The Transport Signal on Sec22 for Packaging into COPII-Coated Vesicles Is a Conformational Epitope  Joseph D. Mancias, Jonathan Goldberg  Molecular Cell  Volume 26, Issue 3, Pages 403-414 (May 2007) DOI: 10.1016/j.molcel.2007.03.017 Copyright © 2007 Elsevier Inc. Terms and Conditions

Figure 1 Sec22b Is Packaged by the a and b Isoforms of Sec24 (A) Vesicles were generated from semi-intact HT-1080 cells using Sar1a, Sec13a/31a, and the four isoforms of human Sec24 (Sec23a/Sec24a–d), in the presence and absence of 0.2 mM GTP and an ATP regenerating system (see Experimental Procedures). The presence of ERGIC-53, Sec22b, and ribophorin in budded vesicles and total membranes (T) was determined by immunoblotting. (B) In vitro budding assay as in (A) from semi-intact HEK293 cells. The packaging of cargo was assessed for wild-type Sec24a and Sec24b and for the C site mutants Sec24a-R541A and Sec24b-R715A. (C) The direct interaction between Sec22 and Sec23/24 was assessed using purified proteins in a pull-down assay. Sec22-GST fusion protein, or GST alone, was incubated with wild-type Sec23/24a or mutant Sec23/24a-R541A (at concentrations from 1.25 to 20 μM), as described in Experimental Procedures. Bound proteins were analyzed by 4%–15% SDS-PAGE and Coomassie blue staining. (D) Binding of wild-type and mutant coat proteins to Sec22 was quantified by densitometry of bands in (C). Molecular Cell 2007 26, 403-414DOI: (10.1016/j.molcel.2007.03.017) Copyright © 2007 Elsevier Inc. Terms and Conditions

Figure 2 Overall Structure of the Sec23/24•Sec22 Complex (A) Ribbon diagram with Sec23 colored gray, Sec24 blue, the Sec22 longin domain red, and the Sec22 NIE segment of the SNARE motif yellow. The two views are related by a 90° rotation; on the left the membrane-proximal surface faces forward, and on the right the subtle curvature of the complex is emphasized by comparison with the surface of a 60 nm sphere (gray line). (B) A close-up view of Sec22 in the complex, with proteins colored as in (A). Amino acid residues of the Sec22 longin domain that interact with the NIE segment of the SNARE motif are colored pink. A difference electron density (simulated-annealing omit) map for the NIE segment is drawn in green, calculated at 2.3 Å resolution and contoured at 1.6 σ. The NIE segment is drawn in yellow with oxygen atoms red and nitrogen atoms blue, and residues Asn152, Ile153, and Glu154 are labeled. (C) Schematic diagram of Sec22 (numbering corresponds to human Sec22b). A previous analysis of S. cerevisiae Sec22 identified two elements required for efficient ER export: the longin domain, and a portion of the SNARE motif between layers −4 and −1 that includes the highly conserved NIE segment (Liu et al., 2004). Molecular Cell 2007 26, 403-414DOI: (10.1016/j.molcel.2007.03.017) Copyright © 2007 Elsevier Inc. Terms and Conditions

Figure 3 Interaction Surfaces on Sec23/24 and Sec22 (A) The molecular surfaces of Sec23/24 and Sec22 are colored according to sequence conservation of the underlying residues in an alignment of Sec23, Sec24, and Sec22 sequences from ten organisms (see Experimental Procedures; sequence alignments for Sec24 are presented in Figures S1 and S2). Picture shows an “open book” view, with Sec22 rotated 140° from the Sec23/24 complex; for comparison, the opposite (180° rotated) surface of Sec23/24 is also shown. Protein contact regions are outlined in black, and a blue line indicates the interface of Sec23 and Sec24. Sar1 (drawn as a backbone worm in cyan) is modeled based on a previous structural analysis of the yeast Sec23/24•Sar1 complex (Bi et al., 2002). (B) Picture shows interactions between the Sec22 longin domain (pink) and Sec24 (blue); Sec23 is colored gray, and the SNARE segment is yellow. Highly conserved residues of the α2-α3 loop of Sec22 are drawn in red; highly conserved interfacial residues of Sec24 are shown in dark blue. Molecular Cell 2007 26, 403-414DOI: (10.1016/j.molcel.2007.03.017) Copyright © 2007 Elsevier Inc. Terms and Conditions

Figure 4 SNARE-Binding Site on the Longin Domain (A) Schematic diagram of the Sec22 longin domain. The sequence comprising the NIE segment of the Sec22 SNARE motif (residues 148–157) is indicated on the yellow line at top, with key interface residues outlined in red; below is the homologous sequence from yeast Ykt6. (B) Comparison of the longin domains of Sec22 (from the Sec23/24•Sec22 structure) and Ykt6 (Tochio et al., 2001). Elements of Sec22 that contact the NIE segment are colored blue. Likewise, residues of Ykt6 that contact an undetermined portion of the SNARE motif (according to NMR chemical shift data) are colored blue (Tochio et al., 2001). Molecular Cell 2007 26, 403-414DOI: (10.1016/j.molcel.2007.03.017) Copyright © 2007 Elsevier Inc. Terms and Conditions

Figure 5 Sec22b Longin Domain Picture shows a comparison of Sec22b from the Sec23/24•Sec22 structure (upper picture) and the crystal structure of the isolated Sec22b longin domain (lower picture, taken from 1IFQ [Gonzalez et al., 2001]). In the Sec23/24•Sec22 complex, Sec22 is drawn with thick lines (and Sec23 is omitted for clarity); the NIE segment of the SNARE motif is drawn in yellow lines, the “acceptor pocket” is indicated by a blue sphere, and the yellow sphere is drawn on the conserved α2-α3 “donor loop” of Sec22 that contacts Sec24. In the lower picture, an aligned copy of the Sec22b longin domain is drawn in thick lines; five additional copies of the domain are shown to indicate the fibre formed by donor-acceptor interactions that runs through the crystal in the direction of the crystallographic c axis. Molecular Cell 2007 26, 403-414DOI: (10.1016/j.molcel.2007.03.017) Copyright © 2007 Elsevier Inc. Terms and Conditions

Figure 6 Composite Model of the COPII Prebudding Complex Molecular-surface depiction of the protein complex is oriented as in Figure 2A. The positions for Sar1-GppNHp (cyan) and the Bet1 transport signal (white) have been added based on structural alignments with crystal structures determined previously (Bi et al., 2002; Mossessova et al., 2003). The dotted lines indicate the polypeptide chains leading to the membrane anchor of Sar1 and the transmembrane domains of Bet1 and Sec22. Molecular Cell 2007 26, 403-414DOI: (10.1016/j.molcel.2007.03.017) Copyright © 2007 Elsevier Inc. Terms and Conditions