› 3j16

Electron Microscopy
7.2Å resolution

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

Released:
DOI: 10.2210/pdb3j16/pdb
PDB entry 3j16 coloured by chain, front view.
PDB entry 3j16 coloured by chain, side view.
PDB entry 3j16 coloured by chain, top view.
Source organism: Saccharomyces cerevisiae
Primary publication:
Structural basis of highly conserved ribosome recycling in eukaryotes and archaea.
Becker T, Franckenberg S, Wickles S, Shoemaker CJ, Anger AM, Armache JP, Sieber H, Ungewickell C, Berninghausen O, Daberkow I, Karcher A, Thomm M, Hopfner KP, Green R, Beckmann R
Nature 482 501-6 (2012)
PMID: 22358840
Related structures: EMD-2010

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero dodecamer (preferred)
PDBe Complex ID:
PDB-CPX-138627 (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:
Large ribosomal subunit protein uL6A 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
Small ribosomal subunit protein eS30A 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
Large ribosomal subunit protein uL10 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:
Small ribosomal subunit protein eS6A 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
Large ribosomal subunit protein uL11A 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:
Large ribosomal subunit protein uL14A 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
Small ribosomal subunit protein eS24A 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:
Ligand MG 1 x MG
Ligand ATP 1 x ATP
Ligand SF4 2 x SF4
No modified residues

Experiments and Validation Details

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

Quick links

Citations

38 review citations

NMD: a multifaceted response to premature translational termination.
Kervestin et al. (2012)
37 more

8 mentions without citation

Recent structural studies on Dom34/aPelota and Hbs1/aEF1α: important factors for solving general problems of ribosomal stall in translation.
Kobayashi et al. (2013)
7 more