› 6wdz

X-ray diffraction
2.03Å resolution

Porcine circovirus 2 Rep domain complexed with a single-stranded DNA 10-mer comprising the cleavage site

Released:
DOI: 10.2210/pdb6wdz/pdb
PDB entry 6wdz coloured by chain, front view.
PDB entry 6wdz coloured by chain, side view.
PDB entry 6wdz coloured by chain, top view.
Source organism: Porcine circovirus 2
Primary publication:
Molecular underpinnings of ssDNA specificity by Rep HUH-endonucleases and implications for HUH-tag multiplexing and engineering.
Tompkins KJ, Houtti M, Litzau LA, Aird EJ, Everett BA, Nelson AT, Pornschloegl L, Limón-Swanson LK, Evans RL, Evans K, Shi K, Aihara H, Gordon WR
OpenAccess logo Nucleic Acids Res 49 1046-1064 (2021)
PMID: 33410911

Function and Biology Details

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

Structure analysis Details

Assemblies composition:
hetero dimer (preferred)
monomeric
Assembly name:
PDBe Complex ID:
PDB-CPX-120826 (preferred)
Entry contents:
1 distinct polypeptide molecule
1 distinct DNA molecule
Macromolecules (2 distinct):
Replication-associated protein Chains: A, D, G
Molecule details ›
Chains: A, D, G
Length: 115 amino acids
Theoretical weight: 13.26 KDa
Source organism: Porcine circovirus 2
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q8BB16 (Residues: 2-116; Coverage: 37%)
Gene names: ORF1, Rep
Sequence domains: Putative viral replication protein
DNA (5'-D(*TP*AP*GP*TP*AP*TP*TP*AP*CP*C)-3') Chains: C, F, I, J
Molecule details ›
Chains: C, F, I, J
Length: 10 nucleotides
Theoretical weight: 3.02 KDa
Source organism: Porcine circovirus 2
Expression system: Not provided

Ligands and Environments

2 bound ligands:
Ligand MN 3 x MN
Ligand EDO 2 x EDO
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 24-ID-C
Spacegroup: P64
Unit cell:
a: 99.527Å b: 99.527Å c: 73.695Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.232 0.229 0.28
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

9 citation in other articles

Mechanism of DNA Interaction and Translocation by the Replicase of a Circular Rep-Encoding Single-Stranded DNA Virus.
Tarasova et al. (2021)
8 more

3 mentions without citation

Molecular underpinnings of ssDNA specificity by Rep HUH-endonucleases and implications for HUH-tag multiplexing and engineering.
Tompkins et al. (2021)
2 more