5WYJ image
Deposition Date 2017-01-13
Release Date 2017-03-29
Last Version Date 2025-09-17
Entry Detail
PDB ID:
5WYJ
Keywords:
RIBOSOME
Title:
Cryo-EM structure of the 90S small subunit pre-ribosome (Dhr1-depleted, Enp1-TAP, state 1)
Biological Source:
Source Organism(s):
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Taxon ID: 559292)
Method Details:
Experimental Method:
ELECTRON MICROSCOPY
Resolution:
8.70 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
5WYJ validation report
Macromolecular Entities
Polymer Type:polyribonucleotide
Molecule:U3 RNA
Chain IDs:A (auth: 3A)
Chain Length:333
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:rRNA 2'-O-methyltransferase fibrillarin
Gene (Uniprot):NOP1
Chain IDs:B (auth: 3B), C (auth: 3C)
Chain Length:327
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
UniProt ID:P15646 Pfam ID:PF01269
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Nucleolar protein 56
Gene (Uniprot):NOP56
Chain IDs:D (auth: 3D)
Chain Length:504
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
UniProt ID:Q12460 Pfam ID:PF08156, PF01798
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Nucleolar protein 58
Gene (Uniprot):NOP58
Chain IDs:E (auth: 3E)
Chain Length:511
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
UniProt ID:Q12499 Pfam ID:PF08156, PF01798
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ribosomal RNA-processing protein 9
Gene (Uniprot):RRP9
Chain IDs:F (auth: 3F)
Chain Length:573
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
UniProt ID:Q06506 Pfam ID:PF00400
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:13 kDa ribonucleoprotein-associated protein
Gene (Uniprot):SNU13
Chain IDs:G (auth: 3G), H (auth: 3H)
Chain Length:126
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
UniProt ID:P39990 Pfam ID:PF01248
Polymer Type:polyribonucleotide
Molecule:5ETS RNA
Chain IDs:I (auth: 5A)
Chain Length:700
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Polymer Type:polypeptide(L)
Molecule:Utp4
Chain IDs:J (auth: AA)
Chain Length:776
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Polymer Type:polypeptide(L)
Molecule:Utp5
Chain IDs:K (auth: AB)
Chain Length:643
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Polymer Type:polypeptide(L)
Molecule:Utp8
Chain IDs:L (auth: AC)
Chain Length:713
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Polymer Type:polypeptide(L)
Molecule:Utp9
Chain IDs:M (auth: AD)
Chain Length:575
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:U3 small nucleolar RNA-associated protein 10,Utp10
Gene (Uniprot):UTP10
Chain IDs:N (auth: AE)
Chain Length:1769
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
UniProt ID:P42945 Pfam ID:PF12397
Polymer Type:polypeptide(L)
Molecule:Utp15
Chain IDs:O (auth: AF)
Chain Length:513
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Polymer Type:polypeptide(L)
Molecule:Utp17
Chain IDs:P (auth: AG)
Chain Length:896
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ribosome biogenesis protein BMS1
Gene (Uniprot):BMS1
Chain IDs:Q (auth: B1)
Chain Length:1183
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
UniProt ID:Q08965 Pfam ID:PF00004, PF08142, PF04950
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Periodic tryptophan protein 2
Gene (Uniprot):PWP2
Chain IDs:R (auth: BA)
Chain Length:923
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
UniProt ID:P25635 Pfam ID:PF00400, PF04003
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:U3 small nucleolar RNA-associated protein 12
Gene (Uniprot):DIP2
Chain IDs:S (auth: BB)
Chain Length:943
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
UniProt ID:Q12220 Pfam ID:PF00400, PF04003
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:U3 small nucleolar RNA-associated protein 13
Gene (Uniprot):UTP13
Chain IDs:T (auth: BC)
Chain Length:817
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
UniProt ID:Q05946 Pfam ID:PF00400, PF08625
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:U3 small nucleolar RNA-associated protein 18
Gene (Uniprot):UTP18
Chain IDs:U (auth: BD)
Chain Length:594
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
UniProt ID:P40362 Pfam ID:PF00400
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:U3 small nucleolar RNA-associated protein 21
Gene (Uniprot):UTP21
Chain IDs:V (auth: BE)
Chain Length:939
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
UniProt ID:Q06078 Pfam ID:PF00400, PF04192
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ribosomal RNA-processing protein 7
Gene (Uniprot):RRP7
Chain IDs:W (auth: CA)
Chain Length:297
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
UniProt ID:P25368 Pfam ID:PF17799, PF12923
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:U3 small nucleolar RNA-associated protein 22
Gene (Uniprot):UTP22
Chain IDs:X (auth: CB)
Chain Length:1237
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
UniProt ID:P53254 Pfam ID:PF03813, PF17403, PF17404, PF17405, PF17406, PF17407
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ribosomal RNA small subunit methyltransferase NEP1
Gene (Uniprot):EMG1
Chain IDs:Y (auth: E1), Z (auth: E2)
Chain Length:252
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
UniProt ID:Q06287 Pfam ID:PF03587
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Essential nuclear protein 1
Gene (Uniprot):ENP1
Chain IDs:AA (auth: E3)
Chain Length:483
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
UniProt ID:P38333 Pfam ID:PF05291
Polymer Type:polypeptide(L)
Molecule:Enp2
Chain IDs:BA (auth: E4)
Chain Length:707
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:KRR1 small subunit processome component
Gene (Uniprot):KRR1
Chain IDs:CA (auth: K1)
Chain Length:316
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
UniProt ID:P25586 Pfam ID:PF17903, PF21800
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:U3 small nucleolar ribonucleoprotein protein IMP3
Gene (Uniprot):IMP3
Chain IDs:DA (auth: MA)
Chain Length:183
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
UniProt ID:P32899 Pfam ID:PF00163, PF01479
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:U3 small nucleolar ribonucleoprotein protein IMP4
Gene (Uniprot):IMP4
Chain IDs:EA (auth: MB)
Chain Length:290
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
UniProt ID:P53941 Pfam ID:PF04427
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Mpp10,U3 small nucleolar RNA-associated protein MPP10
Gene (Uniprot):MPP10
Chain IDs:FA (auth: MC)
Chain Length:593
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
UniProt ID:P47083
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Pre-rRNA-processing protein PNO1
Gene (Uniprot):PNO1
Chain IDs:GA (auth: P1)
Chain Length:274
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
UniProt ID:Q99216 Pfam ID:PF17903, PF22891
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:RNA 3'-terminal phosphate cyclase-like protein
Gene (Uniprot):RCL1
Chain IDs:HA (auth: R1)
Chain Length:367
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
UniProt ID:Q08096 Pfam ID:PF01137, PF05189
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:rRNA biogenesis protein RRP5
Gene (Uniprot):RRP5
Chain IDs:IA (auth: R2)
Chain Length:1729
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
UniProt ID:Q05022 Pfam ID:PF00575, PF05843, PF23240
Polymer Type:polypeptide(L)
Molecule:Sof1
Chain IDs:JA (auth: S1)
Chain Length:489
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Polymer Type:polyribonucleotide
Molecule:18S ribosomal RNA
Chain IDs:KA (auth: SA)
Chain Length:1812
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S1-A
Gene (Uniprot):RPS1A
Chain IDs:LA (auth: SC)
Chain Length:82
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
UniProt ID:P33442 Pfam ID:PF01015
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S4-A
Gene (Uniprot):RPS4A
Chain IDs:MA (auth: SF)
Chain Length:63
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
UniProt ID:P0CX35 Pfam ID:PF08071, PF01479, PF00900, PF00467, PF16121
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S5
Gene (Uniprot):RPS5
Chain IDs:NA (auth: SG)
Chain Length:152
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
UniProt ID:P26783 Pfam ID:PF00177
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S6-A
Gene (Uniprot):RPS6A
Chain IDs:OA (auth: SH)
Chain Length:236
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
UniProt ID:P0CX37 Pfam ID:PF01092
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S7-A
Gene (Uniprot):RPS7A
Chain IDs:PA (auth: SI)
Chain Length:190
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
UniProt ID:P26786 Pfam ID:PF01251
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S8-A
Gene (Uniprot):RPS8A
Chain IDs:QA (auth: SJ)
Chain Length:200
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
UniProt ID:P0CX39 Pfam ID:PF01201
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S9-A
Gene (Uniprot):RPS9A
Chain IDs:RA (auth: SK)
Chain Length:197
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
UniProt ID:O13516 Pfam ID:PF00163, PF01479
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S11-A
Gene (Uniprot):RPS11A
Chain IDs:SA (auth: SM)
Chain Length:156
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
UniProt ID:P0CX47 Pfam ID:PF16205, PF00366
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S12
Gene (Uniprot):RPS12
Chain IDs:TA (auth: SN)
Chain Length:143
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
UniProt ID:P48589 Pfam ID:PF01248
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S13
Gene (Uniprot):RPS13
Chain IDs:UA (auth: SO)
Chain Length:151
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
UniProt ID:P05756 Pfam ID:PF08069, PF00312
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S14-A
Gene (Uniprot):RPS14A
Chain IDs:VA (auth: SP)
Chain Length:137
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
UniProt ID:P06367 Pfam ID:PF00411
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S16-A
Gene (Uniprot):RPS16A
Chain IDs:WA (auth: SR)
Chain Length:143
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
UniProt ID:P0CX51 Pfam ID:PF00380
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S22-A
Gene (Uniprot):RPS22A
Chain IDs:XA (auth: SX)
Chain Length:130
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
UniProt ID:P0C0W1 Pfam ID:PF00410
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S23-A
Gene (Uniprot):RPS23A
Chain IDs:YA (auth: SY)
Chain Length:145
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
UniProt ID:P0CX29 Pfam ID:PF00164
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S24-A
Gene (Uniprot):RPS24A
Chain IDs:ZA (auth: SZ)
Chain Length:135
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
UniProt ID:P0CX31 Pfam ID:PF01282
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S27-A
Gene (Uniprot):RPS27A
Chain IDs:AB (auth: Sc)
Chain Length:82
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
UniProt ID:P35997 Pfam ID:PF01667
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S28-A
Gene (Uniprot):RPS28A
Chain IDs:BB (auth: Sd)
Chain Length:67
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
UniProt ID:Q3E7X9 Pfam ID:PF01200
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S30-A
Gene (Uniprot):RPS30A
Chain IDs:CB (auth: Sf)
Chain Length:63
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
UniProt ID:P0CX33 Pfam ID:PF04758
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ubiquitin-40S ribosomal protein S31
Gene (Uniprot):RPS31
Chain IDs:DB (auth: Sg)
Chain Length:152
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
UniProt ID:P05759 Pfam ID:PF00240, PF01599
Polymer Type:polypeptide(L)
Molecule:Utp7
Chain IDs:EB (auth: U1)
Chain Length:554
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Polymer Type:polypeptide(L)
Molecule:Utp11
Chain IDs:FB (auth: U2)
Chain Length:250
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Polymer Type:polypeptide(L)
Molecule:Utp20
Chain IDs:GB (auth: U3)
Chain Length:2493
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:rRNA-processing protein FCF1
Gene (Uniprot):FCF1
Chain IDs:HB (auth: U4)
Chain Length:189
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
UniProt ID:Q05498 Pfam ID:PF04900
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ribosome biogenesis protein UTP30
Gene (Uniprot):UTP30
Chain IDs:IB (auth: U5)
Chain Length:274
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
UniProt ID:P36144 Pfam ID:PF00687
Polymer Type:polypeptide(L)
Molecule:Helical domain protein
Chain IDs:JB (auth: UA)
Chain Length:1615
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Polymer Type:polypeptide(L)
Molecule:Helical domain protein
Chain IDs:KB (auth: UB)
Chain Length:987
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Polymer Type:polypeptide(L)
Molecule:Unassigned helices
Chain IDs:LB (auth: UC)
Chain Length:1033
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Ligand Molecules
NA
Primary Citation
Molecular architecture of the 90S small subunit pre-ribosome.
Elife 6 ? ? (2017)
PMID: 28244370 DOI: 10.7554/eLife.22086

Abstact

Eukaryotic small ribosomal subunits are first assembled into 90S pre-ribosomes. The complete 90S is a gigantic complex with a molecular mass of approximately five megadaltons. Here, we report the nearly complete architecture of Saccharomyces cerevisiae 90S determined from three cryo-electron microscopy single particle reconstructions at 4.5 to 8.7 angstrom resolution. The majority of the density maps were modeled and assigned to specific RNA and protein components. The nascent ribosome is assembled into isolated native-like substructures that are stabilized by abundant assembly factors. The 5' external transcribed spacer and U3 snoRNA nucleate a large subcomplex that scaffolds the nascent ribosome. U3 binds four sites of pre-rRNA, including a novel site on helix 27 but not the 3' side of the central pseudoknot, and crucially organizes the 90S structure. The 90S model provides significant insight into the principle of small subunit assembly and the function of assembly factors.

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Primary Citation of related structures
5WYJ
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