Cryo-EM structure of a metazoan separase–securin complex at near-atomic resolution

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Separase is a caspase-family protease that initiates chromatid segregation by cleaving the kleisin subunits (Scc1 and Rec8) of cohesin, and regulates centrosome duplication and mitotic spindle function through cleavage of kendrin and Slk19. To understand the mechanisms of securin regulation of separase, we used single-particle cryo-electron microscopy (cryo-EM) to determine a near-atomic-resolution structure of the Caenorhabditis elegans separase–securin complex. Separase adopts a triangular-shaped bilobal architecture comprising an N-terminal tetratricopeptide repeat (TPR)-like α-solenoid domain docked onto the conserved C-terminal protease domain. Securin engages separase in an extended antiparallel conformation, interacting with both lobes. It inhibits separase by interacting with the catalytic site through a pseudosubstrate mechanism, thus revealing that in the inhibited separase–securin complex, the catalytic site adopts a conformation compatible with substrate binding. Securin is protected from cleavage because an aliphatic side chain at the P1 position represses protease activity by disrupting the organization of catalytic site residues.

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Figure 1: Overview of the C. elegans separase–securin complex.
Figure 2: The α-solenoid domain stabilizes the L4 loop.
Figure 3: The interactions between the securin pseudosubstrate motif and separase resemble interactions with Scc1.
Figure 4: Cryo-EM reconstruction of the human separase–securin complex.

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This work was funded by the Medical Research Council (MC_UP_1201/6 to D.B., and MC_UP_A025_1013 to S.H.W.S.), a Cancer Research UK grant (C576/A14109 to D.B.), Long Term EMBO Fellowships (ALTF 79-2014 to A.B., and ALTF 1229-2013 to T.G.M.) and H2020 Marie-Curie Fellowships (657725 to A.B., and 657990 to T.G.M.). We thank members of the Barford group for helpful discussions; T. Tischer for helpful suggestions and support; C. Savva, S. Chen and G. McMullan for maintaining EM facilities; J. Grimmett and T. Darling for computing; and P. Emsley for constant support with COOT. We acknowledge Diamond for access and support of the cryo-EM facilities at the UK national electron bio-imaging centre (eBIC), proposal EM13708, funded by the Wellcome Trust, MRC and BBSRC.

Author information

Z.Z. cloned the separase–securin constructs used in this study. A.B. and J.Y. generated the wild-type and mutant separase–securin viruses, respectively. A.B. established the protein purifications. A.B. and T.G.M. prepared grids and collected EM data, with contributions from X.-c.B. and L.C. A.B. analyzed EM data and determined the 3D reconstructions, aided by T.G.M. and S.H.W.S. A.B. and D.B. built the model ab initio and made the figures. D.B. directed the project and designed experiments with A.B. A.B. and D.B. wrote the manuscript, with input from all other authors.

Correspondence to Andreas Boland or David Barford.

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The authors declare no competing financial interests.

Integrated supplementary information

Supplementary Figure 1 Preparations and EM images of the C. elegans (Ce) separase–securin complex.

a, SDS PAGE gel of Ce separase-securin. b, Size exclusion chromatograph of purified complex. C, Typical cryo-electon micrographs of Ce separase-securin in vitreous ice (representative of 234 micrographs) (left) and on graphene oxide grids (representative of 2,559 micrographs) (right). d, Gallery of two-dimensional class averages of Ce separase-securin showing typical views representative of 100 two-dimensional classes collected in vitreous ice on holey carbon grids (Quantifoil Au R1.2/1.3, 300 mesh). The white scale bar corresponds to a distance of 100 Å. e, Gallery of two-dimensional class averages of Ce separase-securin showing different views representative of 100 two-dimensional classes collected on graphene oxide coated grids. The white scale bar corresponds to a distance of 100 Å. f, Gallery of two-dimensional class averages of 2D-class averages of human separase-securin showing different views representative of 100 two-dimensional classes collected on graphene oxide coated grids (Quantifoil Au R1.2/1.3, 300 mesh). The white scale bar corresponds to a distance of 100 Å. g, Angular distribution plot of C. elegans data sets collected in vitreous ice (left) compared to the angular distribution plot of the data used for the final reconstruction (right) is shown.

Supplementary Figure 2 Resolution estimation and example of de novo model building.

a, Representative EM density for regions of separase with fitted coordinates. b, Gold standard Fourier Shell Correlation (FSC) curve and FSC curve between cryo-EM map and final atomic model of the Ce separase-securin complex. c, Cross-validation of model refinement by half maps. Shown are FSC curves between the atomic model and the half map (maphalf1) it was refined against and FSC curve between the atomic model and the other half map (maphalf2) that was not used during refinement. d, EM density map colour-coded according to local resolution. e, B-factor plot: Cartoon representation of C. elegans separase-securin complex with main-chain atoms colour-coded according to B-factors from low (blue) to high (red).

Supplementary Figure 3 The α-solenoid domain of Ce separase forms a distorted TPR-like superhelix with 11 TPR motifs.

a, α-solenoid domain of Ce separase shown with its 25 α-helices represented as cylinders and colour-ramped from the N- to C-terminus blue to red. TPR motifs TPR1 and TPR11, and α-helices are labeled, as are the positions of insert-1 and insert-2. H2, H16 and H25 are not part of the TPR superhelix. b, An idealized TPR superhelix of eleven TPR motifs superimposed onto the Ce separase α-solenoid TPR-like domain. The Ce separase α-solenoid domain is considerably compressed compared to the idealized TPR superhelix of eleven TPR motifs. H2, H16 and H25 of the Ce separase α-solenoid do not share counterparts in the eleven-motif TPR superhelix.

Supplementary Figure 4 Comparison of H. sapiens and C. elegans separase structures.

a, Schematic of C. elegans separase and b, human separase structures. Human separase comprises an α-helical domain N-terminal to the common TPR domain not present in C. elegans separase. Auto-cleavage and phosphorylation sites in human separase are indicated. c, Structure-based alignment of the TPR domains of C. elegans and human separase. α-helices and corresponding TPR motifs, and Insert-1 and Insert-2 are shown. Human auto-cleavage sites from29,30. Phosphorylation sites from17,28. Sequence alignment figure generated using ALSCRIPT61. The species abbreviations are: Ce (Caenorhabditis elegans), Hs (Homo sapiens).

Supplementary Figure 5 The Ce separase protease domain (SPD) resembles CtSPD.

a, Side by side comparison of CeSPD and CtSPD with the L4 loop highlighted in pink (Ce) and purple (Ct). b, Superposition of Ce and CtSPD domains with the L4 loop highlighted in pink (Ce) and purple (Ct).

Supplementary Figure 6 Structure-based multiple sequence alignment of the SPD.

Secondary structure elements of CeSPD and CtSPD are shown above and below the alignment, respectively. Residues conserved in all aligned sequences are highlighted in red. Residues binding to the securin pseudo-substrate motif P sites P1 to P6 are boxed in wheat, yellow-green, light green, green, cyan and light blue. Catalytic site residues are marked with a red asterisk. The species abbreviations are: Ce (Caenorhabditis elegans), Hs (Homo sapiens), Mm (Mus musculus), Dr (Danio rerio), Sc (Saccharomyces cerevisiae), Ct (Chaetomium thermophilum).

Supplementary Figure 7 Multiple sequence alignment of securin and separase substrates.

Sequence alignment of the separase-binding motif (SBM) of securin. Secondary structure elements are shown above the alignment. Securin pseudo-substrate motif sites P1 to P6 are indicated. Invariant residues are boxed in dark red, conserved residues in light red. b, Sequence alignment of cleavage sites of separase substrates (Scc1, Rec8, kendrin and Slk19) and the securin pseudo-substrate motif. Sites P1 to P6 are indicated. Separase cleaves substrates immediately C-terminal to an Arg residue at P1 (labeled).

Supplementary Figure 8 Comparison of the P1-binding pockets of C. elegans separase and CtSPD.

The P1-binding pockets of C. elegans separase and CtSPD were superimposed and shown with the corresponding C. elegans EM density. EM density for selected separase residues is shown in grey and Met126Sec density is coloured red. Whereas there is a good fit for the C. elegans structure, CtSPD fits poorly, especially Gly2082 and His2083, due to the narrower P1-binding pocket of CtSPD.

Supplementary Figure 9 Three-dimensional classification of the C. elegans separase–securin complex.

The three-dimensional classification was conducted using 665,331 motion-corrected particles that were divided into six classes. The resultant classes did not reveal any major structural rearrangements or classes of free separase. The best-defined and most complete densities were selected for future reconstructions to further improve map quality.

Supplementary information

Supplementary Text and Figures

Supplementary Figures 1–9 (PDF 2502 kb)

Conformational differences at the P1 site of separase with substrate (Scc1) and inhibitor (securin).

This video shows the conformational differences at the P1 site of the catalytic sites of C. elegans separase in complex with securin and the Chaetomium thermophilum separase protease domain (CtSPD) in complex with the Scc1 peptide 13. In the C. elegans separase–securin structure, Met126 of securin (the P1 residue) engages the P1-binding site, whereas in the CtSPD–Scc1 complex the critical Arg residue of the substrate engages the P1 site. In the CtSPD–Scc1 complex, the guanidinium side chain of Arg(P1) restructures the catalytic site by donating hydrogen bonds to the carboxylate side chain of Asp2151 and the main chain carbonyl of Gly2082. The latter contact results in a shift of the imidazole side chain of His2083 (a component of the catalytic dyad with Cys2110) toward Arg(P1). The resultant hydrogen bond between the His2083 imidazole ring and the main chain carbonyl of Arg(P1) generates the oxyanion hole that stabilizes the oxyanion transition state intermediate. In the C. elegans separase–securin complex, the nonpolar Met126(P1) side chain acts to widen the P1-binding pocket. The Met126(P1) side chain forms a van der Waals contact with the carbonyl oxygen atom of Gly1013 (equivalent to Gly2082 of CtSPD), shifting the carbonyl group by 2 Å relative to Gly2082. The imidazole side chain of His1014 (equivalent to Hsi2083 of CtSDP) is displaced away from the main chain carbonyl of Met126(P1) by 1.7 Å, and the oxyanion hole is not created in the C. elegans separase–securin structure. In addition, Met126(P1) is unable to form hydrogen bonds to Asp1082 (equivalent to Asp2151 of CtSPD). The CtSPD in complex with the Scc1 peptide is from ref. 13 (PDB 5FC2). (MP4 940 kb)

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Boland, A., Martin, T., Zhang, Z. et al. Cryo-EM structure of a metazoan separase–securin complex at near-atomic resolution. Nat Struct Mol Biol 24, 414–418 (2017) doi:10.1038/nsmb.3386

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