› 8d6j

X-ray diffraction
2.5Å resolution

Human Ago2 bound to miR122(21nt) with PIWI loop swapped to AtAgo10 sequence

Released:
DOI: 10.2210/pdb8d6j/pdb
PDB entry 8d6j coloured by chain, front view.
PDB entry 8d6j coloured by chain, side view.
PDB entry 8d6j coloured by chain, top view.
Source organisms:
Primary publication:
A tiny loop in the Argonaute PIWI domain tunes small RNA seed strength.
Xiao Y, Liu TM, MacRae IJ
OpenAccess logo EMBO Rep e55806 (2023)
PMID: 37082939

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-215257 (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: 97.48 KDa
Source organism: Homo sapiens
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: Q9UKV8 (Residues: 1-859; Coverage: 100%)
Gene names: AGO2, EIF2C2
Sequence domains:
RNA (5'-R(P*UP*GP*GP*AP*GP*UP*GP*UP*GP*AP*CP*AP*AP*UP*GP*GP*UP*GP*UP*UP*U)-3') Chain: B
Molecule details ›
Chain: B
Length: 21 nucleotides
Theoretical weight: 6.79 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: SSRL BEAMLINE BL9-2
Spacegroup: P21
Unit cell:
a: 63.302Å b: 107.512Å c: 68.706Å
α: 90° β: 106.9° γ: 90°
R-values:
R R work R free
0.234 0.232 0.284
Expression systems:
  • Spodoptera frugiperda
  • Not provided

Quick links

Citations

1 review citation

When Argonaute takes out the ribonuclease sword.
Nakanishi K. (2023)
1 other article