› 4g0r

X-ray diffraction
2.7Å resolution

Structural characterization of H-1 Parvovirus: comparison of infectious virions to replication defective particles

Released:
DOI: 10.2210/pdb4g0r/pdb
PDB entry 4g0r coloured by chain, front view.
PDB entry 4g0r coloured by chain, side view.
PDB entry 4g0r coloured by chain, top view.
Source organism: H-1 parvovirus
Primary publication:
Structural characterization of H-1 parvovirus: comparison of infectious virions to empty capsids.
Halder S, Nam HJ, Govindasamy L, Vogel M, Dinsart C, Salomé N, McKenna R, Agbandje-McKenna M
J Virol 87 5128-40 (2013)
PMID: 23449783

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero 120-mer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-117522 (preferred)
Entry contents:
1 distinct polypeptide molecule
1 distinct DNA molecule
Macromolecules (2 distinct):
Capsid protein VP1 Chain: A
Molecule details ›
Chain: A
Length: 735 amino acids
Theoretical weight: 81.34 KDa
Source organism: H-1 parvovirus
UniProt:
  • Canonical: P03136 (Residues: 1-246, 247-734; Coverage: 100%)
Sequence domains:
Structure domains: Parvovirus coat protein VP1/VP2
DNA (5'-D(P*CP*TP*GP*AP*CP*TP*TP*CP*AP*A)-3') Chain: C
Molecule details ›
Chain: C
Length: 10 nucleotides
Theoretical weight: 3 KDa

Ligands and Environments

5 bound ligands:
Ligand EDO 4 x EDO
Ligand DC 1 x DC
Ligand NA 2 x NA
Ligand CL 1 x CL
Ligand MG 2 x MG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: CHESS BEAMLINE F1
Spacegroup: P21
Unit cell:
a: 255.4Å b: 350.4Å c: 271.6Å
α: 90° β: 90.34° γ: 90°
R-values:
R R work R free
0.216 0.216 0.217

Quick links

Citations

7 review citations

Oncolytic parvoviruses: from basic virology to clinical applications.
Marchini et al. (2015)
6 more

9 mentions without citation

Twenty-Five Years of Structural Parvovirology.
Mietzsch et al. (2019)
8 more