H2A.Bbd, the most divergent histone variant among all known H2A type histones, is involved in gene transcription, spermiogenesis, DNA replication and RNA splicing. Incorporation of H2A.Bbd-H2B dimer, a fundamental unit of H2A.Bbd nucleosome, modulate structures of nucleosome or chromatin, but the underlying mechanism remains elusive. Here we determined a crystal structure of H2A.Bbd-H2B dimer at 2.6 angstrom resolution. Although the H2A.Bbd-H2B dimer structure largely resembles that of H2A-H2B, substitution of H2A citC helix residues by H2A.Bbd counterparts lead to the transition of a long alpha C-helix to the short 3(10)-helix, likely owing to the rearrangement of the hydrogen-bond network. Moreover, structural comparison revealed a strikingly altered electrostatic potential surface for H2A.Bbd-H2B dimer displaying a diminished DNA binding capability. Our study provides the first high-resolution structure of histone variant H2A.Bbd and shed a light on biological function of H2A.Bbd. (C) 2018 Elsevier Inc. All rights reserved.