› 6j80

X-ray diffraction
1.81Å resolution

Human mitochondrial Oligoribonuclease in complex with poly-dT DNA

Released:
DOI: 10.2210/pdb6j80/pdb
PDB entry 6j80 coloured by chain, front view.
PDB entry 6j80 coloured by chain, side view.
PDB entry 6j80 coloured by chain, top view.
Source organisms:
Primary publication:
Structural insights into nanoRNA degradation by human Rexo2.
Chu LY, Agrawal S, Chen YP, Yang WZ, Yuan HS
RNA 25 737-746 (2019)
PMID: 30926754

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-120057 (preferred)
Entry contents:
1 distinct polypeptide molecule
1 distinct DNA molecule
Macromolecules (2 distinct):
Oligoribonuclease, mitochondrial Chains: A, B
Molecule details ›
Chains: A, B
Length: 181 amino acids
Theoretical weight: 20.95 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q9Y3B8 (Residues: 38-216; Coverage: 76%)
Gene names: CGI-114, REXO2, SFN, SMFN
Sequence domains: Exonuclease
DNA (5'-D(P*TP*TP*TP*TP*TP*TP*T)-3') Chain: C
Molecule details ›
Chain: C
Length: 7 nucleotides
Theoretical weight: 2.08 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

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

Experiments and Validation Details

Entry percentile scores
X-ray source: NSRRC BEAMLINE BL15A1
Spacegroup: C2
Unit cell:
a: 130.079Å b: 88.403Å c: 45.939Å
α: 90° β: 105.36° γ: 90°
R-values:
R R work R free
0.194 0.193 0.213
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

3 review citations

Human Mitochondrial RNA Processing and Modifications: Overview.
Jedynak-Slyvka et al. (2021)
2 more

1 mention without citation

Structural insights into nanoRNA degradation by human Rexo2.
Chu et al. (2019)