› 4nca

X-ray diffraction
2.49Å resolution

Structure of Thermus thermophilus Argonaute bound to guide DNA 19-mer and target DNA in the presence of Mg2+

Released:
DOI: 10.2210/pdb4nca/pdb
PDB entry 4nca coloured by chain, front view.
PDB entry 4nca coloured by chain, side view.
PDB entry 4nca coloured by chain, top view.
Source organism: Thermus thermophilus
Primary publication:
Structure-based cleavage mechanism of Thermus thermophilus Argonaute DNA guide strand-mediated DNA target cleavage.
Sheng G, Zhao H, Wang J, Rao Y, Tian W, Swarts DC, van der Oost J, Patel DJ, Wang Y
Proc Natl Acad Sci U S A 111 652-7 (2014)
PMID: 24374628

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-117868 (preferred)
Entry contents:
1 distinct polypeptide molecule
3 distinct DNA molecules
Macromolecules (4 distinct):
Protein argonaute Chains: A, B
Molecule details ›
Chains: A, B
Length: 685 amino acids
Theoretical weight: 76.73 KDa
Source organism: Thermus thermophilus
Expression system: Escherichia coli BL21
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*GP*TP*AP*TP*AP*GP*T)-3' Chains: C, E
Molecule details ›
Chains: C, E
Length: 21 nucleotides
Theoretical weight: 6.59 KDa
Source organism: Thermus thermophilus
Expression system: Not provided
5'-D(P*TP*AP*CP*TP*AP*CP*CP*TP*CP*G)-3' Chains: D, F
Molecule details ›
Chains: D, F
Length: 10 nucleotides
Theoretical weight: 2.98 KDa
Source organism: Thermus thermophilus
Expression system: Not provided
5'-D(*AP*CP*AP*AP*CP*C)-3' Chains: G, H
Molecule details ›
Chains: G, H
Length: 6 nucleotides
Theoretical weight: 1.76 KDa
Source organism: Thermus thermophilus
Expression system: Not provided

Ligands and Environments

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

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRF BEAMLINE BL17U
Spacegroup: P212121
Unit cell:
a: 110.95Å b: 117.561Å c: 160.38Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.203 0.2 0.245
Expression systems:
  • Escherichia coli BL21
  • Not provided

Quick links

Citations

22 review citations

Unravelling the structural and mechanistic basis of CRISPR-Cas systems.
van der Oost et al. (2014)
21 more

7 mentions without citation

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