Surface (S)-layers, para-crystalline arrays of protein, are deposited in the envelope of most bacterial species. These surface organelles are retained in the bacterial envelope through the non-covalent association of proteins with cell wall carbohydrates. Bacillus anthracis, a Gram-positive pathogen, produces S-layers of the protein Sap, which uses three consecutive repeats of the surface-layer homology (SLH) domain to engage secondary cell wall polysaccharides (SCWP). Using x-ray crystallography, we reveal here the structure of these SLH domains, which assume the shape of a three-prong spindle. Each SLH domain contributes to a three-helical bundle at the spindle base, whereas another ␣-helix and its connecting loops generate the three prongs. The inter-prong grooves contain conserved cationic and anionic residues, which are necessary for SLH domains to bind the B. anthracis SCWP. Modeling experiments suggest that the SLH domains of other S-layer proteins also fold into three-prong spindles and capture bacterial envelope carbohydrates by a similar mechanism.Surface layers (S-layers) 3 are para-crystalline sheets of protein, which self-assemble on the surface of microbial cells to form contiguous layers (1, 2). Most organisms that elaborate S-layers do so by abundantly producing and secreting a single protein species (3). Whether an organism produces an S-layer as a component of its envelope structure is assessed by electron microscopy of the cell surface (4). In this manner, species from nearly every branch of the Bacteria and Archaea have been discovered to produce S-layers (2). Proteins within S-layers fulfill variable functions in that they act either as a scaffold or enzyme in the bacterial envelope (5), promote nutrient diffusion or transport (6), or contribute to virulence by enabling microbial adhesion to infected host tissues (7).Most, but not all, S-layer proteins of bacteria share three tandem ϳ55 amino acid repeats of the Surface Layer Homology (SLH) domain (8 -10). Secreted proteins encoding three tandem SLH domains are tethered to the bacterial envelope by non-covalent interactions between the SLH domains and a secondary cell wall carbohydrate (11). SLH domains are remarkable for being both necessary and sufficient for the incorporation of chimeric proteins into S-layers (12, 13). The SbsC protein of Geobacillus stearothermophilus is an example for a class of protein that forms S-layers without SLH domains (14). SbsC binds to the secondary cell wall polysaccharide (SCWP) of G. stearothermophilus via its N-terminal domain, which consists of three triple-helical bundles that are connected by two contiguous helices (14). The N-terminal domain of SbsC has high similarity with S-layer proteins from G. stearothermophilus, Geobacillus kaustophilus, and Geobacillus tepidamans (14) and is not similar to proteins with SLH domains.The Gram-positive bacterium Bacillus anthracis is a rodshaped, spore-forming pathogen of mammalian hosts (15). The envelope of its vegetative forms is composed of a plasma membrane a...