5WLC image
Deposition Date 2017-07-26
Release Date 2017-09-27
Last Version Date 2024-03-13
Entry Detail
PDB ID:
5WLC
Keywords:
RIBOSOME
Title:
The complete structure of the small subunit processome
Biological Source:
Source Organism:
Saccharomyces cerevisiae BY4741 (Taxon ID: 1247190)
Method Details:
Experimental Method:
ELECTRON MICROSCOPY
Resolution:
3.80 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
5WLC validation report
Macromolecular Entities
Polymer Type:polyribonucleotide
Molecule:5' ETS
Chain IDs:A (auth: L0)
Chain Length:700
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
Polymer Type:polyribonucleotide
Molecule:18S pre-rRNA
Chain IDs:B (auth: L1)
Chain Length:1807
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
Polymer Type:polyribonucleotide
Molecule:U3 snoRNA
Chain IDs:C (auth: L2)
Chain Length:333
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
Protein Blast
Polymer Type:polypeptide(L)
Molecule:rpS18_uS13
Gene (Uniprot):RPS18A
Chain IDs:D (auth: L3)
Chain Length:146
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
UniProt ID:P0CX55 Pfam ID:PF00416
Protein Blast
Polymer Type:polypeptide(L)
Molecule:rpS4_eS4
Gene (Uniprot):RPS4A
Chain IDs:E (auth: L4)
Chain Length:261
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
UniProt ID:P0CX35 Pfam ID:PF08071, PF01479, PF00900, PF00467, PF16121
Protein Blast
Polymer Type:polypeptide(L)
Molecule:rpS5_uS7
Gene (Uniprot):RPS5
Chain IDs:F (auth: L5)
Chain Length:225
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
UniProt ID:A0A1L4AA68 Pfam ID:PF00177
Protein Blast
Polymer Type:polypeptide(L)
Molecule:rpS6_eS6
Gene (Uniprot):RPS6A
Chain IDs:G (auth: L6)
Chain Length:236
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
UniProt ID:P0CX37 Pfam ID:PF01092
Protein Blast
Polymer Type:polypeptide(L)
Molecule:rpS7_eS7
Gene (Uniprot):RPS7A
Chain IDs:H (auth: L7)
Chain Length:190
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
UniProt ID:P26786 Pfam ID:PF01251
Protein Blast
Polymer Type:polypeptide(L)
Molecule:rpS8_eS8
Gene (Uniprot):RPS8A
Chain IDs:I (auth: L8)
Chain Length:200
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
UniProt ID:P0CX39 Pfam ID:PF01201
Protein Blast
Polymer Type:polypeptide(L)
Molecule:rpS9_uS4
Gene (Uniprot):RPS9A
Chain IDs:J (auth: L9)
Chain Length:197
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
UniProt ID:O13516 Pfam ID:PF00163, PF01479
Protein Blast
Polymer Type:polypeptide(L)
Molecule:rpS16_uS9
Gene (Uniprot):RPS16A
Chain IDs:K (auth: LC)
Chain Length:143
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
UniProt ID:P0CX51 Pfam ID:PF00380
Protein Blast
Polymer Type:polypeptide(L)
Molecule:rpS11_uS17
Gene (Uniprot):RPS11A
Chain IDs:L (auth: LD)
Chain Length:156
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
UniProt ID:P0CX47 Pfam ID:PF16205, PF00366
Protein Blast
Polymer Type:polypeptide(L)
Molecule:rpS22_uS8
Gene (Uniprot):RPS22A
Chain IDs:M (auth: LE)
Chain Length:130
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
UniProt ID:P0C0W1 Pfam ID:PF00410
Protein Blast
Polymer Type:polypeptide(L)
Molecule:rpS24_eS24
Gene (Uniprot):RPS24A
Chain IDs:N (auth: LF)
Chain Length:135
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
UniProt ID:P0CX31 Pfam ID:PF01282
Protein Blast
Polymer Type:polypeptide(L)
Molecule:rpS28_eS28
Gene (Uniprot):RPS28A
Chain IDs:O (auth: LG)
Chain Length:67
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
UniProt ID:Q3E7X9 Pfam ID:PF01200
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Utp17
Gene (Uniprot):NAN1
Chain IDs:P (auth: LH)
Chain Length:896
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
UniProt ID:Q02931 Pfam ID:PF00400
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Utp8
Gene (Uniprot):UTP8
Chain IDs:Q (auth: LI)
Chain Length:713
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
UniProt ID:P53276 Pfam ID:PF22542
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Utp15
Gene (Uniprot):UTP15
Chain IDs:R (auth: LJ)
Chain Length:513
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
UniProt ID:Q04305 Pfam ID:PF00400, PF09384
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Utp9
Gene (Uniprot):UTP9
Chain IDs:S (auth: LK)
Chain Length:575
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
UniProt ID:P38882
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Utp5
Gene (Uniprot):UTP5
Chain IDs:T (auth: LL)
Chain Length:643
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
UniProt ID:Q04177 Pfam ID:PF04003
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Utp10
Gene (Uniprot):UTP10
Chain IDs:U (auth: LM)
Chain Length:1769
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
UniProt ID:P42945 Pfam ID:PF12397, PF08146
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Utp4
Gene (Uniprot):UTP4
Chain IDs:V (auth: LN)
Chain Length:776
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
UniProt ID:Q06679 Pfam ID:PF00400
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Utp1
Gene (Uniprot):PWP2
Chain IDs:W (auth: LO)
Chain Length:923
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
UniProt ID:P25635 Pfam ID:PF00400, PF04003
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Utp6
Gene (Uniprot):UTP6
Chain IDs:X (auth: LP)
Chain Length:440
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
UniProt ID:Q02354 Pfam ID:PF08640, PF05843
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Utp12
Gene (Uniprot):DIP2
Chain IDs:Y (auth: LQ)
Chain Length:943
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
UniProt ID:Q12220 Pfam ID:PF00400, PF04003
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Utp13
Gene (Uniprot):UTP13
Chain IDs:Z (auth: LR)
Chain Length:817
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
UniProt ID:Q05946 Pfam ID:PF08625
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Utp18
Gene (Uniprot):UTP18
Chain IDs:AA (auth: LS)
Chain Length:594
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
UniProt ID:P40362 Pfam ID:PF00400
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Utp21
Gene (Uniprot):UTP21
Chain IDs:BA (auth: LT)
Chain Length:939
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
UniProt ID:Q06078 Pfam ID:PF00400, PF04192
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Sof1
Gene (Uniprot):SOF1
Chain IDs:CA (auth: LU)
Chain Length:489
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
UniProt ID:P33750 Pfam ID:PF00400, PF04158
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Enp2
Gene (Uniprot):ENP2
Chain IDs:DA (auth: LV)
Chain Length:707
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
UniProt ID:P48234 Pfam ID:PF08159
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Utp7
Gene (Uniprot):UTP7
Chain IDs:EA (auth: LW)
Chain Length:554
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
UniProt ID:P40055 Pfam ID:PF00400, PF08149
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Kre33
Gene (Uniprot):KRE33
Chain IDs:FA (auth: LX), GA (auth: LY)
Chain Length:1056
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae BY4741
UniProt ID:P53914 Pfam ID:PF08351
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Imp3
Gene (Uniprot):IMP3
Chain IDs:HA (auth: LZ)
Chain Length:183
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
UniProt ID:P32899 Pfam ID:PF00163, PF01479
Polymer Type:polypeptide(L)
Molecule:Mpp10
Chain IDs:IA (auth: NA)
Chain Length:593
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Sas10
Gene (Uniprot):SAS10
Chain IDs:JA (auth: NB)
Chain Length:610
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
UniProt ID:Q12136 Pfam ID:PF04000, PF09368
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Lcp5
Gene (Uniprot):LCP5
Chain IDs:KA (auth: NC)
Chain Length:357
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
UniProt ID:P40079 Pfam ID:PF04000
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Bud21
Gene (Uniprot):BUD21
Chain IDs:LA (auth: ND)
Chain Length:214
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
UniProt ID:Q08492 Pfam ID:PF08297
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Faf1
Gene (Uniprot):FAF1
Chain IDs:MA (auth: NE)
Chain Length:346
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
UniProt ID:P40546
Protein Blast
Polymer Type:polypeptide(L)
Molecule:rpS13_uS15
Gene (Uniprot):RPS13
Chain IDs:NA (auth: NF)
Chain Length:151
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
UniProt ID:P05756 Pfam ID:PF08069, PF00312
Protein Blast
Polymer Type:polypeptide(L)
Molecule:rpS14_uS11
Gene (Uniprot):RPS14A
Chain IDs:OA (auth: NG)
Chain Length:137
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
UniProt ID:P06367 Pfam ID:PF00411
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Utp22
Gene (Uniprot):UTP22
Chain IDs:PA (auth: NH)
Chain Length:1237
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
UniProt ID:P53254 Pfam ID:PF03813, PF17403, PF17404, PF17405, PF17406, PF17407
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Rrp7
Gene (Uniprot):RRP7
Chain IDs:QA (auth: NI)
Chain Length:297
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
UniProt ID:P25368 Pfam ID:PF17799, PF12923
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Rrp5
Gene (Uniprot):RRP5
Chain IDs:RA (auth: NJ)
Chain Length:1729
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
UniProt ID:Q05022 Pfam ID:PF00575, PF05843
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Krr1
Gene (Uniprot):KRR1
Chain IDs:SA (auth: NK)
Chain Length:316
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
UniProt ID:B3LU25 Pfam ID:PF17903, PF21800
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Nop56
Gene (Uniprot):NOP56
Chain IDs:TA (auth: SA)
Chain Length:504
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
UniProt ID:Q12460 Pfam ID:PF08156, PF01798
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Nop58
Gene (Uniprot):NOP58
Chain IDs:UA (auth: SB)
Chain Length:511
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
UniProt ID:Q12499 Pfam ID:PF01798
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Nop1
Gene (Uniprot):NOP1
Chain IDs:VA (auth: SC), WA (auth: SD)
Chain Length:327
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae BY4741
UniProt ID:P15646 Pfam ID:PF01269
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Snu13
Gene (Uniprot):SNU13
Chain IDs:XA (auth: SE), YA (auth: SF)
Chain Length:126
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae BY4741
UniProt ID:P39990 Pfam ID:PF01248
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Rrp9
Gene (Uniprot):RRP9
Chain IDs:ZA (auth: SG)
Chain Length:573
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
UniProt ID:Q06506 Pfam ID:PF00400
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Rcl1
Gene (Uniprot):RCL1
Chain IDs:AB (auth: SH)
Chain Length:367
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
UniProt ID:Q08096 Pfam ID:PF01137, PF05189
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Bms1
Gene (Uniprot):BMS1
Chain IDs:BB (auth: SI)
Chain Length:1184
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
UniProt ID:Q08965 Pfam ID:PF00004, PF08142, PF04950
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Emg1
Gene (Uniprot):EMG1
Chain IDs:CB (auth: SJ), DB (auth: SK)
Chain Length:252
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae BY4741
UniProt ID:Q06287 Pfam ID:PF03587
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Utp24
Gene (Uniprot):FCF1
Chain IDs:EB (auth: SL)
Chain Length:189
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
UniProt ID:Q05498 Pfam ID:PF04900
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Imp4
Gene (Uniprot):IMP4
Chain IDs:FB (auth: SM)
Chain Length:290
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
UniProt ID:P53941 Pfam ID:PF04427
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Utp30
Gene (Uniprot):UTP30
Chain IDs:GB (auth: SN)
Chain Length:274
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
UniProt ID:P36144 Pfam ID:PF00687
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Pno1
Gene (Uniprot):PNO1
Chain IDs:HB (auth: SO)
Chain Length:274
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
UniProt ID:Q99216 Pfam ID:PF17903, PF22891
Polymer Type:polypeptide(L)
Molecule:Utp20
Chain IDs:IB (auth: SP)
Chain Length:982
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Fcf2
Gene (Uniprot):FCF2
Chain IDs:JB (auth: SQ)
Chain Length:217
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
UniProt ID:Q12035 Pfam ID:PF08698
Protein Blast
Polymer Type:polypeptide(L)
Molecule:rpS23_uS12
Gene (Uniprot):RPS23A
Chain IDs:KB (auth: SR)
Chain Length:145
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
UniProt ID:P0CY39 Pfam ID:PF00164
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Utp14
Gene (Uniprot):UTP14
Chain IDs:LB (auth: SS)
Chain Length:898
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
UniProt ID:Q04500 Pfam ID:PF04615
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Nop14
Gene (Uniprot):NOP14
Chain IDs:MB (auth: ST)
Chain Length:792
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
UniProt ID:Q99207 Pfam ID:PF04147
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Noc4
Gene (Uniprot):NOC4
Chain IDs:NB (auth: SU)
Chain Length:552
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
UniProt ID:Q06512 Pfam ID:PF03914
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Rrt14
Gene (Uniprot):RRT14, YIL127C
Chain IDs:OB (auth: SV)
Chain Length:206
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
UniProt ID:E9P9B2,B5VKI1 Pfam ID:PF17075
Polymer Type:polypeptide(L)
Molecule:Unassigned peptides
Chain IDs:PB (auth: SX)
Chain Length:103
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Utp11
Gene (Uniprot):UTP11
Chain IDs:QB (auth: SY)
Chain Length:250
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
UniProt ID:B5VM59 Pfam ID:PF03998
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Enp1
Gene (Uniprot):ENP1
Chain IDs:RB (auth: SZ)
Chain Length:483
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
UniProt ID:P38333 Pfam ID:PF05291
Ligand Molecules
ZN
Primary Citation
The complete structure of the small-subunit processome.
Nat. Struct. Mol. Biol. 24 944 953 (2017)
PMID: 28945246 DOI: 10.1038/nsmb.3472

Abstact

The small-subunit processome represents the earliest stable precursor of the eukaryotic small ribosomal subunit. Here we present the cryo-EM structure of the Saccharomyces cerevisiae small-subunit processome at an overall resolution of 3.8 Å, which provides an essentially complete near-atomic model of this assembly. In this nucleolar superstructure, 51 ribosome-assembly factors and two RNAs encapsulate the 18S rRNA precursor and 15 ribosomal proteins in a state that precedes pre-rRNA cleavage at site A1. Extended flexible proteins are employed to connect distant sites in this particle. Molecular mimicry and steric hindrance, as well as protein- and RNA-mediated RNA remodeling, are used in a concerted fashion to prevent the premature formation of the central pseudoknot and its surrounding elements within the small ribosomal subunit.

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Protein

Chemical

Disease

Primary Citation of related structures
5WLC