› 5xpa

X-ray diffraction
2.9Å resolution

Crystal structure of T. thermophilus Argonaute protein complexed with a bulge 9'U10' on the target strand

Released:
DOI: 10.2210/pdb5xpa/pdb
PDB entry 5xpa coloured by chain, front view.
PDB entry 5xpa coloured by chain, side view.
PDB entry 5xpa coloured by chain, top view.
Source organisms:
Primary publication:
Structure/cleavage-based insights into helical perturbations at bulge sites within T. thermophilus Argonaute silencing complexes.
Sheng G, Gogakos T, Wang J, Zhao H, Serganov A, Juranek S, Tuschl T, Patel DJ, Wang Y
OpenAccess logo Nucleic Acids Res 45 9149-9163 (2017)
PMID: 28911094

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-119403 (preferred)
Entry contents:
1 distinct polypeptide molecule
1 distinct DNA molecule
1 distinct RNA molecule
Macromolecules (3 distinct):
Protein argonaute Chain: A
Molecule details ›
Chain: A
Length: 685 amino acids
Theoretical weight: 76.73 KDa
Source organism: Thermus thermophilus HB27
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q746M7 (Residues: 1-685; Coverage: 100%)
Gene names: TT_P0026, ago
Sequence domains:
DNA (5'-D(P*TP*GP*AP*GP*GP*TP*AP*GP*TP*AP*GP*GP*TP*TP*GP*TP*AP*TP*AP*GP*T)-3') Chain: C
Molecule details ›
Chain: C
Length: 21 nucleotides
Theoretical weight: 6.59 KDa
Source organism: Thermus thermophilus
Expression system: Not provided
RNA (5'-R(P*AP*UP*AP*CP*AP*AP*CP*CP*GP*UP*UP*CP*UP*AP*CP*UP*CP*CP*G)-3') Chain: D
Molecule details ›
Chain: D
Length: 20 nucleotides
Theoretical weight: 6.26 KDa
Source organism: Thermus thermophilus
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: SSRF BEAMLINE BL17U1
Spacegroup: P43212
Unit cell:
a: 109.134Å b: 109.134Å c: 184.685Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.218 0.215 0.281
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

3 review citations

Argonaute proteins: structures and their endonuclease activity.
Jin et al. (2021)
2 more

1 mention without citation

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