Figure 1.
Figure 1 Structure of the primer protein VPg in a complex with
3D. (A) Stereo view of a sigma A weighted |F[o]|-|F[c]| electron
density map at 2.9 Å resolution and contoured at 3.0 around
the VPg-UMP molecule (The VPg-UMP and ions were omitted from the
phasing model). The 15 amino acids of VPg, the UMP covalently
linked to the protein and the metal ions are placed inside the
density in ball and stick representation colored in atom type
code. Names for all residues are explicitly labeled in one
letter code. (B) Details of the interactions seen in the active
site of the 3D polymerase during the uridylylation reaction. The
residues Pro2, Tyr3 and Ala4 of VPg are shown in sticks in red
and the UMP, covalently linked to the hydroxyl group of Tyr3, in
light green. The divalent cations Mn2+ and Mg2+ are shown as
magenta and orange spheres, respectively, and the anomalous
difference Fourier map is shown as a chicken wire in blue. The
3D amino acids involved in direct hydrogen bonds with ions and
the uridylylated tyrosine are shown in ball and sticks in atom
type code, and the hydrogen bonds appear as dashed lines. All
residues are explicitly labeled. The predicted position of the
oligo(A) template strand (dark green) was determined using the
3D-RNA template-primer complex (PDB entry 1WNE) as a guide.
around
the VPg-UMP molecule (The VPg-UMP and ions were omitted from the
phasing model). The 15 amino acids of VPg, the UMP covalently
linked to the protein and the metal ions are placed inside the
density in ball and stick representation colored in atom type
code. Names for all residues are explicitly labeled in one
letter code. (B) Details of the interactions seen in the active
site of the 3D polymerase during the uridylylation reaction. The
residues Pro2, Tyr3 and Ala4 of VPg are shown in sticks in red
and the UMP, covalently linked to the hydroxyl group of Tyr3, in
light green. The divalent cations Mn2+ and Mg2+ are shown as
magenta and orange spheres, respectively, and the anomalous
difference Fourier map is shown as a chicken wire in blue. The
3D amino acids involved in direct hydrogen bonds with ions and
the uridylylated tyrosine are shown in ball and sticks in atom
type code, and the hydrogen bonds appear as dashed lines. All
residues are explicitly labeled. The predicted position of the
oligo(A) template strand (dark green) was determined using the
3D-RNA template-primer complex (PDB entry 1WNE) as a guide.