Carboxysome, encapsulating an enzymatic core within an icosahedral-shaped semipermeable protein shell, could enhance CO2 fixation under low CO2 conditions in the environment. The shell of Halothiobacillus neapolitanus alpha-carboxysome possesses two 38% sequence-identical pentameric proteins, namely CsoS4A and CsoS4B. However, the functions of two paralogous pentameric proteins in alpha-carboxysome assembly remain unknown. Here we report the crystal structure of CsoS4B at 2.15 angstrom resolution. It displays as a stable pentamer, each subunit of which consists of a beta-barrel core domain, in addition to an insertion of helix alpha 1 that forms the central pore. Structural comparisons and multiple-sequence alignment strongly indicate that CsoS4A and CsoS4B differ from each other in interacting with various components of alpha-carboxysome, despite they share a similar overall structure. These findings provide the structural basis for further investigations on the self-assembly process of carboxysome. (C) 2019 Elsevier Inc. All rights reserved.