Overview of Crystal Structure of the Sac3^CID:Cdc31:Sus1 Complex
(A) Surface view. (B) Secondary structure schematic. Cdc31 is yellow, Sac3 is red, Sus1A is blue, and Sus1B is cyan. Residues 723–805 of Sac3 form a continuous, 12.5 nm-long, gently undulating, α helix to which one Cdc31 and two Sus1 (Sus1A and Sus1B) chains bind. (C) Schematic of the principal residues that are buried in the interfaces between Sac3 and its partners. Dashed lines represent putative H bonds.

Details of the Sus1:Sac3 Interfaces
(A) Hydrophobic stripe formed by the four-residue repeat in the Sac3 helix in the Sus1A and Sus1B sites. The Sac3 sequence is shown on a helical net, with residues that make a major contribution to the interface shown in bold. Residues forming putative salt bridges or H bonds are shown in red (for acidic) or blue (for basic).
(B) The hydrophobic residues that give rise to the Sac3:Sus1 interface form a four-residue repeating sequence motif in which the first residue, and often the second also, are hydrophobic.

Sac3-CID(723–805) Localization to NPCs Is Dependent on Sus1
GFP-Sac3-CID fragments were expressed from plasmid with an exogenous pNOP promoter in nup133Δ (A) or sac3Δsus1Δ cells (B and C). Strains were complemented with plasmid-born NUP133, SUS1, or the corresponding empty plasmid and visualized by fluorescence microscopy and Nomarski optics. (B and C) The complete Sac3^CID (residues 723–805) is necessary for optimal NPC localization. Fragments of Sac3^CID were fused to GFP and analyzed for NPC association. The percentages of cells showing a clear GFP signal at the NPC are indicated.

Dissection of the Interactions between Sac3, Sus1, and Cdc31 in the TREX-2 Complex
(A) Schematic representation of Sac3 and its homologs, human GANP and Drosophila Xmas-2. The predicted α helix (dark gray cylinder) is located downstream of the conserved Sac3/GANP PFAM domain, PF03399 (gray rectangle). Sac3 mutants within the α-helical region are depicted below with the Sus1 and Cdc31 binding sites inferred from the purifications in (B), (C), and (D).
(B) Cell lysates from sac3Δ cells containing overexpressed Protein A-tagged SAC3 fragments (under GAL1 promoter control) were affinity purified over IgG Sepharose. The acid-released eluates were analyzed by SDS-PAGE and Coomassie staining. Open circles indicate Sac3 fragments. The asterisk indicates, Ssa1, and Ssa2, likely contaminants, identified by mass spectrometry.
(C) Split-tag affinity purification of the TREX-2 complex. Plasmid-based (pNOPPATAIL) Protein-A-tagged Sac3 or mutant derivatives were expressed in sac3Δ, THP1-GST, and SUS1-MYC cells and affinity purified over IgG Sepharose. After TEV cleavage, the eluate was further purified over GSH Sepharose and eluted with glutathione. The final eluate was analyzed by SDS-PAGE and Coomassie staining, (upper panel) or western blotting with anti-GST (to detect Thp1), anti-myc (to detect Sus1), or anti-Cdc31 antibodies (lower panel).
(D) Protein A/Flag split purification of Sus1. Sus1-TAP (via the Protein A tag) was first affinity purified on IgG Sepharose from a yeast strain expressing Sus1-TAP alone or a diploid strain expressing Sus1-TAP and Sus1-FLAG. After TEV cleavage, the eluates (lanes 1 and 2) were subject to Sus1-FLAG purification by anti-FLAG M2 affinity resin and eluted with free FLAG peptide. All eluates were analyzed by SDS-PAGE and Coomassie staining. Indicated copurifying proteins were identified by mass spectrometry. Asterisks denote TEV protease.

Sus1:Sac3 Interaction
(A and B) The hinges between the rigid Sus1 α helices enable the molecule to wrap around the Sac3^CID helix, shown in red.
(C) End-on view showing Sus1 wrapping around the Sac3 helix like fingers gripping a rod.
(D) Sus1 sequences showing the conservation of both the helices (α1, α2, α3, α4, and α5) and the hinges between them. Single Gly residues (yellow) form the hinges between helices α1/α2 and α2/α3. A kink introduced by a Pro in helix α4 enhances the intimacy of the contact with Sac3.

Sac3^CID, Sus1, and Cdc31 Function Together for Efficient Growth and mRNA Export
(A) Sac3 or mutant derivatives were expressed using the endogenous promoter from a single-copy plasmid (pRS315) in sac3Δ cells. Cells were spotted in 10-fold serial dilutions on SDC-Leu plates and growth analyzed after incubation for the indicated time and temperature.
(B) sac3Δ cells expressing Sac3 and mutant derivatives were grown at 30°C, fixed, and poly(A)⁺ mRNA localization determined by fluorescence in situ hybridization (FISH) using a Cy3-labeled oligo-dT probe. DNA was stained with DAPI. Nuclear poly(A)⁺ mRNA retention paralleled the pattern of growth defects observed in (A), with the most pronounced accumulation seen with sac3ΔB, intermediate levels with sac3ΔC, and negligible accumulation with sac3ΔA.
(C) Double-disrupted strains sac3Δmex67Δ or sac3Δyra1Δ harboring pURA3-MEX67 or pURA3-YRA1, respectively, were transformed with the indicated plasmid-borne (pRS315-sac3 or -mex67) gene constructs. Cells were spotted in 10-fold serial dilutions on 5-FOA-containing plates and growth analyzed after incubation for 3 days at 30°C. No growth indicates synthetic lethality.