› 8ok9

X-ray diffraction
2.5Å resolution

Heterodimeric complex of Archaeoglobus fulgidus Argonaute protein Af1318 (AfAgo) with DNA and AfAgo-N protein containing N-L1-L2 domains

Released:
DOI: 10.2210/pdb8ok9/pdb
Model geometry
Fit model/data
PDB entry 8ok9 coloured by chain, front view.
PDB entry 8ok9 coloured by chain, side view.
PDB entry 8ok9 coloured by chain, top view.
Source organism: Archaeoglobus fulgidus DSM 4304
Primary publication:
The missing part: the Archaeoglobus fulgidus Argonaute forms a functional heterodimer with an N-L1-L2 domain protein.
Manakova E, Golovinas E, Pocevičiūtė R, Sasnauskas G, Silanskas A, Rutkauskas D, Jankunec M, Zagorskaitė E, Jurgelaitis E, Grybauskas A, Venclovas Č, Zaremba M
Nucleic Acids Res (2024)
PMID: 38197228

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-268513 (preferred)
Entry contents:
2 distinct polypeptide molecules
1 distinct DNA molecule
Macromolecules (3 distinct):
Piwi protein Chain: A
Molecule details ›
Chain: A
Length: 441 amino acids
Theoretical weight: 50.92 KDa
Source organism: Archaeoglobus fulgidus DSM 4304
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: O28951 (Residues: 1-427; Coverage: 100%)
Gene name: AF_1318
Sequence domains: Piwi domain
Archaeoglobus fulgidus AfAgo-N protein Chain: C
Molecule details ›
Chain: C
Length: 264 amino acids
Theoretical weight: 30.58 KDa
Source organism: Archaeoglobus fulgidus DSM 4304
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: A0A075WKW4 (Residues: 1-250; Coverage: 100%)
Gene name: AFULGI_00014290
DNA (5'-D(P*AP*TP*CP*GP*AP*CP*CP*AP*GP*GP*CP*TP*AP*CP*G)-3') Chains: R, S

Ligands and Environments

4 bound ligands:
Ligand MG 1 x MG
Ligand ACY 8 x ACY
Ligand EDO 6 x EDO
Ligand PEG 1 x PEG
No modified residues

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2)
Spacegroup: P212121
Unit cell:
a: 81.714Å b: 105.893Å c: 144.347Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.201 0.198 0.227
Expression system: Escherichia coli BL21(DE3)

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