› 8jpx

Electron Microscopy
2.9Å resolution

Cryo-EM structure of PfAgo-guide DNA-target DNA complex

Released:
DOI: 10.2210/pdb8jpx/pdb
PDB entry 8jpx coloured by chain, front view.
PDB entry 8jpx coloured by chain, side view.
PDB entry 8jpx coloured by chain, top view.
Source organism: Pyrococcus furiosus DSM 3638
Primary publication:
Molecular mechanism for target recognition, dimerization, and activation of Pyrococcus furiosus Argonaute.
Wang L, Chen W, Zhang C, Xie X, Huang F, Chen M, Mao W, Yu N, Wei Q, Ma L, Li Z
Mol Cell (2024)
PMID: 38295801
Related structures: EMD-36489

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero octamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-239335 (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: 770 amino acids
Theoretical weight: 90.51 KDa
Source organism: Pyrococcus furiosus DSM 3638
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q8U3D2 (Residues: 1-770; Coverage: 100%)
Gene names: PF0537, ago
Sequence domains:
Guide DNA Chains: G, H
Molecule details ›
Chains: G, H
Length: 17 nucleotides
Theoretical weight: 5.34 KDa
Source organism: Pyrococcus furiosus DSM 3638
Expression system: Not provided
Target DNA Chains: T, U
Molecule details ›
Chains: T, U
Length: 17 nucleotides
Theoretical weight: 5.08 KDa
Source organism: Pyrococcus furiosus DSM 3638
Expression system: Not provided
Excess DNA Chains: E, F
Molecule details ›
Chains: E, F
Length: 6 nucleotides
Theoretical weight: 1.78 KDa
Source organism: Pyrococcus furiosus DSM 3638
Expression system: Not provided

Ligands and Environments

1 bound ligand:
Ligand MG 6 x MG
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 2.9Å
Relevant EMDB volumes: EMD-36489
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

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