› 4kpy

X-ray diffraction
2.41Å resolution

DNA binding protein and DNA complex structure

Released:
DOI: 10.2210/pdb4kpy/pdb
PDB entry 4kpy coloured by chain, front view.
PDB entry 4kpy coloured by chain, side view.
PDB entry 4kpy coloured by chain, top view.
Source organisms:
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-117762 (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 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*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: synthetic construct
Expression system: Not provided
DNA (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: synthetic construct
Expression system: Not provided
DNA (5'-D(*TP*AP*TP*AP*CP*AP*AP*CP*C)-3') Chains: M, N
Molecule details ›
Chains: M, N
Length: 9 nucleotides
Theoretical weight: 2.68 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

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

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRF BEAMLINE BL17U
Spacegroup: P212121
Unit cell:
a: 111.329Å b: 118.362Å c: 160.873Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.193 0.19 0.235
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

23 review citations

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

2 mentions without citation

Structure-based cleavage mechanism of Thermus thermophilus Argonaute DNA guide strand-mediated DNA target cleavage.
Sheng et al. (2014)
1 more