Fig 1.
(A) MBP-U14 and MBP-U14-NTD constructs. Arrow heads represent the HRV3c cleavage site. (B) Size-exclusion column chromatography of U14-NTD and MBP. U14-NTD elutes faster than MBP despite the similar molecular sizes of U14-NTD (50 kDa) and MBP (42 kDa). The retention volumes of standard proteins were indicated by arrows.
Table 1.
Data collection and refinement statistics.
Fig 2.
(A) The subdomains (SDs) of U14-NTD. Coloring is according to SDs as follows, SD1: magenta, SD2: cyan, SD3: green, and SD4: khaki. (B) Ribbon representation of the U14-NTD monomer. (C) Secondary structure diagram of U14-NTD. Cylinders and arrows represent α/310 helices and β strands, respectively.
Table 2.
Structural similarity for U14-NTD subdomains suggested by Dali analysis.
Fig 3.
(A) Surface representation of the U14-NTD dimer. For reference, a monomer with a schematic partner is shown at the left in the box. The surface is colored according to the subdomains (SDs), SD1: magenta, SD2: cyan, SD3: green, and SD4: khaki. To distinguish the two molecules, light colors were used for one monomer. (B) Dimerization interface. For simplicity, one of the monomers is shown as a surface model colored in cyan and its contact region is colored in red. The other monomer is represented as a ribbon model colored in yellow. (C) The cavity within the dimer interface is shown as a gray mesh on the surface model (left) and ribbon model (right). For clarity, only one monomer is shown.
Fig 4.
Interactions stabilizing the U14-NTD dimer.
(A) Electrostatic potential of the monomer surface. The positively- and negatively-charged areas are indicated by blue and red brackets, respectively. Note that these areas are separated by the two-fold axis indicated by the black symbol. (B) Hydrogen bond clusters at the dimer interface of U14-NTD. An open-book representation of the surface models of the two monomers, named Mol.1 and Mol.2, is shown, associated with their ribbon representations on the right. The surfaces involving the four hydrogen bonds clusters a, b, c, and d are colored in red, orange, green, and blue, respectively. Their locations are also indicated in the ribbon models with red circles. Detailed interaction modes are depicted in S2 Fig and summarized in S1 Table.
Fig 5.
Potential functional sites on the dimer surface of U14-NTD.
(A) Electrostatic potential of the U14-NTD dimer. The negatively- and positively-charged clusters are indicated by red and blue brackets, respectively. (B) The position of three amino acids, L424, E425, and V426, are shown as stick models. The adjacent residues I414 and L297 that form the hydrophobic patch are also shown. (C) Deep groove along the interface. The position of the groove is indicated by a red dotted line. For reference, a ribbon model in the same orientation is shown at the right with the positions of SD2, SD3, and SD4 indicated.
Fig 6.
Multiple sequence alignment of HHV-6B U14 and its homologs combined with the structural information of U14-NTD.
The sequences of HHV-6A U14, HHV-7 U14, and HCMV UL35 are aligned. For clarity, only the region corresponding to U14-NTD is shown. The cylinders and arrows above the alignment represent α/310 helices and β strands of U14-NTD, respectively. Identical and similar residues among all sequences are highlighted in red and orange, respectively. The blue arrowheads indicate the positions of residues whose side-chains participate in the U14-NTD dimer hydrogen bond network. At these positions, the cyan boxes indicate the residues identical to those of HHV-6B U14. Clustal Omega [25] was used for the alignment. Accession numbers for the sequences are as follows: HHV-6B U14: gi|4996002, HHV-6A U14:gi|9628315, HHV-7 U14: gi|1139615, and HCMV UL35: gi|270355798.
Fig 7.
Structural similarity between the Unc-51-like kinase 3 (ULK3) MIT domain and U14-NTD SD3.
(A) The coordinates of the ULK3 MIT domain (blue) and MIM peptide (red) are superposed on U14-NTD SD3 (green). (B) The MIM binding site of ULK3 MIT corresponds to the U14-NTD SD3 surface that is located at the deep cleft between two monomers.