› 6wdr

Electron Microscopy
3.7Å resolution

Subunit joining exposes nascent pre-40S rRNA for processing and quality control

Released:
DOI: 10.2210/pdb6wdr/pdb
PDB entry 6wdr coloured by chain, front view.
PDB entry 6wdr coloured by chain, side view.
PDB entry 6wdr coloured by chain, top view.
Source organism: Saccharomyces cerevisiae S288C
Primary publication:
An open interface in the pre-80S ribosome coordinated by ribosome assembly factors Tsr1 and Dim1 enables temporal regulation of Fap7.
Rai J, Parker MD, Huang H, Choy S, Ghalei H, Johnson MC, Karbstein K, Stroupe ME
RNA 27 221-233 (2021)
PMID: 33219089
Related structures: EMD-21644

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero 32-mer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-126845 (preferred)
Entry contents:
31 distinct polypeptide molecules
1 distinct RNA molecule
Macromolecules (32 distinct):
Small ribosomal subunit protein uS2A Chain: A
Molecule details ›
Chain: A
Length: 206 amino acids
Theoretical weight: 22.84 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: P32905 (Residues: 2-207; Coverage: 82%)
Gene names: NAB1, NAB1A, RPS0A, YGR214W, YST1
Sequence domains: Ribosomal protein S2
Small ribosomal subunit protein uS5 Chain: C
Molecule details ›
Chain: C
Length: 217 amino acids
Theoretical weight: 23.21 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: P25443 (Residues: 34-250; Coverage: 85%)
Gene names: G2893, RPS2, RPS4, SUP38, SUP44, YGL123W
Sequence domains:
Small ribosomal subunit protein uS3 Chain: D
Molecule details ›
Chain: D
Length: 223 amino acids
Theoretical weight: 24.7 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: P05750 (Residues: 3-225; Coverage: 93%)
Gene names: N1653, RPS3, SUF14, YNL178W
Sequence domains:
Small ribosomal subunit protein eS4A Chain: E
Molecule details ›
Chain: E
Length: 260 amino acids
Theoretical weight: 29.34 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: P0CX35 (Residues: 2-261; Coverage: 100%)
Gene names: J2186, RPS4A, RPS7B, YJR145C
Sequence domains:
Small ribosomal subunit protein uS7 Chain: F
Molecule details ›
Chain: F
Length: 206 amino acids
Theoretical weight: 22.91 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: P26783 (Residues: 20-225; Coverage: 92%)
Gene names: J2045, RPS2, RPS5, YJR123W
Sequence domains: Ribosomal protein S7p/S5e
Small ribosomal subunit protein eS6A Chain: G
Molecule details ›
Chain: G
Length: 232 amino acids
Theoretical weight: 26.65 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: P0CX37 (Residues: 1-232; Coverage: 98%)
Gene names: LPG18C, RPS101, RPS10B, RPS6A, YPL090C
Sequence domains: Ribosomal protein S6e
Small ribosomal subunit protein eS7A Chain: H
Molecule details ›
Chain: H
Length: 184 amino acids
Theoretical weight: 21 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: P26786 (Residues: 4-187; Coverage: 97%)
Gene names: RPS30, RPS7A, YOR096W, YOR3177W
Sequence domains: Ribosomal protein S7e
Small ribosomal subunit protein eS8A Chain: I
Molecule details ›
Chain: I
Length: 199 amino acids
Theoretical weight: 22.41 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: P0CX39 (Residues: 2-200; Coverage: 100%)
Gene names: RPS14A, RPS8A, YBL06.05, YBL0613, YBL072C
Sequence domains: Ribosomal protein S8e
Small ribosomal subunit protein uS4A Chain: J
Molecule details ›
Chain: J
Length: 185 amino acids
Theoretical weight: 21.21 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: O13516 (Residues: 2-186; Coverage: 94%)
Gene names: RPS13A, RPS9A, YPL081W, YS11A
Sequence domains:
Small ribosomal subunit protein eS10A Chain: K
Molecule details ›
Chain: K
Length: 96 amino acids
Theoretical weight: 11.57 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: Q08745 (Residues: 1-96; Coverage: 91%)
Gene names: RPS10A, YOR293W
Sequence domains: Plectin/S10 domain
Small ribosomal subunit protein uS17A Chain: L
Molecule details ›
Chain: L
Length: 140 amino acids
Theoretical weight: 16.03 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: P0CX47 (Residues: 6-145; Coverage: 90%)
Gene names: RPS11A, RPS18A, YD9813.03, YDR025W
Sequence domains:
Small ribosomal subunit protein eS12 Chain: M
Molecule details ›
Chain: M
Length: 125 amino acids
Theoretical weight: 13.43 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: P48589 (Residues: 18-142; Coverage: 87%)
Gene names: RPS12, YOR369C
Sequence domains: Ribosomal protein L7Ae/L30e/S12e/Gadd45 family
Small ribosomal subunit protein uS15 Chain: N
Molecule details ›
Chain: N
Length: 150 amino acids
Theoretical weight: 16.93 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: P05756 (Residues: 2-151; Coverage: 99%)
Gene names: D4252, RPS13, RPS13C, YD9609.18, YDR064W
Sequence domains:
Small ribosomal subunit protein uS19 Chain: P
Molecule details ›
Chain: P
Length: 127 amino acids
Theoretical weight: 14.3 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: Q01855 (Residues: 16-142; Coverage: 89%)
Gene names: RPS15, RPS21, YOL040C
Sequence domains: Ribosomal protein S19
Small ribosomal subunit protein uS9A Chain: Q
Molecule details ›
Chain: Q
Length: 127 amino acids
Theoretical weight: 14.07 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: P0CX51 (Residues: 3-129; Coverage: 89%)
Gene names: RP61R, RPS16A, YM9375.12, YMR143W
Sequence domains: Ribosomal protein S9/S16
Small ribosomal subunit protein eS17A Chain: R
Molecule details ›
Chain: R
Length: 125 amino acids
Theoretical weight: 14.27 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: P02407 (Residues: 2-126; Coverage: 92%)
Gene names: RP51A, RPS17A, YML024W
Sequence domains: Ribosomal S17
Small ribosomal subunit protein uS13A Chain: S
Molecule details ›
Chain: S
Length: 135 amino acids
Theoretical weight: 15.77 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: P0CX55 (Residues: 2-136; Coverage: 93%)
Gene names: D9461.35, RPS18A, YDR450W
Sequence domains: Ribosomal protein S13/S18
Small ribosomal subunit protein eS19A Chain: T
Molecule details ›
Chain: T
Length: 143 amino acids
Theoretical weight: 15.81 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: P07280 (Residues: 2-144; Coverage: 99%)
Gene names: RP55A, RPS16AA, RPS19A, YOL121C
Sequence domains: Ribosomal protein S19e
Small ribosomal subunit protein uS10 Chain: U
Molecule details ›
Chain: U
Length: 103 amino acids
Theoretical weight: 11.68 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: P38701 (Residues: 19-121; Coverage: 85%)
Gene names: RPS20, URP2, YHL015W
Sequence domains: Ribosomal protein S10p/S20e
Small ribosomal subunit protein eS21A Chain: V
Molecule details ›
Chain: V
Length: 87 amino acids
Theoretical weight: 9.76 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: P0C0V8 (Residues: 1-87; Coverage: 100%)
Gene names: RPS21A, RPS25, RPS25A, RPS26A, YKR057W
Sequence domains: Ribosomal protein S21e
Small ribosomal subunit protein uS8A Chain: W
Molecule details ›
Chain: W
Length: 129 amino acids
Theoretical weight: 14.52 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: P0C0W1 (Residues: 2-130; Coverage: 99%)
Gene names: J0355, RPS22A, RPS24, RPS24A, YJL190C
Sequence domains: Ribosomal protein S8
Small ribosomal subunit protein uS12A Chain: X
Molecule details ›
Chain: X
Length: 144 amino acids
Theoretical weight: 15.94 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: P0CX29 (Residues: 2-145; Coverage: 99%)
Gene names: G6178, RPS23A, RPS28A, YGR118W
Sequence domains: Ribosomal protein S12/S23
Small ribosomal subunit protein eS24A Chain: Y
Molecule details ›
Chain: Y
Length: 134 amino acids
Theoretical weight: 15.23 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: P0CX31 (Residues: 2-135; Coverage: 99%)
Gene names: RPS24A, RPS24EA, YER074W
Sequence domains: Ribosomal protein S24e
Small ribosomal subunit protein eS25A Chain: Z
Molecule details ›
Chain: Z
Length: 63 amino acids
Theoretical weight: 7.28 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: Q3E792 (Residues: 42-104; Coverage: 58%)
Gene names: RPS25A, RPS31A, YGR027C
Sequence domains: S25 ribosomal protein
Small ribosomal subunit protein eS27A Chain: b
Molecule details ›
Chain: b
Length: 81 amino acids
Theoretical weight: 8.76 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: P35997 (Residues: 2-82; Coverage: 99%)
Gene names: RPS27A, YKL156W
Sequence domains: Ribosomal protein S27
Small ribosomal subunit protein eS28A Chain: c
Molecule details ›
Chain: c
Length: 63 amino acids
Theoretical weight: 7.12 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: Q3E7X9 (Residues: 5-67; Coverage: 94%)
Gene names: O3600, RPS28A, RPS33, RPS33A, YOR167C
Sequence domains: Ribosomal protein S28e
Small ribosomal subunit protein uS14A Chain: d
Molecule details ›
Chain: d
Length: 37 amino acids
Theoretical weight: 4.37 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: P41057 (Residues: 20-56; Coverage: 66%)
Gene names: L8084.11, RPS29A, RPS36A, YLR388W, YS29A
Sequence domains: Ribosomal protein S14p/S29e
Small ribosomal subunit protein eS30A Chain: e
Molecule details ›
Chain: e
Length: 63 amino acids
Theoretical weight: 7.14 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: P0CX33 (Residues: 1-63; Coverage: 100%)
Gene names: L8003.23, RPS30A, YLR287BC, YLR287C-A
Sequence domains: Ribosomal protein S30
Small ribosomal subunit protein eS31 Chain: f
Molecule details ›
Chain: f
Length: 71 amino acids
Theoretical weight: 8.1 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: P05759 (Residues: 82-152; Coverage: 47%)
Gene names: L9470.14, RPS31, RPS37, UBI3, YLR167W
Sequence domains: Ribosomal protein S27a
Small ribosomal subunit protein RACK1 Chain: g
Molecule details ›
Chain: g
Length: 317 amino acids
Theoretical weight: 34.64 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: P38011 (Residues: 3-319; Coverage: 99%)
Gene names: ASC1, CPC2, YM9718.15C, YMR116C
Sequence domains: WD domain, G-beta repeat
Ribosome biogenesis protein TSR1 Chain: k
Molecule details ›
Chain: k
Length: 788 amino acids
Theoretical weight: 90.88 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: Q07381 (Residues: 1-788; Coverage: 100%)
Gene names: TSR1, YDL060W
Sequence domains:
20S ribosomal RNA Chain: 2
Molecule details ›
Chain: 2
Length: 1910 nucleotides
Theoretical weight: 614.94 KDa
Sequence domains: Eukaryotic small subunit ribosomal RNA

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 3.7Å
Relevant EMDB volumes: EMD-21644
Expression system: Saccharomyces cerevisiae

Quick links

Citations

2 review citations

The World of Stable Ribonucleoproteins and Its Mapping With Grad-Seq and Related Approaches.
Gerovac et al. (2021)
1 more

5 mentions without citation

Quality control ensures fidelity in ribosome assembly and cellular health.
Parker et al. (2023)
4 more