Abstract
Complexes containing a pair of structural maintenance of chromosomes (SMC) family proteins are fundamental for the three-dimensional (3D) organization of genomes in all domains of life. The eukaryotic SMC complexes cohesin and condensin are thought to fold interphase and mitotic chromosomes, respectively, into large loop domains, although the underlying molecular mechanisms have remained unknown. We used cryo-EM to investigate the nucleotide-driven reaction cycle of condensin from the budding yeast Saccharomyces cerevisiae. Our structures of the five-subunit condensin holo complex at different functional stages suggest that ATP binding induces the transition of the SMC coiled coils from a folded-rod conformation into a more open architecture. ATP binding simultaneously triggers the exchange of the two HEAT-repeat subunits bound to the SMC ATPase head domains. We propose that these steps result in the interconversion of DNA-binding sites in the catalytic core of condensin, forming the basis of the DNA translocation and loop-extrusion activities.
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Data availability
The cryo-EM maps and the pseudo-atomic model of the apo condensin structure were deposited in the EM Data Bank (EMDB) and Protein Data Bank (PDB) with accession codes EMD-10951 (non-engaged overall), EMD-10948 (non-engaged arm segment), EMD-10947 (non-engaged head segment), EMD-10954 (bridged overall), EMD-10953 (bridged arm segment), EMD-10952 (bridged head segment), EMD-10944 (+ATP head segment), EMD-10964 (+ATP arm segment) and PDB 6YVU (non-engaged overall model), PDB 6YVV (bridged head segment) and PDB 6YVD (+ATP head segment). Crosslinking MS data are available via the ProteomeXchange with identifiers PXD019275 (BS3) and PXD019274 (sulfo-SDA). Source data are provided with this paper. All other data are available in the main text or the supplementary materials.
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Acknowledgements
We thank D. D’Amours for sharing plasmids and yeast strains. We are grateful to L. Thärichen, S. Perović and C. Stober for help with yeast experiments and W. Hagen and F. Weis of the EMBL Cryo-EM Platform for support with cryo-EM data collection and processing (all EMBL). We thank F. Coscia, G. Cannone, A. Gonzales, J. García-Nafría, K. Zhang, S. Scheres and the MRC-LMB EM facility for assistance and advice with data collection and processing and T. Darling and J. Grimmett for computing (all MRC-LMB). We thank Alejandra F. Cid for help with purifications (MRC-LMS). We acknowledge the Diamond Light Source (eBIC), Astbury Biostructure Electron Microscopy (Leeds) and Cambridge Nano Science Centre for access and help (facilities supported by Wellcome Trust, MRC and BBSRC). T.N. was supported by the Japan Society for the Promotion of Science. This work was funded by the European Molecular Biology Laboratory, the European Research Council (ERC-2015-CoG 681365 to C.H.H.), the Medical Research Council (U105184326 to J.L. and MC-A652-5PY00 to L.A.), the DFG (EXC 2008/1 - 390540038 and 329673113 to J.R.) and the Wellcome Trust (202754/Z/16/Z to J.L. and 100955/Z/13/Z to L.A.).
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Contributions
Cryo-EM of apo condensin: B.-G.L., C.C., P.G.-E., T.N., L.A. and J.L.; cryo-EM of +ATP condensin: F.M., M.A., S.B., M.B. and C.H.H.; biochemical and genetic assays: M.K., L.L., M.H. and C.H.H.; crosslink MS: F.J.O.R., L.R.S. and J.R.; data analysis and manuscript preparation: B.-G.L., F.M., M.H., J.L. and C.H.H.
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Extended data
Extended Data Fig. 1 Cryo-EM structure determination of the nucleotide-free apo condensin complex.
a, Representative micrographs of nucleotide-free (apo) condensin tetramer (Smc2–Smc4–Brn1–Ycs4, left) and pentamer (Smc2–Smc4–Brn1–Ycs4–Ycg1, right). b, Workflow of initial data processing. Representative 2D classes are shown for the tetramer and pentamer data sets. Density map, angular distribution plot and FSC curves of the overall complexes in c, the non-engaged and d, the bridged state.
Extended Data Fig. 2 Focused image processing of the arm segments of nucleotide-free apo condensin.
a, Workflow for the apo non-engaged condensin arm segment and representative 2D classes. Particles of the tetramer complex were initially processed and preliminary angles and translations were assigned as described in Extended Data Fig. 1. b, 5.3 Å cryo-EM density map and its local resolution plot as calculated by RELION (left) and FSC curves (right) for the arm segment. c, Workflow for the apo bridged condensin arm segment and representative 2D classes. Particles of the pentamer bridged class were initially processed and preliminary angles and translations were assigned as described in Extended Data Fig. 1. d, 7.8 Å cryo-EM density map and its local resolution plot as calculated by RELION (left) and FSC curves (right) for the arm segment.
Extended Data Fig. 3 Focused image processing of the head segments of nucleotide-free apo condensin.
a, Workflow for the apo non-engaged condensin head segment. Particles of tetramer and pentamer complexes were initially processed and preliminary angles and translations were assigned as described in Extended Data Fig. 1. b, Representative 2D classes, 4.2 Å cryo-EM density map (top) and its local resolution plot as calculated by RELION (middle) and FSC curves (bottom) for the non-engaged head segment. c, Workflow for the apo bridged condensin head segment. Particles of the bridged class of the pentamer complex were initially processed and preliminary angles and translations were assigned as described in Extended Data Fig. 1. d, Representative 2D classes, 7.5 Å cryo-EM density map (top) and its local resolution plot as calculated by RELION (middle) and FSC curves (bottom) for the bridged head segment.
Extended Data Fig. 4 Crosslink mass spec and pseudo-atomic model of the apo complex.
a, Circle plot of inter-molecular BS3 crosslinks identified in condensin tetramer complexes in the absence of nucleotide with an FDR of < 1%. Bar plot showing the distance distribution of crosslinks (>35 Å; ~23 %). b, Model of the Smc2 and Smc4 coiled coils. c, Pseudo-atomic model of the non-engaged head segment with final electron density map. d, Pseudo-atomic model of the bridged head segment with final electron density map. e, Example images of 2D classes of conformations with the hinge folding back all the way to contact the coiled coils (left) or with lower degrees of elbow bending (right).
Extended Data Fig. 5 Conformational changes and putative DNA binding sites in the apo condensin complex.
a, Structural alignment of pseudo-atomic models of overall apo complexes in the non-engaged and bridged states. b, Electrostatic potential maps of Ycs4 (left) and the Smc2–Smc4 heads and coiled coils (right); red: –5 keT, blue: +5 keT. The dotted line indicates a putative path for a DNA double helix that goes through the coiled coils above the ATPase heads and also includes the positively charged patch on Ycs4 near the ‘proboscis’ protrusion. c, Placement of a DNA double helix in the space between the neck regions of the Smc2 and Smc4 coiled coils in the apo non-engaged state, based on a comparison to a cryo-EM DNA co-structure of the E. coli SbcC (Rad50) head dimer in the engaged state (PDB code 6S85).
Extended Data Fig. 6 Structure determination of the +ATP condensin complex.
a, Workflow of the initial data processing of pentameric condensin in the presence of ATP by reference-free ab initio model estimation, combined with focused refinement and representative 2D class averages of the three major classes of the overall complex. b. 2D class averages of open and rod-shaped coiled coils after re-centering and re-extraction of the arm segments with FSC curves of the cryo-EM density maps. c, 2D class averages of the ATPase heads after re-centering and re-extraction the ATPase head segments with FSC curves of the cryo-EM density maps.
Extended Data Fig. 7 Ycg1 binds Smc2 and Brn1 via a conserved patch in vivo.
a, Surface conservation plot of S. cerevisiae Ycg1–Brn1 (left). Tetrad dissection of diploid S. cerevisiae YCG1/ycg1Δ cells expressing an ectopic PK6-tagged copy of Ycg1 harboring patch 1 or patch 2 mutations, after three days on rich media at 25 °C for 3 days (center). Expression levels of Ycg1-PK6 tested by Western blotting against the PK6 tag (right). b, Western blot analysis of photo-crosslinking products expressing Ycg1-PK6 with bpa substitutions at the indicated residues before (–UV) or after (+UV) exposure to light at 365 nm (left). Shift of endogenously HA-tagged versions Smc4, Smc2, Ycg1 or Brn1 in cells expressing unmodified wild-type (wt) or bpa-substituted Ycg1 at position S435 measured by Western blotting before (–UV) or after (+UV) light exposure (right).
Extended Data Fig. 8 Sub-classification of the + ATP condensin head domain segment.
a, 3D classification of all head particles results in two distinct maps, one with clear density for both coiled coils (open coils, right) and a second one with weak Smc2 coiled coil density (‘single’ coil, left). b, Representative 2D class averages, local resolution as plotted by ResMap52, and FSC curves of the cryo-EM density map of the ‘single’ coil state, as plotted by RELION. c, Representative 2D class averages, local resolution, and FSC curves of the cryo-EM density map of the open coils state.
Extended Data Fig. 9 Conformational changes in the head segment between the apo and +ATP states.
a, Structural alignment based on the RecA-like lobe of the Smc2 head domains of the +ATP (‘open coils’) form (in blue colors) and the apo (nucleotide-free) form (grey colors) highlights the extent of coiled-coil kinking in Smc2. Positioning and extent of the kinking in the carboxy-terminal Smc2 coiled coil are indicated. b, Simultaneous Smc2–Smc4 head engagement and Ycs4 binding to Smc4 would lead to steric clashes. c, Simultaneous binding of Ycs4 and Ycg1 HEAT-repeat subunits to the Smc4 and Smc2 heads, respectively, in the non-engaged state would result in major steric clashes.
Extended Data Fig. 10 Association of Ycs4 with Smc2–Smc4 prevents Ycg1 binding.
a, Size exclusion chromatography of complexes formed between a trimeric Smc2–Smc4–Brn1NC and either Ycs4–Brn1Ycs4 (left), Ycg1–Brn1Ycg1 (center) or both (right). Peak fractions were analyzed by SDS-PAGE and Coomassie Blue staining. b, as in a, but in the presence of 1 mM ATP. One chromatography run of two independent repeats shown for each experiment.
Supplementary information
Supplementary Information
Supplementary Note, Supplementary Figure 1, Supplementary Table 2 and Supplementary References.
Supplementary Table 1
Complete lists of crosslinks identified by mass spectrometry. Worksheets 1–3, crosslinks for the two samples shown in Fig. 3a and the sample shown in Extended Data Fig. 4a, filtered at 1% FDR (false discovery rate) as calculated by xiFDR1.4.1 (ref. 50). Apo pentamer crosslinked with sulfa-SDA, +ATP pentamer crosslinked with sulfo-SDA and apo condensin tetramer crosslinked with BS3. Worksheet 4, S. cerevisiae proteins identified in the upshifted band shown in Fig. 4e before (–UV) and after (+UV) photo-crosslinking of yeast cells expressing Ycg1S435bpa.
Supplementary Video 1
Smc2 head movement between non-engaged and bridged apo states. Conformational changes in the Smc2 and Smc4 head domains and Ycs4 visualized by a morph between the structures for the non-engaged and bridged apo states.
Supplementary Video 2
Ycg1 is flexibly attached to condensin. Animation of a series of 2D classes showing the flexible attachment of Ycg1 to the head segment of condensin in the apo state.
Supplementary Video 3
ATPase head engagement induces coiled-coil kinking in Smc2. Conformational changes in the Smc2 and Smc4 head domains and adjacent coiled coils upon ATP binding as visualized by a morph between the structures for the non-engaged apo and +ATP states.
Source data
Source Data Fig. 4
Unprocessed SDS PAGE gel stained with Coomassie Blue
Source Extended Data Fig. 7
Unprocessed Western blots
Source Extended Data Fig. 10
Unprocessed SDS PAGE gel stained with Coomassie Blue
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Lee, BG., Merkel, F., Allegretti, M. et al. Cryo-EM structures of holo condensin reveal a subunit flip-flop mechanism. Nat Struct Mol Biol 27, 743–751 (2020). https://doi.org/10.1038/s41594-020-0457-x
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DOI: https://doi.org/10.1038/s41594-020-0457-x
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