› 5fir

X-ray diffraction
2.84Å resolution

Crystal structure of C. elegans XRN2 in complex with the XRN2-binding domain of PAXT-1

Released:
DOI: 10.2210/pdb5fir/pdb
PDB entry 5fir coloured by chain, front view.
PDB entry 5fir coloured by chain, side view.
PDB entry 5fir coloured by chain, top view.
Source organism: Caenorhabditis elegans
Primary publication:
Structural basis and function of XRN2 binding by XTB domains.
Richter H, Katic I, Gut H, Großhans H
OpenAccess logo Nat Struct Mol Biol 23 164-71 (2016)
PMID: 26779609

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-173134 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
5'-3' exoribonuclease 2 homolog Chains: A, C, E, G, I, K
Molecule details ›
Chains: A, C, E, G, I, K
Length: 636 amino acids
Theoretical weight: 74.91 KDa
Source organism: Caenorhabditis elegans
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q9U299 (Residues: 1-787; Coverage: 65%)
Gene names: Y48B6A.3, xrn-2
Sequence domains:
Partner of xrn-2 protein 1 Chains: B, D, F, H, J, L
Molecule details ›
Chains: B, D, F, H, J, L
Length: 78 amino acids
Theoretical weight: 8.99 KDa
Source organism: Caenorhabditis elegans
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q21738 (Residues: 2-75; Coverage: 22%)
Gene names: R05D11.6, paxt-1
Sequence domains: XRN-Two Binding Domain, XTBD

Ligands and Environments

1 bound ligand:
Ligand SO4 27 x SO4
1 modified residue:
Ligand MSE 120 x MSE

Experiments and Validation Details

Entry percentile scores
X-ray source: SLS BEAMLINE X10SA
Spacegroup: P212121
Unit cell:
a: 170.21Å b: 200.77Å c: 202.99Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.187 0.185 0.238
Expression system: Escherichia coli BL21(DE3)

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Citations

3 review citations

Comparison of preribosomal RNA processing pathways in yeast, plant and human cells - focus on coordinated action of endo- and exoribonucleases.
Tomecki et al. (2017)
2 more

3 mentions without citation

IT'S 2 for the price of 1: Multifaceted ITS2 processing machines in RNA and DNA maintenance.
Pillon et al. (2019)
2 more