› 5cfd

X-ray diffraction
2.5Å resolution

Crystal Structure of DTT treated Human Cardiovirus SAFV-3

Released:
DOI: 10.2210/pdb5cfd/pdb
PDB entry 5cfd coloured by chain, front view.
PDB entry 5cfd coloured by chain, side view.
PDB entry 5cfd coloured by chain, top view.
Source organism: Saffold virus
Primary publication:
Structure and Genome Release Mechanism of the Human Cardiovirus Saffold Virus 3.
Mullapudi E, Nováček J, Pálková L, Kulich P, Lindberg AM, van Kuppeveld FJ, Plevka P
OpenAccess logo J Virol 90 7628-39 (2016)
PMID: 27279624

Function and Biology Details

Reactions catalysed: 
Nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1)
Selective cleavage of Gln-|-Gly bond in the poliovirus polyprotein. In other picornavirus reactions Glu may be substituted for Gln, and Ser or Thr for Gly.
ATP + H(2)O = ADP + phosphate
Biochemical function:
Biological process:
  • not assigned
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero 240-mer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-503788 (preferred)
Entry contents:
4 distinct polypeptide molecules
Macromolecules (4 distinct):
Capsid protein VP1 Chain: A
Molecule details ›
Chain: A
Length: 252 amino acids
Theoretical weight: 28.3 KDa
Source organism: Saffold virus
Expression system: Homo sapiens
UniProt:
  • Canonical: C0MHL9 (Residues: 647-898; Coverage: 11%)
Sequence domains: Picornavirus coat protein
Structure domains: Jelly Rolls
Capsid protein VP3 Chain: B
Molecule details ›
Chain: B
Length: 232 amino acids
Theoretical weight: 25.61 KDa
Source organism: Saffold virus
Expression system: Homo sapiens
UniProt:
  • Canonical: C0MHL9 (Residues: 415-646; Coverage: 10%)
Sequence domains: picornavirus capsid protein
Structure domains: Jelly Rolls
Capsid protein VP2 Chain: C
Molecule details ›
Chain: C
Length: 258 amino acids
Theoretical weight: 28.7 KDa
Source organism: Saffold virus
Expression system: Homo sapiens
UniProt:
  • Canonical: C0MHL9 (Residues: 154-411; Coverage: 11%)
Sequence domains: picornavirus capsid protein
Structure domains: Jelly Rolls
VP4 Chain: D
Molecule details ›
Chain: D
Length: 24 amino acids
Theoretical weight: 2.69 KDa
Source organism: Saffold virus
Expression system: Homo sapiens
UniProt:
  • Canonical: C3U5A3 (Residues: 116-139; Coverage: 1%)
Gene name: gp1
Sequence domains: Viral protein VP4 subunit

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I03
Spacegroup: P3221
Unit cell:
a: 299.946Å b: 299.946Å c: 723.471Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.216 not available not available
Expression system: Homo sapiens

Quick links

Citations

3 review citations

Evolutionary and Structural Overview of Human Picornavirus Capsid Antibody Evasion.
Cifuente et al. (2019)
2 more

2 mentions without citation

Structure and Genome Release Mechanism of the Human Cardiovirus Saffold Virus 3.
Mullapudi et al. (2016)
1 more