7D5S image
Deposition Date 2020-09-28
Release Date 2021-10-06
Last Version Date 2024-05-29
Entry Detail
PDB ID:
7D5S
Keywords:
RIBOSOME
Title:
Cryo-EM structure of 90S preribosome with inactive Utp24 (state A2)
Biological Source:
Source Organism:
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Taxon ID: 559292)
Method Details:
Experimental Method:
ELECTRON MICROSCOPY
Resolution:
4.60 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
7D5S validation report
Macromolecular Entities
Polymer Type:polyribonucleotide
Molecule:U3 snoRNA
Chain IDs:A (auth: 3A)
Chain Length:333
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Protein Blast
Polymer Type:polypeptide(L)
Molecule:rRNA 2'-O-methyltransferase fibrillarin
Gene (Uniprot):NOP1
Chain IDs:M (auth: 3B), N (auth: 3C)
Chain Length:327
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
UniProt ID:P15646 Pfam ID:PF01269
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Nucleolar protein 56
Gene (Uniprot):NOP56
Chain IDs:O (auth: 3D)
Chain Length:504
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
UniProt ID:Q12460 Pfam ID:PF08156, PF01798
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Nucleolar protein 58
Gene (Uniprot):NOP58
Chain IDs:P (auth: 3E)
Chain Length:511
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
UniProt ID:Q12499 Pfam ID:PF08156, PF01798
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ribosomal RNA-processing protein 9
Gene (Uniprot):RRP9
Chain IDs:Q (auth: 3F)
Chain Length:573
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
UniProt ID:Q06506 Pfam ID:PF00400
Protein Blast
Polymer Type:polypeptide(L)
Molecule:13 kDa ribonucleoprotein-associated protein
Gene (Uniprot):SNU13
Chain IDs:R (auth: 3G), S (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:5' ETS
Chain IDs:B (auth: 5A)
Chain Length:700
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Bud site selection protein 21
Gene (Uniprot):BUD21
Chain IDs:GA (auth: 5B)
Chain Length:214
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
UniProt ID:Q08492 Pfam ID:PF08297
Protein Blast
Polymer Type:polypeptide(L)
Molecule:U3 small nucleolar RNA-associated protein 7
Gene (Uniprot):UTP7
Chain IDs:HA (auth: 5C)
Chain Length:554
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
UniProt ID:P40055 Pfam ID:PF00400, PF08149
Protein Blast
Polymer Type:polypeptide(L)
Molecule:U3 small nucleolar RNA-associated protein 11
Gene (Uniprot):UTP11
Chain IDs:IA (auth: 5D)
Chain Length:250
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
UniProt ID:P34247 Pfam ID:PF03998
Protein Blast
Polymer Type:polypeptide(L)
Molecule:U3 small nucleolar RNA-associated protein MPP10
Gene (Uniprot):MPP10
Chain IDs:JA (auth: 5E)
Chain Length:593
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
UniProt ID:P47083 Pfam ID:PF04006
Protein Blast
Polymer Type:polypeptide(L)
Molecule:U3 small nucleolar ribonucleoprotein protein IMP3
Gene (Uniprot):IMP3
Chain IDs:KA (auth: 5F)
Chain Length:183
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
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:LA (auth: 5G)
Chain Length:290
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
UniProt ID:P53941 Pfam ID:PF04427
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Something about silencing protein 10
Gene (Uniprot):SAS10
Chain IDs:MA (auth: 5H)
Chain Length:610
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
UniProt ID:Q12136 Pfam ID:PF04000, PF09368
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Protein SOF1
Gene (Uniprot):SOF1
Chain IDs:NA (auth: 5I)
Chain Length:489
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
UniProt ID:P33750 Pfam ID:PF00400, PF04158
Protein Blast
Polymer Type:polypeptide(L)
Molecule:rRNA-processing protein FCF2
Gene (Uniprot):FCF2
Chain IDs:OA (auth: 5J)
Chain Length:217
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
UniProt ID:Q12035 Pfam ID:PF08698
Protein Blast
Polymer Type:polypeptide(L)
Molecule:rRNA-processing protein FCF1
Gene (Uniprot):FCF1
Chain IDs:PA (auth: 5K)
Chain Length:189
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
UniProt ID:Q05498 Pfam ID:PF04900
Protein Blast
Polymer Type:polypeptide(L)
Molecule:U3 small nucleolar RNA-associated protein 4
Gene (Uniprot):UTP4
Chain IDs:T (auth: A4)
Chain Length:776
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
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:U (auth: A5)
Chain Length:643
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
UniProt ID:Q04177 Pfam ID:PF04003
Protein Blast
Polymer Type:polypeptide(L)
Molecule:U3 small nucleolar RNA-associated protein 8
Gene (Uniprot):UTP8
Chain IDs:V (auth: A8)
Chain Length:713
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
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:W (auth: A9)
Chain Length:575
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
UniProt ID:P38882
Protein Blast
Polymer Type:polypeptide(L)
Molecule:U3 small nucleolar RNA-associated protein 10
Gene (Uniprot):UTP10
Chain IDs:X (auth: AE)
Chain Length:1769
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
UniProt ID:P42945 Pfam ID:PF12397, PF08146
Protein Blast
Polymer Type:polypeptide(L)
Molecule:U3 small nucleolar RNA-associated protein 15
Gene (Uniprot):UTP15
Chain IDs:Y (auth: AF)
Chain Length:513
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
UniProt ID:Q04305 Pfam ID:PF00400, PF09384
Protein Blast
Polymer Type:polypeptide(L)
Molecule:NET1-associated nuclear protein 1
Gene (Uniprot):NAN1
Chain IDs:Z (auth: AG)
Chain Length:896
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
UniProt ID:Q02931 Pfam ID:PF00400
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Periodic tryptophan protein 2
Gene (Uniprot):PWP2
Chain IDs:AA (auth: B1)
Chain Length:923
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
UniProt ID:P25635 Pfam ID:PF00400, PF04003
Protein Blast
Polymer Type:polypeptide(L)
Molecule:U3 small nucleolar RNA-associated protein 12
Gene (Uniprot):DIP2
Chain IDs:BA (auth: B2)
Chain Length:943
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
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:CA (auth: B3)
Chain Length:817
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
UniProt ID:Q05946 Pfam ID:PF00400, PF08625
Protein Blast
Polymer Type:polypeptide(L)
Molecule:U3 small nucleolar RNA-associated protein 6
Gene (Uniprot):UTP6
Chain IDs:FA (auth: B6)
Chain Length:440
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
UniProt ID:Q02354 Pfam ID:PF08640, PF05843
Protein Blast
Polymer Type:polypeptide(L)
Molecule:U3 small nucleolar RNA-associated protein 18
Gene (Uniprot):UTP18
Chain IDs:DA (auth: B8)
Chain Length:594
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
UniProt ID:P40362 Pfam ID:PF00400
Protein Blast
Polymer Type:polypeptide(L)
Molecule:U3 small nucleolar RNA-associated protein 21
Gene (Uniprot):UTP21
Chain IDs:EA (auth: BE)
Chain Length:939
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
UniProt ID:Q06078 Pfam ID:PF00400, PF04192
Protein Blast
Polymer Type:polypeptide(L)
Molecule:KRR1 small subunit processome component
Gene (Uniprot):KRR1
Chain IDs:QA (auth: RC)
Chain Length:316
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
UniProt ID:P25586 Pfam ID:PF17903, PF21800
Protein Blast
Polymer Type:polypeptide(L)
Molecule:rRNA biogenesis protein RRP5
Gene (Uniprot):RRP5
Chain IDs:RA (auth: RD)
Chain Length:1729
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
UniProt ID:Q05022 Pfam ID:PF00575, PF05843
Protein Blast
Polymer Type:polypeptide(L)
Molecule:U3 small nucleolar RNA-associated protein 22
Gene (Uniprot):UTP22
Chain IDs:SA (auth: RE)
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
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ribosomal RNA-processing protein 7
Gene (Uniprot):RRP7
Chain IDs:TA (auth: RF)
Chain Length:297
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
UniProt ID:P25368 Pfam ID:PF17799, PF12923
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ribosomal RNA small subunit methyltransferase NEP1
Gene (Uniprot):EMG1
Chain IDs:UA (auth: RG), VA (auth: RH)
Chain Length:252
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
UniProt ID:Q06287 Pfam ID:PF03587
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ribosome biogenesis protein UTP30
Gene (Uniprot):UTP30
Chain IDs:WA (auth: RI)
Chain Length:274
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
UniProt ID:P36144 Pfam ID:PF00687
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ribosome biogenesis protein BMS1
Gene (Uniprot):BMS1
Chain IDs:XA (auth: RJ)
Chain Length:1183
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
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:YA (auth: RK)
Chain Length:367
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
UniProt ID:Q08096 Pfam ID:PF01137, PF05189
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Nucleolar complex protein 14
Gene (Uniprot):NOP14
Chain IDs:ZA (auth: RN)
Chain Length:810
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
UniProt ID:Q99207 Pfam ID:PF04147
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Nucleolar complex protein 4
Gene (Uniprot):NOC4
Chain IDs:AB (auth: RO)
Chain Length:552
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
UniProt ID:Q06512 Pfam ID:PF03914
Protein Blast
Polymer Type:polypeptide(L)
Molecule:U3 small nucleolar RNA-associated protein 14
Gene (Uniprot):UTP14
Chain IDs:BB (auth: RQ)
Chain Length:899
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
UniProt ID:Q04500 Pfam ID:PF04615
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Essential nuclear protein 1
Gene (Uniprot):ENP1
Chain IDs:CB (auth: RS)
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:Pno1
Chain IDs:DB (auth: RT)
Chain Length:326
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Regulator of rDNA transcription protein 14
Gene (Uniprot):RRT14
Chain IDs:EB (auth: RW)
Chain Length:206
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
UniProt ID:P40470 Pfam ID:PF17075
Polymer Type:polyribonucleotide
Molecule:18S rRNA
Chain IDs:C (auth: SA)
Chain Length:1808
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S5
Gene (Uniprot):RPS5
Chain IDs:D (auth: SG)
Chain Length:225
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
UniProt ID:P26783 Pfam ID:PF00177
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S9-A
Gene (Uniprot):RPS9A
Chain IDs:E (auth: SK)
Chain Length:197
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
UniProt ID:O13516 Pfam ID:PF00163, PF01479
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S12
Gene (Uniprot):RPS12
Chain IDs:F (auth: SN)
Chain Length:143
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
UniProt ID:P48589 Pfam ID:PF01248
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S13
Gene (Uniprot):RPS13
Chain IDs:G (auth: SO)
Chain Length:151
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
UniProt ID:P05756 Pfam ID:PF08069, PF00312
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S14-A
Gene (Uniprot):RPS14A
Chain IDs:H (auth: SP)
Chain Length:137
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
UniProt ID:P06367 Pfam ID:PF00411
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S16-A
Gene (Uniprot):RPS16A
Chain IDs:I (auth: SR)
Chain Length:143
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
UniProt ID:P0CX51 Pfam ID:PF00380
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S18-A
Gene (Uniprot):RPS18A
Chain IDs:J (auth: ST)
Chain Length:146
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
UniProt ID:P0CX55 Pfam ID:PF00416
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S23-A
Gene (Uniprot):RPS23A
Chain IDs:K (auth: SY)
Chain Length:145
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
UniProt ID:P0CX29 Pfam ID:PF00164
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S28-A
Gene (Uniprot):RPS28A
Chain IDs:L (auth: Sd)
Chain Length:67
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
UniProt ID:Q3E7X9 Pfam ID:PF01200
Polymer Type:polypeptide(L)
Molecule:Unassigned peptides 1
Chain IDs:FB (auth: X1)
Chain Length:347
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Ligand Molecules
GTP
MG
ZN
Primary Citation
Cryo-EM structure of 90S preribosome with inactive Utp24 (state A2)
Ye, K.Show
To Be Published ? ? ? (?)
Primary Citation of related structures
7D5S