› 2y35

X-ray diffraction
3.2Å resolution

Crystal structure of Xrn1-substrate complex

Released:
DOI: 10.2210/pdb2y35/pdb
PDB entry 2y35 coloured by chain, front view.
PDB entry 2y35 coloured by chain, side view.
PDB entry 2y35 coloured by chain, top view.
Source organisms:
Primary publication:
Coupled 5' nucleotide recognition and processivity in Xrn1-mediated mRNA decay.
Jinek M, Coyle SM, Doudna JA
Mol Cell 41 600-8 (2011)
PMID: 21362555

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-115948 (preferred)
Entry contents:
1 distinct polypeptide molecule
1 distinct DNA molecule
Macromolecules (2 distinct):
5'-3' exoribonuclease 1 Chain: A
Molecule details ›
Chain: A
Length: 1140 amino acids
Theoretical weight: 132.4 KDa
Source organism: Drosophila melanogaster
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: E1JJR3 (Residues: 1-1140; Coverage: 71%)
Gene names: CG3291, DmXrn1, Dmel\CG3291, Dmel_CG3291, Pcm, XRN1, XRN1/pcm, Xrn1, Xrn1p, dXRN1, pcm
Sequence domains:
DT11 (5'-D(*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP)-3' Chain: B
Molecule details ›
Chain: B
Length: 11 nucleotides
Theoretical weight: 3.3 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

1 bound ligand:
Ligand MG 1 x MG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 8.2.2
Spacegroup: P42212
Unit cell:
a: 149.99Å b: 149.99Å c: 154.86Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.226 0.225 0.271
Expression systems:
  • Spodoptera frugiperda
  • Not provided

Quick links

Citations

22 review citations

RNA degradation in Saccharomyces cerevisae.
Parker R. (2012)
21 more

18 mentions without citation

XRN 5'→3' exoribonucleases: structure, mechanisms and functions.
Nagarajan et al. (2013)
17 more