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Structure of the eukaryotic MCM complex at 3.8 Å

Nature volume 524, pages 186–191 (2015)Cite this article

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Abstract

DNA replication in eukaryotes is strictly regulated by several mechanisms. A central step in this replication is the assembly of the heterohexameric minichromosome maintenance (MCM2–7) helicase complex at replication origins during G1 phase as an inactive double hexamer. Here, using cryo-electron microscopy, we report a near-atomic structure of the MCM2–7 double hexamer purified from yeast G1 chromatin. Our structure shows that two single hexamers, arranged in a tilted and twisted fashion through interdigitated amino-terminal domain interactions, form a kinked central channel. Four constricted rings consisting of conserved interior β-hairpins from the two single hexamers create a narrow passageway that tightly fits duplex DNA. This narrow passageway, reinforced by the offset of the two single hexamers at the double hexamer interface, is flanked by two pairs of gate-forming subunits, MCM2 and MCM5. These unusual features of the twisted and tilted single hexamers suggest a concerted mechanism for the melting of origin DNA that requires structural deformation of the intervening DNA.

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Figure 1: Overall structure and domain organization of the MCM2–7 double hexamer.
Figure 2: Inter-hexamer interactions contributed by NTEs and NTIs.
Figure 3: Inactive ATPase centres of 2:6 and 5:2 dimers.
Figure 4: Spatial distribution of conserved hairpins in the single hexamer.
Figure 5: Central channel and its implication in origin melting.

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Electron Microscopy Data Bank

Protein Data Bank

Data deposits

The cryo-EM density map has been deposited in the Electron Microscopy Data Bank (EMDB) under accession number EMD-6338; and the atomic model has been deposited in the Protein Data Bank (PDB) under accession number 3JA8.

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Acknowledgements

We thank X. Li for providing programs in data collection, motion correction and framed-based analysis, and J. Wang for advices on modelling and model refinement. We also thank the National Center for Protein Sciences (Beijing, China) for technical support with cryo-EM data collection and for computation resource. This work was supported by the Ministry of Science and Technology of China (2013CB910404 to N.G.), the National Natural Science Foundation of China (31422016 to N.G.), the Research Grants Council of Hong Kong (GRF664013 and HKUST12/CRF/13G to Yu.Z.) and the Hong Kong University of Science & Technology (B.-K.T.).

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Author notes

  1. Ningning Li and Yuanliang Zhai: These authors contributed equally to this work.

Authors and Affiliations

  1. Ministry of Education Key Laboratory of Protein Sciences, Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China

    Ningning Li, Yixiao Zhang, Wanqiu Li, Maojun Yang, Jianlin Lei & Ning Gao

  2. Division of Life Science, Hong Kong Universityof Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China

    Yuanliang Zhai & Bik-Kwoon Tye

  3. Institute for Advanced Study, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China

    Yuanliang Zhai

  4. Department of Molecular Biology and Genetics, College of Agriculture and Life Sciences, Cornell University, Ithaca, 14853, New York, USA

    Bik-Kwoon Tye

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  1. Ningning Li
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Contributions

Yu.Z. purified sample; N.L. collected cryo-EM data (with J.L., Yi.Z. and W.L), performed image processing, and analyzed structures. N.L., N.G. and M.Y. performed atomic modelling. N.L., Yu.Z., B.-K.T. and N.G. designed experiments, interpreted the structure and wrote the manuscript.

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Correspondence to Yuanliang Zhai, Bik-Kwoon Tye or Ning Gao.

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Extended data figures and tables

Extended Data Figure 1 MCM2–7 double hexamer purification and structural determination.

a, A flowchart of the procedure for MCM2–7 double hexamer purification from G1 chromatin of the yeast strain MCM4-TEV-3×Flag. b, Fractions taken were analysed by SDS–PAGE and immunoblotting of the indicated MCM subunits. c, The eluted MCM2–7 complexes were subjected to 20–40% glycerol gradient sedimentation at 175,000g for 6.5 h. Collected fractions were analysed by SDS–PAGE and visualized by silver staining. Molecular size markers used are: ALP 140 kDa and thyroglobulin 670 kDa. Fractions 10–12 were pooled and concentrated for cryo-EM analysis. d, A representative raw micrograph of the negatively stained MCM2–7 double hexamer. Representative 2D class averages of negatively stained particles produced by reference-free classification are shown at the top-right corner. The initial 3D model generated using RELION is shown at the bottom-right corner. e, A representative raw micrograph of cryo-EM data. f, Representative 2D class averages of cryo-EM particles from reference-free classification. g, Two typical side views of the average images from f, in enlarged forms, highlighting well-resolved secondary structure elements. Extra densities with poor quality on the two ends of double hexamer could be attributed to the flexible winged-helix motifs (WH) within the CTEs of MCM proteins. h, i, Distribution of particle orientations in the last round of structural refinement, showing in side (h) and top (i) views. The heights of blue cylinders at different projection directions on the surface of a hemisphere are proportional to their particle numbers. Two areas (red asterisks) of a dense equator belt are slightly enriched with particles. j, The density map of the MCM2–7 double hexamer (sharpened) is shown in two views, for the outer (left) and inner (right) surfaces. The map is colour-coded to indicate the range of the local resolution. k, Fourier shell correlation (FSC) curves for the final 3D density map after RELION-based post-processing (red, gold-standard FSC), and for the cross-examination between final atomic model and the 3D density map (blue, final refined model versus map). At a FSC 0.143 cut-off, the overall resolution for the map is 3.8 Å. l, FSC curves for the atomic model cross-validation. See Methods for details.

Extended Data Figure 2 Sequence alignment of the MCM2–7 proteins.

The sequences of archaeal (SS, Sulfolobus solfataricus) and yeast (Saccharomyces cerevisiae) MCM proteins were aligned using BioEdit73. The alignment was further adjusted manually according to the secondary structure prediction and 3D structural alignment. Conserved hairpins and loops are labelled (H2I, EXT, PS1 and β-turn). CTEs were aligned by the predicted secondary elements in the winged-helix (WH) motifs. Eukaryote-specific sequences (numbered 1–9) well resolved in our structure as in Extended Data Fig. 4a are labelled.

Extended Data Figure 3 Structural diversity of ZFs and structural flexibility of CTEs in the MCM2–7 double hexamer.

a–c, Ribbon representation of ZF motifs of MCM7 (a), MCM3 (b) and MCM5 (c), superimposed with sharpened density map (transparent cyan) at 4σ contour level. Positions of zinc are denoted by red balls. Zinc-binding was not observed in the ZF of MCM3. d, e, Surface representation of the density map (unsharpened, at 1σ contour level) superimposed with colour-coded atomic structures for each MCM subunit, viewed from the CTD ring. Four segmented extra densities are coloured in deep grey (d), with tentative fitting of a winged-helix motif from a crystal structure (PDB code 2KLQ)74 into these four density pieces. e, Same as d, but displayed without extra densities.

Extended Data Figure 4 Subunit-specific structural features of the MCM2–7 subunits.

a, Schematic illustration of domain organization and subunit-specific features of MCM2–7 subunits, with comparison to the archaeal MCM (SS, Sulfolobus solfataricus) (see also Extended Data Fig. 2). Numbered regions correspond to numbered extensions and insertions highlighted in d–i. ‘-’ symbols denote corresponding regions with reliable densities to trace the main chain direction, but not sufficient for atomic modelling. ‘--’ symbols denote sequences with highly disordered densities. b, c, A protomer of the crystal structure of a chimaeric archaeal MCM hexamer structure (PDB code 4R7Y)30 used as the template for modelling. The archaeal MCM was aligned globally (b) or domain-based flexibly fitted (c) to the atomic model of MCM2. d–i, Side-by-side structural comparison of MCM2–7 proteins, with MCM3-7 globally aligned to the atomic model of MCM2. The well-resolved insertions and extensions of each MCM subunit (d–i) are numbered and coloured in red.

Extended Data Figure 5 Intersubunit interactions in the MCM2–7 single hexamer.

a, Interactions at the CTD ring exemplified by the 7:3 interface. The EXT hairpin of MCM3 facilitates the packing of one helix (the α-linker of the α/β subdomain) from MCM7 with another helix (located at the α subdomain of the CTD) from MCM3. b, Interactions at the neck region, as exemplified by the 6:4 interface. PS1-HP of MCM4 is sandwiched between ACL and H2I-N (N-terminal loop/helix of H2I) of MCM6. At the same time, ACL of MCM6 also interacts with H2I-C (C-terminal helix of H2I) of MCM4. c, Interactions at the NTD ring exemplified by the 6:4 interface. The first loop of OB (OB-L1) that flanks NTD-A, and the extended β-turn loop from MCM6 form a cradle for docking the ZF from MCM4. Asterisks mark sites of strong interactions. d–i, Zoomed-in views of intersubunit interactions between NTD-As of each adjacent MCM pair. The unsharpened density map (transparent grey), contoured at the 2.7σ level, is superimposed with the atomic model. Four of the six MCM proteins (3, 5, 6 and 7) contain NTIs at varying locations of their NTD-As (see also Extended Data Fig. 4). Only the NTI of MCM7 is modelled in our structure. Superimposition of the atomic model with the density map indicates that these NTIs all interact with the NTD-As of the adjacent subunit on the left. Extra densities indicating interactions are marked by red asterisks.

Extended Data Figure 6 Cryo-EM densities for different regions of the MCM2–7 double hexamer.

a, Electron microscopy density map (cyan mesh) superimposed with atomic model for NTD-A of MCM7. Two representative α-helices with side chains (right) were displayed in stick representation. b, Electron microscopy density map for the OB and ZF of MCM3. A representative loop of the OB and a strand connecting the OB and ZF with side chains are shown on the right. c, A representative region of inter-hexamer interaction, highlighting the interactions between the β-strands of MCM5-NTE and MCM7-ZF. d, A representative region of intersubunit interaction (MCM4–MCM6), highlighting the hydrophobic interaction between Met342, Phe391 of MCM4 and neighbouring Ile284 of MCM6. e, A representative region of conserved hairpin loops, highlighting H2I of MCM4. Segmented density maps in all panels are displayed at the 5–6σ contour level.

Extended Data Figure 7 A unique side channel between MCM2 and MCM6.

a–f, Outer surface representation of the six subunit interfaces within MCM2–7 single hexamer. a, A unique side channel in the neck region of the M2–M6 interface. The boxed region is shown in a zoomed-in view (right) with individual components (H2I-N, EXT, PS1 and ACL) coloured individually. The size of this side channel is large enough to act as a pore for ssDNA exiting from the central channel during DNA unwinding along with basic residues (Arg566, Lys557 and Lys564) of the EXT hairpin from MCM6. The H2I-N is partially disordered. b–f, Same as a, but at different subunit interfaces. In the case of the 3:5 interface (e), the N–C linker of MCM3 also contributes to the blocking of the channel.

Extended Data Figure 8 ATP-binding site configuration at MCM intersubunit interfaces.

a–f, Zoomed-in views of ATP-binding sites for each MCM dimer. The Walker A and B (WA and WB, respectively) residues of the left subunit, and sensor 3, sensor 2 and arginine finger (AF) residues of the right subunit, are shown in stick model. g, Superimposition of all six active centres. The sensor 3 residues of MCM2 (orange asterisk) and MCM6 (blue asterisk) in the 5:2 and 2:6 dimers display sharply different configurations, resulting in two relatively loose centres. h, i, Superimposition of two representative compact ATPase centres (dimers of 7:3 and 4:7) with that of E1 hexameric helicase (active form)40. j, The ATPase centre (inactive conformation) of an archaeal MCM (PDB code 4R7Y)30. k, l, Superimposition of j with the centres of 2:6 (k) and 7:3 (l). Walker A and B motifs are used as a reference for alignment in all panels. l, A large shift in the sensor 3 of MCM3 is shown by red arrow, compared with the inactive conformation.

Extended Data Figure 9 Nucleotide occupancy at the six ATPase centres of MCM2–7 single hexamer.

a–f, Zoomed-in views of the active centres for all MCM subunit pairs. The conserved ATPase elements of the active centres are labelled. Segmented nucleotide densities at a contour level of 5.5σ were superimposed (transparent grey). Note that nucleotide occupancies at the centres of 6:4 and 3:5 are relatively low. For the 7:3 dimer, there seems to be extra density for γ-phosphate or Mg2+, but could not be confirmed at the current resolution (3.8 Å). Nucleotides were modelled using ADP.

Extended Data Table 1 Statistics of structural determination, model refinement and interface analysis.
Full size table

Supplementary information

Overall structure of the MCM2-7 DH and arrangement of the two ZF rings.

The cryo-EM density map (unsharpened) of the MCM2-7 DH is first shown in surface representation, followed by superimposition of atomic models for each of the MCM proteins one by one. The unique side-channel between MCM2 and MCM6 is highlighted. Subsequently, only the two rings of ZFs, with their atomic models converted to surface representation, are shown in zoom-in views. The two stacked ZF rings are rotated in different directions to highlight the diameter and wall components of a major channel and two minor channels at the DH interface. At last, the surface representation of two ZF pairs of MCM2:MCM5 is hidden, highlighting the proposed fusion of three channels into a larger one upon the gap opening between MCM2 and MCM5. A thumbnail map of the MCM2-7 DH, with the 2-fold axis displayed as a red rod, is shown on the top right corner to illustrate the orientations of individual movie frames relative to the DH. (MP4 18712 kb)

Sharpened density map of the MCM2-7 DH

The cryo-EM density map of the MCM2-7 DH (sharpened) is displayed in surface representation, zoomed into selected regions with atomic models superimposed. (MP4 20759 kb)

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Li, N., Zhai, Y., Zhang, Y. et al. Structure of the eukaryotic MCM complex at 3.8 Å. Nature 524, 186–191 (2015). https://doi.org/10.1038/nature14685

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