› 4j7l

X-ray diffraction
1.8Å resolution

Crystal structure of mouse DXO in complex with PRODUCT RNA AND two MAGNESIUM ions

Released:
DOI: 10.2210/pdb4j7l/pdb
PDB entry 4j7l coloured by chain, front view.
PDB entry 4j7l coloured by chain, side view.
PDB entry 4j7l 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-130693 (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*UP*UP*UP*U)-3') Chain: B
Molecule details ›
Chain: B
Length: 5 nucleotides
Theoretical weight: 1.49 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

2 bound ligands:
Ligand UBD 1 x UBD
Ligand MG 2 x MG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X29A
Spacegroup: P21
Unit cell:
a: 50.01Å b: 87.66Å c: 53.94Å
α: 90° β: 112.18° γ: 90°
R-values:
R R work R free
0.195 0.183 0.215
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

8 mentions without citation

eIF3d: A driver of noncanonical cap-dependent translation of specific mRNAs and a trigger of biological/pathological processes.
Ma et al. (2023)
7 more