Article | Published:

Structure of the eukaryotic MCM complex at 3.8 Å

Nature volume 524, pages 186191 (13 August 2015) | Download Citation

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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Accessions

Primary accessions

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.).

Author information

Author notes

    • Ningning Li
    •  & Yuanliang Zhai

    These authors contributed equally to this work.

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, New York 14853, USA

    • Bik-Kwoon Tye

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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.

Competing interests

The authors declare no competing financial interests.

Corresponding authors

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

Extended data

Supplementary information

Videos

  1. 1.

    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.

  2. 2.

    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.

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https://doi.org/10.1038/nature14685

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