Cryo-EM Structure of the TOM Core Complex from Neurospora crassa Thomas Bausewein, Deryck J. Mills, Julian D. Langer, Beate Nitschke, Stephan Nussberger, Werner Kühlbrandt  Cell  Volume 170, Issue 4, Pages 693-700.e7 (August 2017) DOI: 10.1016/j.cell.2017.07.012 Copyright © 2017 Elsevier Inc. Terms and Conditions

Cell 2017 170, 693-700.e7DOI: (10.1016/j.cell.2017.07.012) Copyright © 2017 Elsevier Inc. Terms and Conditions

Figure 1 Overall Structure of TOM-CC (A) Side view at low density threshold (sigma level 0.04) showing the detergent belt and α-helical subunits protruding on both membrane surfaces. (B) Same view at a higher density threshold (sigma level 0.0665) showing protein features. (C) View of the two pores from the top. (D) Sectional view shows the pore dimensions and their orientation in the membrane. See also Figures S1 and S4. Cell 2017 170, 693-700.e7DOI: (10.1016/j.cell.2017.07.012) Copyright © 2017 Elsevier Inc. Terms and Conditions

Figure 2 Fit of the Tom40 Homology Model (A and B) Top view (A) and side view (B) of the cryo-EM map with the model of two Tom40 β-barrels fitted into the density. β strands are colored purple; helical segments are green. (C) Close-up view of the fitted cytosolic loops of Tom40. β strands are numbered from 1 to 19 in ascending order from N to C terminus. (D) The helical N terminus of Tom40 (N-Tom40) inserts into the pore and continues into the periphery of the complex. (E) The short C-terminal helix (Tom40-C) at the end of β strand 19 interacts with the loop between strands 3 and 4. (F) Close-up view of the dimer interface. See also Figure S2. Cell 2017 170, 693-700.e7DOI: (10.1016/j.cell.2017.07.012) Copyright © 2017 Elsevier Inc. Terms and Conditions

Figure 3 Dimensions and Interactions in the Tom40 Pore (A) Map of one protomer sectioned along the 2-fold axis. (B) Fitted model of Tom40 in the region of the proposed seam in the β-barrel. Blue dashed lines indicate H bonds between antiparallel β strands; red dashed lines are H bonds between the parallel β strands 1 and 19. (C) Tom40 residues close to Tom22 as indicated by chemical crosslinking (Shiota et al., 2015) are blue. (D) Residues that crosslink to Tom5 (Shiota et al., 2015) are red. Cell 2017 170, 693-700.e7DOI: (10.1016/j.cell.2017.07.012) Copyright © 2017 Elsevier Inc. Terms and Conditions

Figure 4 Subunit Assignment (A) The β-barrel of Tom40 is yellow and the elongated density of Tom22 is blue. Map volumes assigned to the small α-helical Tom proteins are red (Tom5), green (Tom6), and purple (Tom7). (B) Side view of the complex with Tom5 in front. (C) Two side views indicate the orientations of the small α-helical subunits relative to the lipid bilayer. See also Figures S2 and S3. Cell 2017 170, 693-700.e7DOI: (10.1016/j.cell.2017.07.012) Copyright © 2017 Elsevier Inc. Terms and Conditions

Figure 5 Model of Preprotein Import through TOM-CC Tom22 (blue), the central TOM-CC receptor, accepts the preprotein from Tom20 (pale blue) on the cytosolic side of the membrane. Together with the Tom5 subunit (red) on the edge of the complex, Tom20 guides the preprotein to either of the two β-barrel pores of Tom40 (yellow). The IMS domains of Tom22 in the center of the complex accept the incoming preprotein and transfer it to the mitochondrial import machineries of the inner membrane. Cell 2017 170, 693-700.e7DOI: (10.1016/j.cell.2017.07.012) Copyright © 2017 Elsevier Inc. Terms and Conditions

Figure S1 Cryo-EM of TOM-CC, Related to Figure 1 (A) Typical micrograph (scale bar 500 Å). (B) Representative 2D class averages. (C) Coomassie blue-stained SDS-PAGE of TOM-CC. The small Tom subunits were not resolved on the gel, but were identified unambiguously by mass spectrometry (see Figure S3). (D) Fourier shell correlation (FSC) curve generated by RELION post-processing. The 0.143 threshold indicates an average gold-standard resolution of 6.8 Å. (E) Angular particle distribution in the final reconstruction. Each column represents one view; the length of the column is proportional to the number of particles in each view. Blue columns indicate rare views; red columns indicate frequent views. (F) Local map resolution as determined in RELION 2.0. Blue indicates higher local resolution; lower local resolution is red. Cell 2017 170, 693-700.e7DOI: (10.1016/j.cell.2017.07.012) Copyright © 2017 Elsevier Inc. Terms and Conditions

Figure S2 Secondary Structure Prediction, Related to Figures 2 and 4 (A) Tom40. (B) Tom5, Tom6 and Tom7. Residues predicted to be in the transmembrane region are green. Light green: consistent predictions by all algorithms used; dark green: predictions by some algorithms. Cell 2017 170, 693-700.e7DOI: (10.1016/j.cell.2017.07.012) Copyright © 2017 Elsevier Inc. Terms and Conditions

Figure S3 Mass Spectrometry, Related to Figure 4 (A) MALDI spectrum of the small subunits Tom5 (5.460 kDa), Tom6 (6.332 kDa) and Tom7 (6.061 kDa). (B) MALDI spectrum of Tom22 (17.95 kDa) and Tom40 (38.1 kDa, showing a second peak for the doubly charged Tom40 at m/z 19.07). (C) High-resolution MALDI-MS in the m/z range 5000-7000 and polypeptide sequences (Figure S2B) indicate that Tom5 is acetylated and oxidized, while Tom6 appears to lack the N-terminal methionine. (D) annotated ESI-MS/MS spectrum acquired on an Orbitrap Elite following proteolytic digest and chromatographic separation, matched to the sequence MFGGFQPPALSREELQAAEAEATFTIQR (aa 1-28 of Tom5, indicating acetylation on M1, m/z 1046.516, z = +3). Cell 2017 170, 693-700.e7DOI: (10.1016/j.cell.2017.07.012) Copyright © 2017 Elsevier Inc. Terms and Conditions

Figure S4 Comparison of the 6.8 Å Map of N. crassa TOM-CC to the ∼20 Å Map of the Yeast TOM Complex as Published by Model et al., 2008, Related to Figure 1 (A) Superposition of the yeast two-pore complex in side and top view. (B) Comparison to the yeast three-pore complex. Cell 2017 170, 693-700.e7DOI: (10.1016/j.cell.2017.07.012) Copyright © 2017 Elsevier Inc. Terms and Conditions