› 5xp8

X-ray diffraction
3.1Å resolution

Crystal structure of T. thermophilus Argonaute protein complexed with a bulge 4A5 on the guide strand

Released:
DOI: 10.2210/pdb5xp8/pdb
PDB entry 5xp8 coloured by chain, front view.
PDB entry 5xp8 coloured by chain, side view.
PDB entry 5xp8 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
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 tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-119402 (preferred)
Entry contents:
1 distinct polypeptide molecule
3 distinct DNA molecules
Macromolecules (4 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*AP*GP*TP*AP*GP*TP*AP*GP*GP*TP*TP*GP*T)-3') Chain: E
Molecule details ›
Chain: E
Length: 22 nucleotides
Theoretical weight: 6.9 KDa
Source organism: Thermus thermophilus
Expression system: Not provided
DNA (5'-D(*CP*AP*AP*CP*C*AP*TP*AP*CP*TP*AP*CP*CP*TP*CP*G)-3') Chain: F
Molecule details ›
Chain: F
Length: 19 nucleotides
Theoretical weight: 5.71 KDa
Source organism: Thermus thermophilus
Expression system: Not provided
DNA (5'-D(*AP*GP*T)-3') Chain: C
Molecule details ›
Chain: C
Length: 3 nucleotides
Theoretical weight: 902 Da
Source organism: Thermus thermophilus
Expression system: Not provided

Ligands and Environments

1 bound ligand:
Ligand MG 3 x MG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: PHOTON FACTORY BEAMLINE BL-1A
Spacegroup: P4132
Unit cell:
a: 202.14Å b: 202.14Å c: 202.14Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.217 0.214 0.276
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

2 mentions without citation

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