5TZS image
Deposition Date 2016-11-22
Release Date 2016-12-21
Last Version Date 2024-03-13
Entry Detail
PDB ID:
5TZS
Keywords:
TRANSLATION
Title:
Architecture of the yeast small subunit processome
Biological Source:
Source Organism:
Saccharomyces cerevisiae S288c (Taxon ID: 559292)
Method Details:
Experimental Method:
ELECTRON MICROSCOPY
Resolution:
5.10 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
5TZS validation report
Macromolecular Entities
Polymer Type:polyribonucleotide
Molecule:5' external transcribed spacer
Chain IDs:A (auth: 0)
Chain Length:364
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
Polymer Type:polyribonucleotide
Molecule:18S ribosomal RNA
Chain IDs:B (auth: 1)
Chain Length:1800
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C
Polymer Type:polyribonucleotide
Molecule:U3 snoRNA
Chain IDs:C (auth: 2)
Chain Length:126
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S6-A
Gene (Uniprot):RPS6A
Chain IDs:D (auth: 3)
Chain Length:236
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C
UniProt ID:P0CX37 Pfam ID:PF01092
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S4-A
Gene (Uniprot):RPS4A
Chain IDs:E (auth: 5)
Chain Length:261
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C
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:F (auth: 6)
Chain Length:225
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C
UniProt ID:P26783 Pfam ID:PF00177
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S7-A
Gene (Uniprot):RPS7A
Chain IDs:G (auth: 7)
Chain Length:190
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C
UniProt ID:P26786 Pfam ID:PF01251
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S8-A
Gene (Uniprot):RPS8A
Chain IDs:H (auth: 8)
Chain Length:200
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C
UniProt ID:P0CX39 Pfam ID:PF01201
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S9-A
Gene (Uniprot):RPS9A
Chain IDs:I (auth: 9)
Chain Length:197
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C
UniProt ID:O13516 Pfam ID:PF00163, PF01479
Polymer Type:polydeoxyribonucleotide
Molecule:5' domain-associated
Chain IDs:J (auth: A)
Chain Length:312
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
Polymer Type:polydeoxyribonucleotide
Molecule:3' domain-associated
Chain IDs:K (auth: B)
Chain Length:108
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S16-A
Gene (Uniprot):RPS16A
Chain IDs:L (auth: C)
Chain Length:143
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C
UniProt ID:P0CX51 Pfam ID:PF00380
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S11-A
Gene (Uniprot):RPS11A
Chain IDs:M (auth: D)
Chain Length:216
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C
UniProt ID:P0CX47 Pfam ID:PF16205, PF00366
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S22-A
Gene (Uniprot):RPS22A
Chain IDs:N (auth: E)
Chain Length:126
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C
UniProt ID:P0C0W1 Pfam ID:PF00410
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S24-A
Gene (Uniprot):RPS24A
Chain IDs:O (auth: F)
Chain Length:126
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C
UniProt ID:P0CX31 Pfam ID:PF01282
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S28-A
Gene (Uniprot):RPS28A
Chain IDs:P (auth: G)
Chain Length:67
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C
UniProt ID:Q3E7X9 Pfam ID:PF01200
Polymer Type:polypeptide(L)
Molecule:Utp4
Chain IDs:Q (auth: H)
Chain Length:367
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
Polymer Type:polypeptide(L)
Molecule:UtpA_CTD1
Chain IDs:R (auth: I)
Chain Length:511
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
Polymer Type:polypeptide(L)
Molecule:UtpA_CTD2
Chain IDs:S (auth: J), T (auth: K)
Chain Length:107
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae S288c
Polymer Type:polypeptide(L)
Molecule:Beta-propeller 2
Chain IDs:U (auth: M)
Chain Length:258
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
Polymer Type:polypeptide(L)
Molecule:Utp17
Chain IDs:V (auth: N)
Chain Length:160
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
Polymer Type:polypeptide(L)
Molecule:Utp1
Chain IDs:W (auth: O)
Chain Length:175
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
Polymer Type:polypeptide(L)
Molecule:Utp6
Chain IDs:X (auth: P)
Chain Length:924
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
Polymer Type:polypeptide(L)
Molecule:Utp12
Chain IDs:Y (auth: Q)
Chain Length:710
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
Polymer Type:polypeptide(L)
Molecule:Utp13
Chain IDs:Z (auth: R)
Chain Length:717
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
Polymer Type:polypeptide(L)
Molecule:Utp18
Chain IDs:AA (auth: S)
Chain Length:250
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
Protein Blast
Polymer Type:polypeptide(L)
Molecule:U3 small nucleolar RNA-associated protein 21,Utp21
Gene (Uniprot):UTP21
Chain IDs:BA (auth: T)
Chain Length:290
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C, Saccharomyces cerevisiae S288c
UniProt ID:Q06078 Pfam ID:PF00400
Polymer Type:polypeptide(L)
Molecule:Beta-propeller 5
Chain IDs:CA (auth: U)
Chain Length:290
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
Polymer Type:polypeptide(L)
Molecule:Enp2
Chain IDs:DA (auth: V)
Chain Length:580
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
Polymer Type:polypeptide(L)
Molecule:UtpA_CTD4
Chain IDs:EA (auth: W)
Chain Length:104
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
Polymer Type:polypeptide(L)
Molecule:Kre33
Chain IDs:FA (auth: X)
Chain Length:640
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
Polymer Type:polypeptide(L)
Molecule:Kre33
Chain IDs:GA (auth: Y)
Chain Length:507
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
Polymer Type:polypeptide(L)
Molecule:Imp3
Chain IDs:HA (auth: Z)
Chain Length:76
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
Polymer Type:polypeptide(L)
Molecule:Nop56
Chain IDs:IA (auth: a)
Chain Length:312
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
Polymer Type:polypeptide(L)
Molecule:Nop58
Chain IDs:JA (auth: b)
Chain Length:108
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
Polymer Type:polypeptide(L)
Molecule:Nop1
Chain IDs:KA (auth: c)
Chain Length:143
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
Polymer Type:polypeptide(L)
Molecule:Nop1
Chain IDs:LA (auth: d)
Chain Length:216
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
Protein Blast
Polymer Type:polypeptide(L)
Molecule:13 kDa ribonucleoprotein-associated protein
Gene (Uniprot):SNU13
Chain IDs:MA (auth: e), NA (auth: f)
Chain Length:126
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae S288C
UniProt ID:P39990 Pfam ID:PF01248
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ribosomal RNA-processing protein 9
Gene (Uniprot):RRP9
Chain IDs:OA (auth: g)
Chain Length:67
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C
UniProt ID:Q06506 Pfam ID:PF00400
Protein Blast
Polymer Type:polypeptide(L)
Molecule:RNA 3'-terminal phosphate cyclase-like protein
Gene (Uniprot):RCL1
Chain IDs:PA (auth: h)
Chain Length:367
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C
UniProt ID:Q08096 Pfam ID:PF01137, PF05189
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Bms1,Ribosome biogenesis protein BMS1,Bms1,Ribosome biogenesis protein BMS1
Gene (Uniprot):BMS1
Chain IDs:QA (auth: i)
Chain Length:511
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c, Saccharomyces cerevisiae S288C
UniProt ID:Q08965
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ribosomal RNA small subunit methyltransferase NEP1
Gene (Uniprot):EMG1
Chain IDs:RA (auth: j), SA (auth: k)
Chain Length:107
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae S288C
UniProt ID:Q06287 Pfam ID:PF03587
Polymer Type:polypeptide(L)
Molecule:Utp24
Chain IDs:TA (auth: l)
Chain Length:124
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
Polymer Type:polypeptide(L)
Molecule:Imp4
Chain IDs:UA (auth: m)
Chain Length:258
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
Polymer Type:polypeptide(L)
Molecule:Utp30
Chain IDs:VA (auth: n)
Chain Length:160
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
Polymer Type:polypeptide(L)
Molecule:Unassigned KH domain
Chain IDs:WA (auth: o)
Chain Length:175
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
Polymer Type:polypeptide(L)
Molecule:Utp20
Chain IDs:XA (auth: p)
Chain Length:924
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
Polymer Type:polypeptide(L)
Molecule:Repeat protein 2
Chain IDs:YA (auth: q)
Chain Length:710
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S23-A
Gene (Uniprot):RPS23A
Chain IDs:ZA (auth: r)
Chain Length:717
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C
UniProt ID:P0CX29 Pfam ID:PF00164
Polymer Type:polypeptide(L)
Molecule:Beta-propeller 1
Chain IDs:AB (auth: s), BB (auth: t), CB (auth: u)
Chain Length:250
Number of Molecules:3
Biological Source:Saccharomyces cerevisiae S288c
Polymer Type:polypeptide(L)
Molecule:Repeat protein 1
Chain IDs:DB (auth: v)
Chain Length:580
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
Polymer Type:polypeptide(L)
Molecule:Unassigned protein helices
Chain IDs:EB (auth: y)
Chain Length:507
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
Polymer Type:polydeoxyribonucleotide
Molecule:Unassigned RNA helices
Chain IDs:FB (auth: z)
Chain Length:76
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
Ligand Molecules
NA
Primary Citation
Architecture of the yeast small subunit processome.
Science 355 ? ? (2017)
PMID: 27980088 DOI: 10.1126/science.aal1880

Abstact

The small subunit (SSU) processome, a large ribonucleoprotein particle, organizes the assembly of the eukaryotic small ribosomal subunit by coordinating the folding, cleavage, and modification of nascent pre-ribosomal RNA (rRNA). Here, we present the cryo-electron microscopy structure of the yeast SSU processome at 5.1-angstrom resolution. The structure reveals how large ribosome biogenesis complexes assist the 5' external transcribed spacer and U3 small nucleolar RNA in providing an intertwined RNA-protein assembly platform for the separate maturation of 18S rRNA domains. The strategic placement of a molecular motor at the center of the particle further suggests a mechanism for mediating conformational changes within this giant particle. This study provides a structural framework for a mechanistic understanding of eukaryotic ribosome assembly in the model organism Saccharomyces cerevisiae.

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Primary Citation of related structures
5TZS