› 3hvr

X-ray diffraction
3.21Å resolution

Crystal structure of T. thermophilus Argonaute complexed with DNA guide strand and 19-nt RNA target strand with two Mg2+ at the cleavage site

Released:
DOI: 10.2210/pdb3hvr/pdb
PDB entry 3hvr coloured by chain, front view.
PDB entry 3hvr coloured by chain, side view.
PDB entry 3hvr coloured by chain, top view.
Source organism: Thermus thermophilus HB27
Primary publication:
Nucleation, propagation and cleavage of target RNAs in Ago silencing complexes.
Wang Y, Juranek S, Li H, Sheng G, Wardle GS, Tuschl T, Patel DJ
Nature 461 754-61 (2009)
PMID: 19812667

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-116379 (preferred)
Entry contents:
1 distinct polypeptide molecule
1 distinct DNA molecule
1 distinct RNA molecule
Macromolecules (3 distinct):
Protein argonaute Chains: A, B
Molecule details ›
Chains: A, B
Length: 685 amino acids
Theoretical weight: 76.73 KDa
Source organism: Thermus thermophilus HB27
Expression system: Escherichia coli
UniProt:
  • Canonical: Q746M7 (Residues: 1-685; Coverage: 100%)
Gene names: TT_P0026, ago
Sequence domains:
Structure domains:
5'-D(P*TP*GP*AP*GP*GP*TP*AP*GP*TP*AP*GP*GP*TP*TP*TP*GP*AP*TP*AP*GP*T)-3' Chains: C, M
Molecule details ›
Chains: C, M
Length: 21 nucleotides
Theoretical weight: 6.59 KDa
Source organism: Thermus thermophilus HB27
Expression system: Not provided
5'-R(*UP*AP*UP*AP*CP*AP*AP*CP*CP*UP*AP*CP*UP*AP*CP*CP*UP*CP*G)-3' Chains: D, N
Molecule details ›
Chains: D, N
Length: 19 nucleotides
Theoretical weight: 5.94 KDa
Source organism: Thermus thermophilus HB27
Expression system: Not provided

Ligands and Environments

2 bound ligands:
Ligand MG 6 x MG
Ligand PO4 2 x PO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 24-ID-C
Spacegroup: P212121
Unit cell:
a: 111.252Å b: 116.903Å c: 170.504Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.229 0.226 0.273
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

75 review citations

The widespread regulation of microRNA biogenesis, function and decay.
Krol et al. (2010)
74 more

8 mentions without citation

Molecular mechanisms of RNA interference.
Wilson et al. (2013)
7 more