to form for 6 h at room temperature. Microsomes were sedi mented and the pellet resuspended in solubilization buffer, for 15 s agi tated on a Vortex Mixer and incubated for 15 min on ice. The solubilized microsomes were layered on a 0 15% sucrose gradient and centrifuged in an ultracentrifuge. After centrifugation, 13 fractions of 310 ul each were collected from the top, pre cipitated with TCA, resuspended in 40 ul SDS sample buffer, heated to 65 C for 10 min and protein resolved by SDS PAGE. Proteins were transferred to nitrocellulose and incubated with the indicated antibodies as described above. Crosslinking of the Sec61 complex in intact microsomes Microsomes were crosslinked in 50 ul B88, pH 7. 9, by addition of 6 ul freshly made 5 mg ml DSS in dry DMSO.
After 20 min at 20 C crosslinking was quenched by addition of 7. 5 ul 8. 4 M ammonium acetate. Proteins were denatured in SDS sample buffer at 65 C, separated by SDS PAGE and Sec61p, Sbh1p and Sss1p detected by immunoblotting with specific polyclonal antisera. Isolation of the heptameric Sec complex Microsomes were prepared as described in. Micro somes were sedimented and the pellet was resuspended in 100 ul solubilization buffer Glycerol, 0. 05% B Mercaptoethanol, 1x PI Entinostat Solubilization buffer with 3. 75% digitonin was added, and membranes solubilized for 30 min on ice. Insoluble debris were removed by centrifugation, the supernatant collected and the pellet treated again with 300 ul solubilization buffer with 3. 75% digitonin and centrifuged again.
The resulting super natant was united with the first supernatant and centrifuged in an ultracentrifuge to remove the ribosome associated hetero trimeric Sec61 complex. The supernatant was subse quently referred as digitonin extract. Solubilization buffer was added to 150 ul digitonin extract and heptameric Sec complex containing the Sec71p glycopro tein precipitated with ConA Sepharose. To con trol for the saturation of the ConA precipitation, the supernatant was centrifuged for 10 min, 4 C and 10000 g, and precipitated again with 100 ul ConA Sepharose. The supernatant was collected. Both, ConA precipitates were centrifuged and washed with equilibration buffer. This step was repeated 2��. The ConA beads and the TCA precipitated extracts were resuspended in 40 ul SDS sample buffer with DTT, heated to 65 C for 10 min and resolved in SDS PAGE as described above.
Proteasome binding Proteasomes were isolated and proteasome binding experi ments to proteoliposomes performed as in Kalies et al. Modelling of Sec61L7p We homology modeled S. cerevisiae Sec61p and Sec61L7p using the software MODELLER 9. 10. In order to obtain better homology models we used the multi template hom ology modeling approach with default parameters. We identified the templates considering both sequence similarity and resolution of the crystal structures. The pu tative templates can be classified into two groups, The first group consists of prokaryotic crystal structures with rela t