The Zalpha domain (yabaZalpha(E3L)) of the E3L protein homologue from Yaba-like disease virus, a yatavirus, was co-crystallized with d(TCGCGCG)(2) in the Z-conformation. The crystals belong to the P2(1)2(1)2 space group, with unit-cell parameters a=51.20 Angstroms, b=92.45 Angstroms, c=48.02 Angstroms, alpha=beta= gamma=90 degrees. The diffraction data were collected up to a resolution of 2.2 Angstroms. The structure of viral Zalpha motif will provide an insight into how diverse Zalpha motifs recognize Z-DNA.