The carbon fixation machinery α-carboxysome of the marine cyanobacterium Prochlorococcus is composed of an icosahedral-like proteinaceous shell that encapsulates the enzymes RuBisCO and carbonic anhydrase. Our cryo-EM structure reveals how thousands of protein components self-assemble into the α-carboxysome and characterizes the multivalent interactions by which the scaffolding protein CsoS2 crosslinks the shell with internal RuBisCO molecules.