› 6d92

X-ray diffraction
1.81Å resolution

Ternary RsAgo Complex with Guide RNA and Target DNA Containing A-A non-canonical pair at position 3

Released:
DOI: 10.2210/pdb6d92/pdb
PDB entry 6d92 coloured by chain, front view.
PDB entry 6d92 coloured by chain, side view.
PDB entry 6d92 coloured by chain, top view.
Source organism: Cereibacter sphaeroides ATCC 17025
Primary publication:
Accommodation of Helical Imperfections in Rhodobacter sphaeroides Argonaute Ternary Complexes with Guide RNA and Target DNA.
Liu Y, Esyunina D, Olovnikov I, Teplova M, Kulbachinskiy A, Aravin AA, Patel DJ
Cell Rep 24 453-462 (2018)
PMID: 29996105

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-218862 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
1 distinct RNA molecule
Macromolecules (4 distinct):
Protein argonaute Chains: A, F
Molecule details ›
Chains: A, F
Length: 791 amino acids
Theoretical weight: 89.04 KDa
Source organism: Cereibacter sphaeroides ATCC 17025
Expression system: Escherichia coli
UniProt:
  • Canonical: A4WYU7 (Residues: 2-777; Coverage: 100%)
Gene names: Rsph17025_3694, ago
Sequence domains: Piwi domain
DNA (5'-D(P*TP*CP*GP*TP*CP*AP*CP*CP*TP*GP*TP*GP*CP*AP*GP*AP*AP*AP*C)-3') Chain: G
Molecule details ›
Chain: G
Length: 19 nucleotides
Theoretical weight: 5.79 KDa
Source organism: Cereibacter sphaeroides ATCC 17025
Expression system: Not provided
DNA (5'-D(P*TP*GP*TP*CP*GP*TP*CP*AP*CP*CP*TP*GP*TP*GP*CP*AP*GP*AP*AP*AP*C)-3') Chain: J
Molecule details ›
Chain: J
Length: 21 nucleotides
Theoretical weight: 6.42 KDa
Source organism: Cereibacter sphaeroides ATCC 17025
Expression system: Not provided
RNA (5'-R(P*UP*UP*AP*CP*UP*GP*CP*AP*CP*AP*GP*GP*UP*GP*AP*CP*GP*A)-3') Chains: C, H
Molecule details ›
Chains: C, H
Length: 18 nucleotides
Theoretical weight: 5.77 KDa
Source organism: Cereibacter sphaeroides ATCC 17025
Expression system: Not provided

Ligands and Environments

3 bound ligands:
Ligand ACT 4 x ACT
Ligand MG 2 x MG
Ligand MPD 1 x MPD
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 24-ID-C
Spacegroup: P21
Unit cell:
a: 68.237Å b: 118.942Å c: 118.559Å
α: 90° β: 95.72° γ: 90°
R-values:
R R work R free
0.2 0.198 0.24
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

1 review citation

A Structural View of miRNA Biogenesis and Function.
Leitão et al. (2022)
23 other articles

2 mentions without citation

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