› 1rk8

X-ray diffraction
1.9Å resolution

Structure of the cytosolic protein PYM bound to the Mago-Y14 core of the exon junction complex

Released:
DOI: 10.2210/pdb1rk8/pdb
PDB entry 1rk8 coloured by chain, front view.
PDB entry 1rk8 coloured by chain, side view.
PDB entry 1rk8 coloured by chain, top view.
Source organism: Drosophila melanogaster
Primary publication:
Molecular insights into the interaction of PYM with the Mago-Y14 core of the exon junction complex.
Bono F, Ebert J, Unterholzner L, Güttler T, Izaurralde E, Conti E
EMBO Rep 5 304-10 (2004)
PMID: 14968132

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-155844 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
RNA-binding protein 8A Chain: A
Molecule details ›
Chain: A
Length: 165 amino acids
Theoretical weight: 19.04 KDa
Source organism: Drosophila melanogaster
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9V535 (Residues: 1-165; Coverage: 100%)
Gene names: CG8781, Y14, tsu
Sequence domains: RNA recognition motif
Structure domains: Alpha-Beta Plaits
Protein mago nashi Chain: B
Molecule details ›
Chain: B
Length: 147 amino acids
Theoretical weight: 17.34 KDa
Source organism: Drosophila melanogaster
Expression system: Escherichia coli
UniProt:
  • Canonical: P49028 (Residues: 1-147; Coverage: 100%)
Gene names: CG9401, mago, mgn
Sequence domains: Mago nashi protein
Structure domains: Mago nashi
Partner of Y14 and mago Chain: C
Molecule details ›
Chain: C
Length: 58 amino acids
Theoretical weight: 6.61 KDa
Source organism: Drosophila melanogaster
Expression system: Escherichia coli
UniProt:
  • Canonical: P82804 (Residues: 1-58; Coverage: 28%)
Gene names: CG30176, Pym, wibg
Sequence domains: Mago binding

Ligands and Environments

1 bound ligand:
Ligand CA 3 x CA
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID29
Spacegroup: P43212
Unit cell:
a: 106.357Å b: 106.357Å c: 58.139Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.235 0.235 0.249
Expression system: Escherichia coli

Quick links

Citations

25 review citations

The nonsense-mediated decay RNA surveillance pathway.
Chang et al. (2007)
24 more

6 mentions without citation

Molecular insights into the interaction of PYM with the Mago-Y14 core of the exon junction complex.
Bono et al. (2004)
5 more