› 6whm

X-ray diffraction
1.92Å resolution

The crystal structure of the 2009/H1N1/California PA endonuclease wild type bound to DNA oligomer TAGC (cleaved TTAGCATT, 5mM overnight DNA soak)

Released:
DOI: 10.2210/pdb6whm/pdb
PDB entry 6whm coloured by chain, front view.
PDB entry 6whm coloured by chain, side view.
PDB entry 6whm coloured by chain, top view.
Source organism: Influenza A virus
Primary publication:
Structural insights into the substrate specificity of the endonuclease activity of the influenza virus cap-snatching mechanism.
Kumar G, Cuypers M, Webby RR, Webb TR, White SW
OpenAccess logo Nucleic Acids Res 49 1609-1618 (2021)
PMID: 33469660

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-111580 (preferred)
Entry contents:
1 distinct polypeptide molecule
1 distinct DNA molecule
Macromolecules (2 distinct):
Protein PA-X Chain: A
Molecule details ›
Chain: A
Length: 197 amino acids
Theoretical weight: 23.15 KDa
Source organism: Influenza A virus
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: C6H0Y9 (Residues: 1-50, 74-196; Coverage: 42%)
Gene name: PA
Sequence domains: Influenza RNA-dependent RNA polymerase subunit PA
DNA (5'-D(P*TP*AP*GP*C)-3') Chain: B
Molecule details ›
Chain: B
Length: 8 nucleotides
Theoretical weight: 2.42 KDa

Ligands and Environments

4 bound ligands:
Ligand GOL 2 x GOL
Ligand MG 2 x MG
Ligand MN 1 x MN
Ligand SO4 2 x SO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 22-ID
Spacegroup: I422
Unit cell:
a: 89.885Å b: 89.885Å c: 134.295Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.179 0.177 0.216
Expression system: Escherichia coli BL21(DE3)

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Citations

1 review citation

Not making the cut: Techniques to prevent RNA cleavage in structural studies of RNase-RNA complexes.
Jones et al. (2022)
7 other articles

1 mention without citation

Structural insights into the substrate specificity of the endonuclease activity of the influenza virus cap-snatching mechanism.
Kumar et al. (2021)