The type III secretion system machinery, also known as the injectisome, delivers bacterial effector proteins into eukaryotic cells during infection. The outer membrane YscC secretin is a major part of Yersinia enterocolitica's injectisome and is among the first components to assemble, solely assisted by its pilotin, YscW. We have determined the three-dimensional structures of the native complex and its protease-resistant core to 12 Å resolution by cryo-electron microscopy (cryo-EM) and show that YscC forms a dodecameric complex. Cryo-EM of YscC reconstituted into proteoliposomes defines the secretin's membrane-spanning region. Native YscC consists of an outer membrane ring connected via a thin cylindrical wall to a conical, periplasmic region that exposes N-terminal petals connected by flexible linkers. These petals harbor the binding site of YscD, a component of the inner membrane ring. A change in their orientation adapts the length of the YscC secretin and facilitates its interaction with YscD.