› 4ncb

X-ray diffraction
2.19Å resolution

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

Released:
DOI: 10.2210/pdb4ncb/pdb
PDB entry 4ncb coloured by chain, front view.
PDB entry 4ncb coloured by chain, side view.
PDB entry 4ncb 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-117869 (preferred)
Entry contents:
1 distinct polypeptide molecule
4 distinct DNA molecules
Macromolecules (5 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(*TP*AP*TP*AP*CP*AP*AP*CP*C)-3' Chains: H, P
Molecule details ›
Chains: H, P
Length: 9 nucleotides
Theoretical weight: 2.68 KDa
Source organism: Thermus thermophilus
Expression system: Not provided
5'-D(*TP*AP*TP*AP*CP*AP*AP*CP*CP*TP*AP*CP*TP*AP*CP*CP*TP*CP*G)-3' Chain: D
Molecule details ›
Chain: D
Length: 19 nucleotides
Theoretical weight: 5.71 KDa
Source organism: Thermus thermophilus
Expression system: Not provided
5'-D(P*TP*AP*CP*TP*AP*CP*CP*TP*CP*G)-3' Chain: F
Molecule details ›
Chain: F
Length: 10 nucleotides
Theoretical weight: 2.98 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: P21
Unit cell:
a: 84.736Å b: 105.363Å c: 92.058Å
α: 90° β: 94.25° γ: 90°
R-values:
R R work R free
0.178 0.175 0.23
Expression systems:
  • Escherichia coli BL21
  • Not provided

Quick links

Citations

18 review citations

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

23 mentions without citation

The evolutionary journey of Argonaute proteins.
Swarts et al. (2014)
22 more