› 3f73

X-ray diffraction
3Å resolution

Alignment of guide-target seed duplex within an argonaute silencing complex

Released:
DOI: 10.2210/pdb3f73/pdb
PDB entry 3f73 coloured by chain, front view.
PDB entry 3f73 coloured by chain, side view.
PDB entry 3f73 coloured by chain, top view.
Source organism: Thermus thermophilus HB27
Primary publication:
Structure of an argonaute silencing complex with a seed-containing guide DNA and target RNA duplex.
Wang Y, Juranek S, Li H, Sheng G, Tuschl T, Patel DJ
Nature 456 921-6 (2008)
PMID: 19092929

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-116238 (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:
DNA (5'-D(P*DTP*DGP*DAP*DGP*DGP*DTP*DAP*DGP*DTP*DAP*DGP*DGP*DTP*DTP*DGP*DTP*DA*DTP*DAP*DGP*DT)-3') Chains: C, X
Molecule details ›
Chains: C, X
Length: 21 nucleotides
Theoretical weight: 6.59 KDa
Source organism: Thermus thermophilus HB27
Expression system: Not provided
RNA (5'-R(*UP*AP*UP*AP*CP*AP*A*CP*UP*CP*AP*CP*UP*AP*CP*CP*UP*CP*GP*U)-3') Chains: H, Y
Molecule details ›
Chains: H, Y
Length: 20 nucleotides
Theoretical weight: 6.25 KDa
Source organism: Thermus thermophilus HB27
Expression system: Not provided

Ligands and Environments

2 bound ligands:
Ligand MG 3 x MG
Ligand PO4 1 x PO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 24-ID-E
Spacegroup: P21
Unit cell:
a: 61.162Å b: 120.527Å c: 109.085Å
α: 90° β: 105.3° γ: 90°
R-values:
R R work R free
0.221 0.221 0.282
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

82 review citations

Origins and Mechanisms of miRNAs and siRNAs.
Carthew et al. (2009)
81 more

23 mentions without citation

DNA interference and beyond: structure and functions of prokaryotic Argonaute proteins.
Lisitskaya et al. (2018)
22 more