› 7sez

X-ray diffraction
1.7Å resolution

Crystal structure of Vaccinia Virus decapping enzyme D9 in complex with m7GDP

Released:
DOI: 10.2210/pdb7sez/pdb
PDB entry 7sez coloured by chain, front view.
PDB entry 7sez coloured by chain, side view.
PDB entry 7sez coloured by chain, top view.
Source organism: Vaccinia virus Western Reserve
Primary publication:
Structure of the poxvirus decapping enzyme D9 reveals its mechanism of cap recognition and catalysis.
Peters JK, Tibble RW, Warminski M, Jemielity J, Gross JD
Structure 30 721-732.e4 (2022)
PMID: 35290794

Function and Biology Details

Biochemical function:
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-137591 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
mRNA-decapping protein OPG121 Chain: A
Molecule details ›
Chain: A
Length: 221 amino acids
Theoretical weight: 26.1 KDa
Source organism: Vaccinia virus Western Reserve
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P04311 (Residues: 1-213; Coverage: 100%)
Gene names: D9R, OPG121, VACWR114
Sequence domains: NUDIX domain

Ligands and Environments

2 bound ligands:
Ligand M7G 1 x M7G
Ligand NA 9 x NA
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 8.3.1
Spacegroup: C2221
Unit cell:
a: 52.55Å b: 140.1Å c: 75.98Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.195 0.193 0.224
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

1 review citation

Eukaryotic mRNA Decapping Activation.
Vidya et al. (2022)

3 mentions without citation

In silico identification of potential inhibitors of vital monkeypox virus proteins from FDA approved drugs.
Sahoo et al. (2023)
2 more