Volume 28, Issue 6, Pages 1083-1092 (December 2007) Ribosome Binding of a Single Copy of the SecY Complex: Implications for Protein Translocation  Jean-François Ménétret, Julia Schaletzky, William M. Clemons, Andrew R. Osborne, Sigrid S. Skånland, Carilee Denison, Steven P. Gygi, Don S. Kirkpatrick, Eunyong Park, Steven J. Ludtke, Tom A. Rapoport, Christopher W. Akey  Molecular Cell  Volume 28, Issue 6, Pages 1083-1092 (December 2007) DOI: 10.1016/j.molcel.2007.10.034 Copyright © 2007 Elsevier Inc. Terms and Conditions

Figure 1 The 3D Structure of Ribosome-SecY Complexes in Detergent (A) The ribosome-SecY complex is shown at 16 Å resolution in a frontal view, with the SecY density aligned horizontally within a hypothetical membrane. This view reveals an open junction created by the tilt of the ribosome relative to SecY. The small subunit (S) is yellow, the large subunit (L) is blue, and the SecY density is magenta. (B) A bottom view is shown of the ribosome-SecY complex in (A). (C) Connections 1 and 2 in the ribosome-SecY junction are shown in maps from specimens imaged on a carbon film in DDM (left) and over holes in DBC (right). The maps have been filtered to 16 Å resolution. The orientation of the complexes is shown in a small icon view on the right. (D) A broad grazing contact forms connection c3. This contact is similar in both maps. (E) The archaeal SecYEβ model (as ribbons) is shown within the SecY density (in magenta) of a ribosome complex imaged on a carbon film. A space-filling envelope for the archaeal SecY is shown in blue, and the subunits are colored as follows: SecY (blue), SecE (red), and SecG (yellow). This view is enlarged relative to (C) and (D). The orientation of the complex is shown in the icon view. (F) The archaeal SecYEβ model is shown within the SecY density of a ribosome complex imaged over holes. Molecular Cell 2007 28, 1083-1092DOI: (10.1016/j.molcel.2007.10.034) Copyright © 2007 Elsevier Inc. Terms and Conditions

Figure 2 Docking an Atomic Model of the Ribosome into a 3D Map of the Ribosome-SecY Complex (A) A front view of the ribosome is shown at a resolution of ∼9.6 Å. This ribosome is from the ribosome-SecY complex imaged on a carbon film in DDM. The small subunit (S) is yellow, and the large subunit (L) is blue. (B) The atomic structure of the E. coli ribosome (2I2P, 2I2T) and a region of the T. thermophilus L1 stalk (2J03) have been docked into a transparent surface rendering of the ribosome. The rRNAs are yellow and blue for the small and large subunits, while the corresponding proteins are magenta and green. (C) The atomic structure of the E. coli small subunit is shown within a transparent surface rendering of the subunit, as viewed from the back. (Icon view) The orientation of the small subunit is shown relative to the large subunit. (D) The large subunit is shown in a crown view, as seen from the interface side. The view is the same as in the icon view (center) but with the small subunit removed. Note that the L1- and L7/L12 stalks were not present in the crystal structures. (E) Individual proteins from the 3D map. (Left) Close-ups are shown of S6p with a mixed α/β architecture. (Middle) Two views are shown of the α-helical features in S20p. (Right) Two views of the L9p protein are shown in density after modeling this protein, which is extended in the crystal structures. Molecular Cell 2007 28, 1083-1092DOI: (10.1016/j.molcel.2007.10.034) Copyright © 2007 Elsevier Inc. Terms and Conditions

Figure 3 Connections between SecY and the Ribosome (A) A bottom view of the ribosome-SecY complex is shown with SecY in magenta. The docked SecYEβ model is shown as ribbons. The atomic model of the E. coli large subunit is shown within the map of the ribosome and oriented as in the icon view (center). This map corresponds to particles imaged on a carbon film. (B) The transmembrane region of the SecY density was removed to reveal a cross-sectional view of the channel docking surface. The cut plane is semitransparent, and components on the docking surface are labeled. A surface depression (see circled area in the icon view, [A]) is partly filled by density (in gold) from connections 1 and 2. (C) A tilted side view of the large subunit and SecY density (magenta) reveals the key-like insertion of the connections (in gold) within the tunnel entrance. (D) A close-up is shown of the c1 and c2 connections that are formed by the 8/9 and 6/7 loops. The loops are magenta, basic residues are in blue, and the cytoplasmic helix of SecE is in red. (Inset) A cross-section of the connection density is shown with docked loops, as viewed from the channel. The cut plane is shown in gray and reveals the two connections. (E) The 8/9 loop interacts with H59 and H50 while the 6/7 loop contacts H7 and perhaps H24 (RNA helices are shown in gold). (F) The insert in the 6/7 loop extends into the tunnel entrance. The tunnel is marked by black dots in this cutaway view. (G) The cytoplasmic helix of SecE (in red) forms connection 3 and contacts L23 (in purple). An overview is shown by the icon view on the right. Molecular Cell 2007 28, 1083-1092DOI: (10.1016/j.molcel.2007.10.034) Copyright © 2007 Elsevier Inc. Terms and Conditions

Figure 4 SecY Binding to the Ribosome (A) Sucrose gradient profiles are shown for ribosome-SecY complexes. Unbound SecY remains at the top of the gradient and sedimentation is from left to right. The mutants that were tested are the following: loop 8/9 (R357E), loop 6/7 (R255E/R256E), and loop 2/3 (E108C). (B) Increasing amounts of the purified complexes were run on SDS PAGE, transferred, and then immunoblotted with an anti-SecY antibody (top) or silver stained to reveal the characteristic ribosomal protein pattern (bottom). (C) The SecY density (in gray) derived from a ribosome-tandem SecY complex is shown. The extra density (asterisk) indicates the approximate positions of the N and C termini. The position of TM1 is indicated. The small subunit would be positioned on the left in the icon view. (D) (Left) Based on our studies, the first SecY monomer to bind to the ribosome is oriented as shown with the lateral gate indicated by an arrow. (Middle) The position of the small subunit (in yellow) and the tunnel exit are indicated. (Right) A SecY dimer with a face-to-face orientation is shown beneath the ribosome (Mitra et al., 2005), using our ribosome map to provide a common reference frame. The lateral gates of each monomer in the model of Mitra et al. (2005) face roughly toward the tunnel exit (marked with an asterisk). SecE is shown in red and SecG in dark blue. Molecular Cell 2007 28, 1083-1092DOI: (10.1016/j.molcel.2007.10.034) Copyright © 2007 Elsevier Inc. Terms and Conditions