomal RNA-processing protein 9
Gene (Uniprot):RRP9
Chain IDs:PA (auth: CH)
Chain Length:573
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:Q06506 Pfam ID:PF00400
Protein Blast
Polymer Type:polypeptide(L)
Molecule:U3 small nucleolar ribonucleoprotein protein IMP3
Gene (Uniprot):IMP3
Chain IDs:Y (auth: CI)
Chain Length:183
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P32899 Pfam ID:PF00163, PF01479
Protein Blast
Polymer Type:polypeptide(L)
Molecule:U3 small nucleolar ribonucleoprotein protein IMP4
Gene (Uniprot):IMP4
Chain IDs:D (auth: CJ)
Chain Length:290
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P53941 Pfam ID:PF04427
Protein Blast
Polymer Type:polypeptide(L)
Molecule:U3 small nucleolar RNA-associated protein MPP10
Gene (Uniprot):MPP10
Chain IDs:E (auth: CK)
Chain Length:593
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P47083 Pfam ID:PF04006
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ribosome biogenesis protein BMS1
Gene (Uniprot):BMS1
Chain IDs:F (auth: CL)
Chain Length:1183
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:Q08965 Pfam ID:PF00004, PF08142, PF04950
Protein Blast
Polymer Type:polypeptide(L)
Molecule:RNA 3'-terminal phosphate cyclase-like protein
Gene (Uniprot):RCL1
Chain IDs:ZA (auth: CM)
Chain Length:367
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:Q08096 Pfam ID:PF01137, PF05189
Polymer Type:polyribonucleotide
Molecule:5' ETS
Chain IDs:B (auth: D2)
Chain Length:700
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polyribonucleotide
Molecule:18S rRNA
Chain IDs:A (auth: D3)
Chain Length:1808
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polyribonucleotide
Molecule:U3 snoRNA
Chain IDs:C (auth: D4)
Chain Length:333
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S4-A
Gene (Uniprot):RPS4A
Chain IDs:KA (auth: DE)
Chain Length:261
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P0CX35 Pfam ID:PF08071, PF01479, PF00900, PF00467, PF16121
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S5
Gene (Uniprot):RPS5
Chain IDs:FA (auth: DF)
Chain Length:225
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P26783 Pfam ID:PF00177
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S6-A
Gene (Uniprot):RPS6A
Chain IDs:NA (auth: DG)
Chain Length:236
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P0CX37 Pfam ID:PF01092
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S7-A
Gene (Uniprot):RPS7A
Chain IDs:JB (auth: DH)
Chain Length:190
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P26786 Pfam ID:PF01251
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S8-A
Gene (Uniprot):RPS8A
Chain IDs:GA (auth: DI)
Chain Length:200
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P0CX39 Pfam ID:PF01201
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S9-A
Gene (Uniprot):RPS9A
Chain IDs:HA (auth: DJ)
Chain Length:197
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:O13516 Pfam ID:PF00163, PF01479
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S11-A
Gene (Uniprot):RPS11A
Chain IDs:OA (auth: DL)
Chain Length:156
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P0CX47 Pfam ID:PF16205, PF00366
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S16-A
Gene (Uniprot):RPS16A
Chain IDs:RA (auth: DQ)
Chain Length:143
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P0CX51 Pfam ID:PF00380
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S18-A
Gene (Uniprot):RPS18A
Chain IDs:IA (auth: DS)
Chain Length:146
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P0CX55 Pfam ID:PF00416
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S22-A
Gene (Uniprot):RPS22A
Chain IDs:MA (auth: DW)
Chain Length:130
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P0C0W1 Pfam ID:PF00410
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S23-A
Gene (Uniprot):RPS23A
Chain IDs:LA (auth: DX)
Chain Length:145
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P0CX29 Pfam ID:PF00164
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S24-A
Gene (Uniprot):RPS24A
Chain IDs:G (auth: DY)
Chain Length:135
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P0CX31 Pfam ID:PF01282
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S28-A
Gene (Uniprot):RPS28A
Chain IDs:QA (auth: Dc)
Chain Length:67
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:Q3E7X9 Pfam ID:PF01200
Protein Blast
Polymer Type:polypeptide(L)
Molecule:RNA cytidine acetyltransferase
Gene (Uniprot):KRE33
Chain IDs:LB (auth: JA), MB (auth: JB)
Chain Length:1056
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
UniProt ID:P53914 Pfam ID:PF08351, PF05127, PF13718, PF13725
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ribosome biogenesis protein ENP2
Gene (Uniprot):ENP2
Chain IDs:JA (auth: JC)
Chain Length:707
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P48234 Pfam ID:PF08159
Protein Blast
Polymer Type:polypeptide(L)
Molecule:U3 small nucleolar ribonucleoprotein protein LCP5
Gene (Uniprot):LCP5
Chain IDs:Z (auth: JE)
Chain Length:357
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P40079 Pfam ID:PF04000
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ribosomal RNA small subunit methyltransferase NEP1
Gene (Uniprot):EMG1
Chain IDs:I (auth: JG), J (auth: JF)
Chain Length:252
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
UniProt ID:Q06287 Pfam ID:PF03587
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Essential nuclear protein 1
Gene (Uniprot):ENP1
Chain IDs:AA (auth: JH)
Chain Length:483
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P38333 Pfam ID:PF05291
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Pre-rRNA-processing protein PNO1
Gene (Uniprot):PNO1
Chain IDs:BA (auth: JJ)
Chain Length:274
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:Q99216 Pfam ID:PF17903, PF22891
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Protein BFR2
Gene (Uniprot):BFR2
Chain IDs:CA (auth: JK)
Chain Length:534
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:Q06631 Pfam ID:PF13339, PF08164
Protein Blast
Polymer Type:polypeptide(L)
Molecule:rRNA-processing protein FCF2
Gene (Uniprot):FCF2
Chain IDs:DA (auth: JM)
Chain Length:217
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:Q12035 Pfam ID:PF08698
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Protein FAF1
Gene (Uniprot):FAF1
Chain IDs:XA (auth: JN)
Chain Length:346
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P40546
Protein Blast
Polymer Type:polypeptide(L)
Molecule:KRR1 small subunit processome component
Gene (Uniprot):KRR1
Chain IDs:YA (auth: JO)
Chain Length:316
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P25586 Pfam ID:PF17903, PF21800
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Protein SOF1
Gene (Uniprot):SOF1
Chain IDs:BB (auth: JP)
Chain Length:489
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P33750 Pfam ID:PF00400, PF04158
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Regulator of rDNA transcription protein 14
Gene (Uniprot):RRT14
Chain IDs:EA (auth: JQ)
Chain Length:206
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P40470 Pfam ID:PF17075
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Periodic tryptophan protein 2
Gene (Uniprot):PWP2
Chain IDs:GB (auth: UA)
Chain Length:923
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P25635 Pfam ID:PF00400, PF04003
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Nucleolar complex protein 14
Gene (Uniprot):NOP14
Chain IDs:M (auth: UB)
Chain Length:810
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:Q99207 Pfam ID:PF04147
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Something about silencing protein 10
Gene (Uniprot):SAS10
Chain IDs:N (auth: UC)
Chain Length:610
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:Q12136 Pfam ID:PF04000, PF09368
Protein Blast
Polymer Type:polypeptide(L)
Molecule:U3 small nucleolar RNA-associated protein 4
Gene (Uniprot):UTP4
Chain IDs:EB (auth: UD)
Chain Length:776
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:Q06679 Pfam ID:PF00400
Protein Blast
Polymer Type:polypeptide(L)
Molecule:U3 small nucleolar RNA-associated protein 5
Gene (Uniprot):UTP5
Chain IDs:O (auth: UE)
Chain Length:643
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:Q04177 Pfam ID:PF04003
Protein Blast
Polymer Type:polypeptide(L)
Molecule:U3 small nucleolar RNA-associated protein 6
Gene (Uniprot):UTP6
Chain IDs:VA (auth: UF)
Chain Length:440
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:Q02354 Pfam ID:PF08640, PF05843
Protein Blast
Polymer Type:polypeptide(L)
Molecule:U3 small nucleolar RNA-associated protein 7
Gene (Uniprot):UTP7
Chain IDs:WA (auth: UG)
Chain Length:554
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P40055 Pfam ID:PF00400, PF08149
Protein Blast
Polymer Type:polypeptide(L)
Molecule:U3 small nucleolar RNA-associated protein 8
Gene (Uniprot):UTP8
Chain IDs:P (auth: UH)
Chain Length:713
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P53276 Pfam ID:PF10395, PF22542
Protein Blast
Polymer Type:polypeptide(L)
Molecule:U3 small nucleolar RNA-associated protein 9
Gene (Uniprot):UTP9
Chain IDs:HB (auth: UI)
Chain Length:575
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P38882
Protein Blast
Polymer Type:polypeptide(L)
Molecule:U3 small nucleolar RNA-associated protein 10
Gene (Uniprot):UTP10
Chain IDs:IB (auth: UJ)
Chain Length:1769
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P42945 Pfam ID:PF12397, PF08146
Protein Blast
Polymer Type:polypeptide(L)
Molecule:U3 small nucleolar RNA-associated protein 11
Gene (Uniprot):UTP11
Chain IDs:Q (auth: UK)
Chain Length:250
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P34247 Pfam ID:PF03998
Protein Blast
Polymer Type:polypeptide(L)
Molecule:U3 small nucleolar RNA-associated protein 12
Gene (Uniprot):DIP2
Chain IDs:R (auth: UL)
Chain Length:943
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:Q12220 Pfam ID:PF00400, PF04003
Protein Blast
Polymer Type:polypeptide(L)
Molecule:U3 small nucleolar RNA-associated protein 13
Gene (Uniprot):UTP13
Chain IDs:S (auth: UM)
Chain Length:817
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:Q05946 Pfam ID:PF00400, PF08625
Protein Blast
Polymer Type:polypeptide(L)
Molecule:U3 small nucleolar RNA-associated protein 14
Gene (Uniprot):UTP14
Chain IDs:UA (auth: UN)
Chain Length:899
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:Q04500 Pfam ID:PF04615
Protein Blast
Polymer Type:polypeptide(L)
Molecule:U3 small nucleolar RNA-associated protein 15
Gene (Uniprot):UTP15
Chain IDs:T (auth: UO)
Chain Length:513
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:Q04305 Pfam ID:PF00400, PF09384
Protein Blast
Polymer Type:polypeptide(L)
Molecule:U3 small nucleolar RNA-associated protein 16
Gene (Uniprot):BUD21
Chain IDs:U (auth: UP)
Chain Length:214
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:Q08492 Pfam ID:PF08297
Protein Blast
Polymer Type:polypeptide(L)
Molecule:NET1-associated nuclear protein 1
Gene (Uniprot):NAN1
Chain IDs:FB (auth: UQ)
Chain Length:896
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:Q02931 Pfam ID:PF00400
Protein Blast
Polymer Type:polypeptide(L)
Molecule:U3 small nucleolar RNA-associated protein 18
Gene (Uniprot):UTP18
Chain IDs:CB (auth: UR)
Chain Length:594
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P40362 Pfam ID:PF00400
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Nucleolar complex protein 4
Gene (Uniprot):NOC4
Chain IDs:V (auth: US)
Chain Length:552
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:Q06512 Pfam ID:PF03914
Protein Blast
Polymer Type:polypeptide(L)
Molecule:U3 small nucleolar RNA-associated protein 20
Gene (Uniprot):UTP20
Chain IDs:KB (auth: UT)
Chain Length:2493
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P35194 Pfam ID:PF07539, PF20416
Protein Blast
Polymer Type:polypeptide(L)
Molecule:U3 small nucleolar RNA-associated protein 21
Gene (Uniprot):UTP21
Chain IDs:DB (auth: UU)
Chain Length:939
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:Q06078 Pfam ID:PF00400, PF04192
Protein Blast
Polymer Type:polypeptide(L)
Molecule:rRNA-processing protein FCF1
Gene (Uniprot):FCF1
Chain IDs:H (auth: UX)
Chain Length:189
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:Q05498 Pfam ID:PF04900
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ribosome biogenesis protein UTP30
Gene (Uniprot):UTP30
Chain IDs:AB (auth: UZ)
Chain Length:274
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P36144 Pfam ID:PF00687
Ligand Molecules
GTP
ZN
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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Protein

Chemical

Disease

Primary Citation of related structures
9G33