› 4n41

X-ray diffraction
2.25Å resolution

Structure of Thermus thermophilus Argonaute bound to guide DNA and 15-mer target DNA

Released:
DOI: 10.2210/pdb4n41/pdb
PDB entry 4n41 coloured by chain, front view.
PDB entry 4n41 coloured by chain, side view.
PDB entry 4n41 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 trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-218974 (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*T*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*AP*CP*CP*TP*AP*CP*TP*AP*CP*CP*TP*CP*G)-3' Chain: D
Molecule details ›
Chain: D
Length: 13 nucleotides
Theoretical weight: 3.87 KDa
Source organism: Thermus thermophilus
Expression system: Not provided
5'-D(*AP*AP*CP*CP*TP*AP*CP*TP*GP*CP*CP*TP*CP*G)-3' Chain: F
Molecule details ›
Chain: F
Length: 14 nucleotides
Theoretical weight: 4.18 KDa
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: SSRF BEAMLINE BL17U
Spacegroup: P21
Unit cell:
a: 59.513Å b: 101.699Å c: 153.019Å
α: 90° β: 93.52° γ: 90°
R-values:
R R work R free
0.225 0.223 0.259
Expression systems:
  • Escherichia coli BL21
  • Not provided

Quick links

Citations

21 review citations

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

6 mentions without citation

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