PDBe 3j16

Electron Microscopy
7.2Å resolution

Models of ribosome-bound Dom34p and Rli1p and their ribosomal binding partners

Released:

Function and Biology Details

Structure analysis Details

Assembly composition:
hetero 12-mer (preferred)
Entry contents:
9 distinct polypeptide molecules
3 distinct RNA molecules
Macromolecules (12 distinct):
Protein DOM34 Chain: A
Molecule details ›
Chain: A
Length: 386 amino acids
Theoretical weight: 44.12 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P33309 (Residues: 1-386; Coverage: 100%)
Gene names: DOM34, N2016, YNL001W
Sequence domains:
Translation initiation factor RLI1 Chain: B
Molecule details ›
Chain: B
Length: 608 amino acids
Theoretical weight: 68.43 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: Q03195 (Residues: 1-608; Coverage: 100%)
Gene names: RLI1, YDR091C
Sequence domains:
60S ribosomal protein L9-A Chain: F
Molecule details ›
Chain: F
Length: 191 amino acids
Theoretical weight: 21.61 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P05738 (Residues: 1-191; Coverage: 100%)
Gene names: RPL8A, RPL9, RPL9A, YGL147C
Sequence domains: Ribosomal protein L6
40S ribosomal protein S30-A Chain: E
Molecule details ›
Chain: E
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
60S acidic ribosomal protein P0 Chain: G
Molecule details ›
Chain: G
Length: 312 amino acids
Theoretical weight: 33.75 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P05317 (Residues: 1-312; Coverage: 100%)
Gene names: L10E, L8300.8, RPA0, RPL10E, RPLA0, RPP0, YLR340W
Sequence domains:
40S ribosomal protein S6-A Chain: C
Molecule details ›
Chain: C
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
60S ribosomal protein L12-A Chain: H
Molecule details ›
Chain: H
Length: 165 amino acids
Theoretical weight: 17.85 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P0CX53 (Residues: 1-165; Coverage: 100%)
Gene names: RPL12A, RPL15B, YEL054C
Sequence domains:
60S ribosomal protein L23-A Chain: I
Molecule details ›
Chain: I
Length: 137 amino acids
Theoretical weight: 14.49 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P0CX41 (Residues: 1-137; Coverage: 100%)
Gene names: RPL17A, RPL17AA, RPL23A, YBL0713, YBL087C
Sequence domains: Ribosomal protein L14p/L23e
40S ribosomal protein S24-A Chain: D
Molecule details ›
Chain: D
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
28S ribosomal RNA Chain: J
Molecule details ›
Chain: J
Length: 233 nucleotides
Theoretical weight: 75.11 KDa
Sequence domains: Eukaryotic small subunit ribosomal RNA
18S Ribosomal RNA Chain: K
Molecule details ›
Chain: K
Length: 155 nucleotides
Theoretical weight: 49.86 KDa
Sequence domains: Eukaryotic large subunit ribosomal RNA
P-site tRNA Chain: L
Molecule details ›
Chain: L
Length: 75 nucleotides
Theoretical weight: 24.14 KDa
Sequence domains: tRNA

Ligands and Environments

3 bound ligands:

No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 7.2Å
Relevant EMDB volumes: EMD-2010