› 6qzk

X-ray diffraction
3.55Å resolution

Structure of Clostridium butyricum Argonaute bound to a guide DNA (5' deoxycytidine) and a 19-mer target DNA

Released:
DOI: 10.2210/pdb6qzk/pdb
PDB entry 6qzk coloured by chain, front view.
PDB entry 6qzk coloured by chain, side view.
PDB entry 6qzk coloured by chain, top view.
Source organisms:
Primary publication:
DNA-guided DNA cleavage at moderate temperatures by Clostridium butyricum Argonaute.
Hegge JW, Swarts DC, Chandradoss SD, Cui TJ, Kneppers J, Jinek M, Joo C, van der Oost J
Nucleic Acids Res 47 5809-5821 (2019)
PMID: 31069393

Function and Biology Details

Biochemical function:
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
PDBe Complex ID:
PDB-CPX-120517 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
Clostridium butyricum Argonaute Chain: A
Molecule details ›
Chain: A
Length: 748 amino acids
Theoretical weight: 85.83 KDa
Source organism: Clostridium butyricum
Expression system: Escherichia coli BL21
siDNA guide (5'-D(P*CP*GP*AP*GP*GP*TP*AP*GP*TP*AP*GP*GP*TP*TP*GP*TP*AP*TP*AP*GP*T)-3') Chain: B
Molecule details ›
Chain: B
Length: 21 nucleotides
Theoretical weight: 6.57 KDa
Source organism: synthetic construct
Expression system: Not provided
DNA target (5'-D(T*AP*TP*AP*CP*AP*AP*CP*CP*TP*AP*CP*TP*AP*CP*CP*TP*CP*T)-3') Chain: C
Molecule details ›
Chain: C
Length: 19 nucleotides
Theoretical weight: 5.68 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

2 bound ligands:
Ligand MG 1 x MG
Ligand FMT 5 x FMT
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SLS BEAMLINE X06DA
Spacegroup: P6322
Unit cell:
a: 181.45Å b: 181.45Å c: 142.99Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.25 0.247 0.276
Expression systems:
  • Escherichia coli BL21
  • Not provided

Quick links

Citations

10 review citations

Bacterial origins of human cell-autonomous innate immune mechanisms.
Wein et al. (2022)
9 more

6 mentions without citation

A Structural View of miRNA Biogenesis and Function.
Leitão et al. (2022)
5 more