› 4xrp

X-ray diffraction
3.3Å resolution

Structure of the Pnkp1/Rnl/Hen1 RNA repair complex

Released:
DOI: 10.2210/pdb4xrp/pdb
PDB entry 4xrp coloured by chain, front view.
PDB entry 4xrp coloured by chain, side view.
PDB entry 4xrp coloured by chain, top view.
Source organism: Capnocytophaga gingivalis ATCC 33624
Primary publication:
Reconstitution and structure of a bacterial Pnkp1-Rnl-Hen1 RNA repair complex.
Wang P, Selvadurai K, Huang RH
Nat Commun 6 6876 (2015)
PMID: 25882814

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero hexamer (preferred)
PDBe Complex ID:
PDB-CPX-111150 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
Polynucleotide kinase Chains: A, D
Molecule details ›
Chains: A, D
Length: 312 amino acids
Theoretical weight: 36.32 KDa
Source organism: Capnocytophaga gingivalis ATCC 33624
Expression system: Escherichia coli
UniProt:
  • Canonical: C2M8N3 (Residues: 1-312; Coverage: 100%)
Gene name: CAPGI0001_2485
Sequence domains: AAA domain
Polynucleotide kinase-phosphatase ligase domain-containing protein Chains: B, E
Molecule details ›
Chains: B, E
Length: 394 amino acids
Theoretical weight: 46.56 KDa
Source organism: Capnocytophaga gingivalis ATCC 33624
Expression system: Escherichia coli
UniProt:
  • Canonical: C2M8N4 (Residues: 1-394; Coverage: 100%)
Gene name: CAPGI0001_2487
Sequence domains: PNKP adenylyltransferase domain, ligase domain
Small RNA 2'-O-methyltransferase Chains: C, F
Molecule details ›
Chains: C, F
Length: 436 amino acids
Theoretical weight: 51.56 KDa
Source organism: Capnocytophaga gingivalis ATCC 33624
Expression system: Escherichia coli
UniProt:
  • Canonical: C2M7I7 (Residues: 1-436; Coverage: 100%)
Gene name: CAPGI0001_1566

Ligands and Environments

4 bound ligands:
Ligand PO4 2 x PO4
Ligand MG 4 x MG
Ligand SO4 8 x SO4
Ligand GOL 5 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 21-ID-D
Spacegroup: P21
Unit cell:
a: 111.16Å b: 179.201Å c: 114.333Å
α: 90° β: 103.7° γ: 90°
R-values:
R R work R free
0.177 0.175 0.238
Expression system: Escherichia coli

Quick links

Citations

1 review citation

RNA damage in biological conflicts and the diversity of responding RNA repair systems.
Burroughs et al. (2016)
7 other articles

2 mentions without citation

Reconstitution and structure of a bacterial Pnkp1-Rnl-Hen1 RNA repair complex.
Wang et al. (2015)
1 more