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TitleCryo-EM structure of DNA-bound Smc5/6 reveals DNA clamping enabled by multi-subunit conformational changes.
Journal, issue, pagesProc Natl Acad Sci U S A, Vol. 119, Issue 23, Page e2202799119, Year 2022
Publish dateJun 7, 2022
AuthorsYou Yu / Shibai Li / Zheng Ser / Huihui Kuang / Thane Than / Danying Guan / Xiaolan Zhao / Dinshaw J Patel /
PubMed AbstractStructural maintenance of chromosomes (SMC) complexes are essential for chromatin organization and functions throughout the cell cycle. The cohesin and condensin SMCs fold and tether DNA, while ...Structural maintenance of chromosomes (SMC) complexes are essential for chromatin organization and functions throughout the cell cycle. The cohesin and condensin SMCs fold and tether DNA, while Smc5/6 directly promotes DNA replication and repair. The functions of SMCs rely on their abilities to engage DNA, but how Smc5/6 binds and translocates on DNA remains largely unknown. Here, we present a 3.8 Å cryogenic electron microscopy (cryo-EM) structure of DNA-bound Saccharomyces cerevisiae Smc5/6 complex containing five of its core subunits, including Smc5, Smc6, and the Nse1-3-4 subcomplex. Intricate interactions among these subunits support the formation of a clamp that encircles the DNA double helix. The positively charged inner surface of the clamp contacts DNA in a nonsequence-specific manner involving numerous DNA binding residues from four subunits. The DNA duplex is held up by Smc5 and 6 head regions and positioned between their coiled-coil arm regions, reflecting an engaged-head and open-arm configuration. The Nse3 subunit secures the DNA from above, while the hook-shaped Nse4 kleisin forms a scaffold connecting DNA and all other subunits. The Smc5/6 DNA clamp shares similarities with DNA-clamps formed by other SMCs but also exhibits differences that reflect its unique functions. Mapping cross-linking mass spectrometry data derived from DNA-free Smc5/6 to the DNA-bound Smc5/6 structure identifies multi-subunit conformational changes that enable DNA capture. Finally, mutational data from cells reveal distinct DNA binding contributions from each subunit to Smc5/6 chromatin association and cell fitness. In summary, our integrative study illuminates how a unique SMC complex engages DNA in supporting genome regulation.
External linksProc Natl Acad Sci U S A / PubMed:35648833 / PubMed Central
MethodsEM (single particle)
Resolution3.8 Å
Structure data

26140

7tve

EMDB-26140, PDB-7tve:
ATP and DNA bound SMC5/6 core complex
Method: EM (single particle) / Resolution: 3.8 Å

Chemicals

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM

Source
  • saccharomyces cerevisiae w303 (yeast)
  • synthetic construct (others)
KeywordsDNA BINDING PROTEIN/DNA / Nse1 / Nse3 / Nse4 / Smc5 / Smc6 / Nse2 / ATP / DNA BINDING PROTEIN-DNA complex

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