› 7sp3

X-ray diffraction
1.6Å resolution

E. coli RppH bound to Ap4A

Released:
DOI: 10.2210/pdb7sp3/pdb
PDB entry 7sp3 coloured by chain, front view.
PDB entry 7sp3 coloured by chain, side view.
PDB entry 7sp3 coloured by chain, top view.
Source organism: Escherichia coli
Primary publication:
A distinct RNA recognition mechanism governs Np4 decapping by RppH.
Levenson-Palmer R, Luciano DJ, Vasilyev N, Nuthanakanti A, Serganov A, Belasco JG
OpenAccess logo Proc Natl Acad Sci U S A 119 (2022)
PMID: 35131855

Function and Biology Details

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

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-532043 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
RNA pyrophosphohydrolase Chain: A
Molecule details ›
Chain: A
Length: 161 amino acids
Theoretical weight: 18.97 KDa
Source organism: Escherichia coli
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P0A776 (Residues: 1-158; Coverage: 90%)
Gene names: JW2798, b2830, nudH, rppH, ygdP
Sequence domains: NUDIX domain

Ligands and Environments

4 bound ligands:
Ligand B4P 1 x B4P
Ligand MG 3 x MG
Ligand F 1 x F
Ligand CL 1 x CL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU R-AXIS
Spacegroup: C2
Unit cell:
a: 79.39Å b: 36.384Å c: 57.801Å
α: 90° β: 102.101° γ: 90°
R-values:
R R work R free
0.185 0.183 0.22
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

1 review citation

Recent insights into noncanonical 5' capping and decapping of RNA.
Doamekpor et al. (2022)

2 mentions without citation

The mysterious diadenosine tetraphosphate (AP4A).
Zegarra et al. (2023)
1 more