› 5js2

X-ray diffraction
2.95Å resolution

Human Argonaute-2 Bound to a Modified siRNA

Released:
DOI: 10.2210/pdb5js2/pdb
PDB entry 5js2 coloured by chain, front view.
PDB entry 5js2 coloured by chain, side view.
PDB entry 5js2 coloured by chain, top view.
Source organisms:
Primary publication:
Structural Analysis of Human Argonaute-2 Bound to a Modified siRNA Guide.
Schirle NT, Kinberger GA, Murray HF, Lima WF, Prakash TP, MacRae IJ
J Am Chem Soc 138 8694-7 (2016)
PMID: 27380263

Function and Biology Details

Reaction catalysed: 
Endonucleolytic cleavage to 5'-phosphomonoester
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-193881 (preferred)
Entry contents:
1 distinct polypeptide molecule
1 distinct RNA molecule
Macromolecules (2 distinct):
Protein argonaute-2 Chain: A
Molecule details ›
Chain: A
Length: 859 amino acids
Theoretical weight: 97.38 KDa
Source organism: Homo sapiens
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: Q9UKV8 (Residues: 1-859; Coverage: 100%)
Gene names: AGO2, EIF2C2
Sequence domains:
Structure domains:
modified siRNA Chain: B
Molecule details ›
Chain: B
Length: 6 nucleotides
Theoretical weight: 1.96 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

3 bound ligands:
Ligand IPH 2 x IPH
Ligand PO4 1 x PO4
Ligand MG 1 x MG
4 modified residues:
Ligand F2T 1 x F2T
Ligand 6NW 1 x 6NW
Ligand UFT 2 x UFT
Ligand 6OO 1 x 6OO

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRL BEAMLINE BL11-1
Spacegroup: P21
Unit cell:
a: 63.102Å b: 107.552Å c: 68.893Å
α: 90° β: 107.39° γ: 90°
R-values:
R R work R free
0.224 0.222 0.261
Expression systems:
  • Spodoptera frugiperda
  • Not provided

Quick links

Citations

12 review citations

The chemical evolution of oligonucleotide therapies of clinical utility.
Khvorova et al. (2017)
11 more

3 mentions without citation

Structural Analysis of Human Argonaute-2 Bound to a Modified siRNA Guide.
Schirle et al. (2016)
2 more