Labeling experiments with formyl-[uS]-methionyl sulfone methylphosphate and crosslinking studies with dimethylsuberimidate suggest that the spike glycoproteins of Semliki Forest virus extend through the viral membrane into close contact with the nucleocapsid. Based on this finding, we present a mechanism for the formation of virus-specific patches in the host cell plasma membrane during virus assembly.We have been studying the membrane of Semliki Forest virus (SFV), a group A togavirus, to investigate the structure and assembly of biological membranes (1). SFV is composed of a smooth-surfaced nucleocapsid, which is surrounded by a lipid membrane (2, 3). The nucleocapsid is assembled in the cytoplasm of the host cell (2). It consists of the viral RNA and one lysine-rich protein species [molecular weight (MW) 33, 000] (4). The viral membrane is acquired from the host cell plasma membrane by a budding process in the final stage of SFV maturation (2). It has a lipid composition similar to that of the host cell plasma membrane (5), and its lipids seem to be arranged in a bilayer structure (6). Three virus-specific glycosylated proteins have been found in about equimolar ratios in the SFV membrane: El, E2 (both with a MW of about 50,000), and E3 (MW about 10,000) (H. Garoff, K.Simons, and 0. Renkonen, Virology, in press). The glycoproteins form spikes on the external surface of the bilayer, and are responsible for the hemagglutinating activity of the virus (7). The spikes can be cleaved off by thermolysin, leaving two hydrophobic peptides in the membrane derived from El and E2 (7). The peptides are large enough (MW about 5000 for each) to span the viral membrane like the intramembranous region of the MN glycoprotein (glycophorin) in the human erythrocyte membrane (8).Since no host cell proteins are found in the viral membrane of the mature virus particle, this membrane must be derived from a segment of the plasma membrane from which all host cell proteins are excluded (1). How such patches of viral membrane are generated is an enigma (9). In this report we present results suggesting that one or both of the viral spike glycoproteins El and E2 extend through the SFV membrane into close contact with the nucleocapsid. Based on this finding, a mechanism is presented that could explain the formation of virus-specific patches in the host cell plasma membrane, during virus assembly. of Na2CO3 buffer (pH 9.7) was mixed with 40 Mll of the [MS]-FMMP reagent and incubated at room temperature for 10 min. Excess reagent was removed by sucrose density gradient centrifugation (16). Viral membranes were released from another virus preparation containing 540 gg of protein by treatment with 170 j.g of Triton X-100 in 170 ul of the Na2CO3 buffer for 10 min at room temperature as described (17) before the labeling reagent (50 Md of ["S]FMMP) was added. The released membranes were separated from the nucleocapsids by centrifugation in a 15-30% (w/w) sucrose density gradient containing 0.1 M NaCl-0.05 M Tris buffer (pH 7.4) and 0.013...