The 100-kDa S-layer protein from Thermus thermophilus HB8 is able to form three kinds of crystalline aggregates with different morphologies and symmetries when extracted from crude membranes using slightly different extractive procedures. Interestingly, only the structure showing P6 symmetry represents the native S-layer (called S1), while the others show a very different morphology. In this paper, the three dimensional structure of each of these crystals revealing their topographic features at 2-3 nm resolution has been analyzed by electron microscopy and image processing. The S1 crystals contain an hexagonal center, probably build up by six monomers, where most of the protein mass is concentrated. These P6 centers account for the width of the native S-layer, being the connective domains of the subunits (two per subunit) located at the outermost part of the structure. Such connections radiating from different P6 centers are mediated through centers with P3 symmetry. The other two crystals are also consistent with a lattice based on trimeric subunits probably related to those found in the connections between P6 centers of S1. The most conspicuous feature of these two latter forms is the presence of trimers of channels that traverse the crystal in the direction perpendicular to the plane of the membrane. Their distinct morphology, quite different from other S-layer assemblies, shows a surprising adaptive potential of this protein, and suggests interesting evolutive relationships to other membrane proteins. (C) 1994 Academic Press, Inc.