› 4j7m

X-ray diffraction
1.7Å resolution

Crystal structure of mouse DXO in complex with substrate mimic RNA and calcium ion

Released:
DOI: 10.2210/pdb4j7m/pdb
PDB entry 4j7m coloured by chain, front view.
PDB entry 4j7m coloured by chain, side view.
PDB entry 4j7m coloured by chain, top view.
Source organisms:
Primary publication:
A mammalian pre-mRNA 5' end capping quality control mechanism and an unexpected link of capping to pre-mRNA processing.
Jiao X, Chang JH, Kilic T, Tong L, Kiledjian M
Mol Cell 50 104-15 (2013)
PMID: 23523372

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-130694 (preferred)
Entry contents:
1 distinct polypeptide molecule
1 distinct RNA molecule
Macromolecules (2 distinct):
Decapping and exoribonuclease protein Chain: A
Molecule details ›
Chain: A
Length: 378 amino acids
Theoretical weight: 43.13 KDa
Source organism: Mus musculus
Expression system: Escherichia coli
UniProt:
  • Canonical: O70348 (Residues: 27-384; Coverage: 90%)
Gene names: Dom3z, Dxo, Ng6
Sequence domains: RAI1 like PD-(D/E)XK nuclease
RNA (5'-R(P*UP*(U37)P*(U37)P*UP*U)-3') Chain: B
Molecule details ›
Chain: B
Length: 5 nucleotides
Theoretical weight: 1.52 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

2 bound ligands:
Ligand UBD 2 x UBD
Ligand CA 1 x CA
1 modified residue:
Ligand U37 2 x U37

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X29A
Spacegroup: P21
Unit cell:
a: 49.985Å b: 87.837Å c: 54.356Å
α: 90° β: 111.69° γ: 90°
R-values:
R R work R free
0.195 0.183 0.213
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

36 review citations

Coupling mRNA processing with transcription in time and space.
Bentley DL. (2014)
35 more

4 mentions without citation

A mammalian pre-mRNA 5' end capping quality control mechanism and an unexpected link of capping to pre-mRNA processing.
Jiao et al. (2013)
3 more