Mammalian and bacterial ribosome-channel complexes

Nascent secretory proteins are translocated into the lumen of the ER in higher eukaryotes and across the plasma membrane in bacteria. Conversely, membrane proteins are gated laterally into the lipid bilayer by the Sec61 and SecYEG channels.

80S Mammalian ribosome channel complex

In a collaboration with Dr. Tom Rapoport (Harvard Medical School), we imaged native ribosome-Sec61 channel complexes isolated from canine endoplasmic reticulum. This allowed us to describe the architecture of the ribosome-channel complex; single Sec61 heterotrimers are present with highly conserved connections formed by the 6/7 and 8/9 loops of Sec61 alpha. A conserved gap is present between the cytoplasmic surface of the channel and the exit tunnel of the large ribosomal subunit that may allow nascent chains to access cytosolic factors during translocation. Previous work had suggested that a tight seal may be present between the large subunit and the channel. This gap may be used in quality control when large proteins are not properly folded as they enter the ER lumen and may also be used by cytoplasmic domains of membrane proteins as they begin folding during translocation. This analysis also allowed us to position single copies of Sec61 and TRAP complexes within the translocon.

Segmented 3D density maps for ribosomal proteins, RNAs, Sec61 and TRAP complexes in the mammalian ribosome-channel complex. [Ménétret et al., 2008; Chandramouli et al. 2008]
This work also led to the first sub-nanometer 3D map of a mammalian 80S ribosome at ~8.7 Å resolution, in which alpha helices in ribosomal proteins and double RNA helices were resolved; this enabled a nearly complete model to be constructed for the small and large ribosomal subunits.

(left) Cross-sections through the 80S ribosome; (right) segmented views of selected ribosomal components. [Chandramouli et al. 2008]

Bacterial ribosome-channel complexes

Current studies are targeting the bacterial ribosome-channel complex to provide new insights into translocation at the cytoplasmic membrane. This analysis suggests how the lateral gate of the SecYEG channel may open in the plane of the lipid bilayer.

A model for opening the lateral gate of the E. coli SecYEG channel. [Park et al., 2014]

Click on figure for animation

Density map for the E. coli ribosome-SecYEG channel complex in detergent obtained with a direct electron detector. [T. Guettler, T. Rapoport and C. Akey, unpublished]
Researchers Capture Images of Open Channel That Moves Proteins Across Cell Membranes | School of Medicine – bumc.bu.edu

Selected Publications:

Park, E., Ménétret, J. F., Gumbart, J.C., Ludtke, S.J., Li, W., Whynot, A., Rapoport, T. A., and Akey, C. W. (2014). Structure of the SecY channel during initiation of protein translocation. Nature 506, 102-106. PMID: 24153188

Ménétret, J. F., Hegde, R.S., Woong, K., Gygi, S.P., Rapoport, T. A., and Akey, C. W. (2008). Single copies of Sec61 and TRAP associate with a non-translating mammalian ribosome. Structure 16, 1126-1137. PMID:18611385

Chandramouli, P., Topf, M., Ménétret, J.F., Eswar, N., Gutell, R.R., Sali, A., and Akey, C.W. (2008). Structure of the mammalian 80S ribosome at 8.7Å resolution. Structure 16, 535-548. PMID:18400176

Ribosome-Sec Channels PubMed list
Ribosome and Sec channel EMDB entries