› 8k88

Electron Microscopy
2.6Å resolution

Structure of procaryotic Ago

Released:
DOI: 10.2210/pdb8k88/pdb
PDB entry 8k88 coloured by chain, front view.
PDB entry 8k88 coloured by chain, side view.
PDB entry 8k88 coloured by chain, top view.
Source organism: Geobacter sulfurreducens
Primary publication:
Nucleic acid-induced NADase activation of a short Sir2-associated prokaryotic Argonaute system.
Sun D, Zhu K, Wang L, Mu Z, Wu K, Hua L, Qin B, Gao X, Wang Y, Cui S
Cell Rep 43 114391 (2024)
PMID: 38923459
Related structures: EMD-36947

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-270238 (preferred)
Entry contents:
2 distinct polypeptide molecules
1 distinct DNA molecule
1 distinct DNA/RNA hybrid molecule
Macromolecules (4 distinct):
Piwi domain protein Chain: A
Molecule details ›
Chain: A
Length: 473 amino acids
Theoretical weight: 53.33 KDa
Source organism: Geobacter sulfurreducens
Expression system: Expression vector pET-mod
UniProt:
  • Canonical: Q74DF5 (Residues: 1-473; Coverage: 100%)
Gene name: GSU1361
SIR2-like domain-containing protein Chain: B
Molecule details ›
Chain: B
Length: 587 amino acids
Theoretical weight: 66.65 KDa
Source organism: Geobacter sulfurreducens
Expression system: Expression vector pET-mod
UniProt:
  • Canonical: Q74DF6 (Residues: 1-587; Coverage: 100%)
Gene name: GSU1360
Sequence domains: SIR2-like domain
DNA (41-mer) Chain: C
Molecule details ›
Chain: C
Length: 41 nucleotides
Theoretical weight: 12.53 KDa
DNA/RNA (21-mer) Chain: D
Molecule details ›
Chain: D
Length: 21 nucleotides
Theoretical weight: 6.68 KDa

Ligands and Environments

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

Experiments and Validation Details

Entry percentile scores
Resolution: 2.6Å
Relevant EMDB volumes: EMD-36947
Expression system: Expression vector pET-mod

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