› 7wtp

Electron Microscopy
3.8Å resolution

Cryo-EM structure of a yeast pre-40S ribosomal subunit - State Tsr1-2 (with Rps2)

Released:
DOI: 10.2210/pdb7wtp/pdb
PDB entry 7wtp coloured by chain, front view.
PDB entry 7wtp coloured by chain, side view.
PDB entry 7wtp coloured by chain, top view.
Source organism: Saccharomyces cerevisiae
Primary publication:
The nucleoplasmic phase of pre-40S formation prior to nuclear export.
Cheng J, Lau B, Thoms M, Ameismeier M, Berninghausen O, Hurt E, Beckmann R
Nucleic Acids Res (2022)
PMID: 36321656
Related structures: EMD-32794

Function and Biology Details

Reaction catalysed: 
S-adenosyl-L-methionine + guanine(1575) in 18S rRNA = S-adenosyl-L-homocysteine + N(7)-methylguanine(1575) in 18S rRNA
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero nonadecamer (preferred)
PDBe Complex ID:
PDB-CPX-216236 (preferred)
Entry contents:
18 distinct polypeptide molecules
1 distinct RNA molecule
Macromolecules (19 distinct):
Small ribosomal subunit protein eS1A Chain: SB
Molecule details ›
Chain: SB
Length: 255 amino acids
Theoretical weight: 28.8 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P33442 (Residues: 1-255; Coverage: 100%)
Gene names: L9753.9, PLC1, RPS10A, RPS1A, YLR441C
Sequence domains: Ribosomal S3Ae family
Small ribosomal subunit protein uS5 Chain: SC
Molecule details ›
Chain: SC
Length: 254 amino acids
Theoretical weight: 27.49 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P25443 (Residues: 1-254; Coverage: 100%)
Gene names: G2893, RPS2, RPS4, SUP38, SUP44, YGL123W
Sequence domains:
Small ribosomal subunit protein eS4A Chain: SE
Molecule details ›
Chain: SE
Length: 261 amino acids
Theoretical weight: 29.47 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P0CX35 (Residues: 1-261; Coverage: 100%)
Gene names: J2186, RPS4A, RPS7B, YJR145C
Sequence domains:
Small ribosomal subunit protein eS6A Chain: SG
Molecule details ›
Chain: SG
Length: 236 amino acids
Theoretical weight: 27.05 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P0CX37 (Residues: 1-236; Coverage: 100%)
Gene names: LPG18C, RPS101, RPS10B, RPS6A, YPL090C
Sequence domains: Ribosomal protein S6e
Small ribosomal subunit protein eS7A Chain: SH
Molecule details ›
Chain: SH
Length: 190 amino acids
Theoretical weight: 21.66 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P26786 (Residues: 1-190; Coverage: 100%)
Gene names: RPS30, RPS7A, YOR096W, YOR3177W
Sequence domains: Ribosomal protein S7e
Small ribosomal subunit protein eS8A Chain: SI
Molecule details ›
Chain: SI
Length: 200 amino acids
Theoretical weight: 22.54 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P0CX39 (Residues: 1-200; Coverage: 100%)
Gene names: RPS14A, RPS8A, YBL06.05, YBL0613, YBL072C
Sequence domains: Ribosomal protein S8e
Small ribosomal subunit protein uS4A Chain: SJ
Molecule details ›
Chain: SJ
Length: 197 amino acids
Theoretical weight: 22.49 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: O13516 (Residues: 1-197; Coverage: 100%)
Gene names: RPS13A, RPS9A, YPL081W, YS11A
Sequence domains:
Small ribosomal subunit protein uS17A Chain: SL
Molecule details ›
Chain: SL
Length: 156 amino acids
Theoretical weight: 17.79 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P0CX47 (Residues: 1-156; Coverage: 100%)
Gene names: RPS11A, RPS18A, YD9813.03, YDR025W
Sequence domains:
Small ribosomal subunit protein uS15 Chain: SN
Molecule details ›
Chain: SN
Length: 151 amino acids
Theoretical weight: 17.06 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P05756 (Residues: 1-151; Coverage: 100%)
Gene names: D4252, RPS13, RPS13C, YD9609.18, YDR064W
Sequence domains:
Small ribosomal subunit protein uS11A Chain: SO
Molecule details ›
Chain: SO
Length: 137 amino acids
Theoretical weight: 14.56 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P06367 (Residues: 1-137; Coverage: 100%)
Gene names: CRY1, RPL59, RPS14A, YCR031C, YCR31C
Sequence domains: Ribosomal protein S11
Small ribosomal subunit protein uS8A Chain: SW
Molecule details ›
Chain: SW
Length: 130 amino acids
Theoretical weight: 14.65 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P0C0W1 (Residues: 1-130; Coverage: 100%)
Gene names: J0355, RPS22A, RPS24, RPS24A, YJL190C
Sequence domains: Ribosomal protein S8
Small ribosomal subunit protein uS12A Chain: SX
Molecule details ›
Chain: SX
Length: 145 amino acids
Theoretical weight: 16.07 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P0CX29 (Residues: 1-145; Coverage: 100%)
Gene names: G6178, RPS23A, RPS28A, YGR118W
Sequence domains: Ribosomal protein S12/S23
Small ribosomal subunit protein eS24A Chain: SY
Molecule details ›
Chain: SY
Length: 135 amino acids
Theoretical weight: 15.36 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P0CX31 (Residues: 1-135; Coverage: 100%)
Gene names: RPS24A, RPS24EA, YER074W
Sequence domains: Ribosomal protein S24e
Small ribosomal subunit protein eS27A Chain: Sb
Molecule details ›
Chain: Sb
Length: 82 amino acids
Theoretical weight: 8.89 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P35997 (Residues: 1-82; Coverage: 100%)
Gene names: RPS27A, YKL156W
Sequence domains: Ribosomal protein S27
Small ribosomal subunit protein eS30A Chain: Se
Molecule details ›
Chain: Se
Length: 63 amino acids
Theoretical weight: 7.14 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P0CX33 (Residues: 1-63; Coverage: 100%)
Gene names: L8003.23, RPS30A, YLR287BC, YLR287C-A
Sequence domains: Ribosomal protein S30
Pre-rRNA-processing protein PNO1 Chain: CA
Molecule details ›
Chain: CA
Length: 274 amino acids
Theoretical weight: 30.38 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: Q99216 (Residues: 1-274; Coverage: 100%)
Gene names: DIM2, O3513, PNO1, RRP20, YOR145C, YOR3513C
Sequence domains: Krr1 KH1 domain
18S rRNA (guanine(1575)-N(7))-methyltransferase Chain: CB
Molecule details ›
Chain: CB
Length: 275 amino acids
Theoretical weight: 30.79 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P25627 (Residues: 1-275; Coverage: 100%)
Gene names: BUD23, YCR047C, YCR47C
Sequence domains:
Ribosome biogenesis protein TSR1 Chain: CC
Molecule details ›
Chain: CC
Length: 788 amino acids
Theoretical weight: 90.88 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: Q07381 (Residues: 1-788; Coverage: 100%)
Gene names: TSR1, YDL060W
Sequence domains:
18S Ribosomal RNA Chain: C2
Molecule details ›
Chain: C2
Length: 1800 nucleotides
Theoretical weight: 579.76 KDa
Sequence domains: Eukaryotic small subunit ribosomal RNA

Ligands and Environments

1 bound ligand:
Ligand ZN 1 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 3.8Å
Relevant EMDB volumes: EMD-32794

Quick links

Citations

2 review citations

Ribosome biogenesis factors-from names to functions.
Dörner et al. (2023)
1 more

1 mention without citation

The nucleoplasmic phase of pre-40S formation prior to nuclear export.
Cheng et al. (2022)