8I13

Cryo-EM structure of 6-subunit Smc5/6


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 6.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


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Literature

Cryo-EM structures of Smc5/6 in multiple states reveal its assembly and functional mechanisms.

Li, Q.Zhang, J.Haluska, C.Zhang, X.Wang, L.Liu, G.Wang, Z.Jin, D.Cheng, T.Wang, H.Tian, Y.Wang, X.Sun, L.Zhao, X.Chen, Z.Wang, L.

(2024) Nat Struct Mol Biol 

  • DOI: https://doi.org/10.1038/s41594-024-01319-1
  • Primary Citation of Related Structures:  
    7YLM, 7YMD, 7YQH, 8HQS, 8I13, 8I21, 8I4U, 8I4V, 8I4W, 8I4X, 8WJL, 8WJN, 8WJO

  • PubMed Abstract: 

    Smc5/6 is a member of the eukaryotic structural maintenance of chromosomes (SMC) family of complexes with important roles in genome maintenance and viral restriction. However, limited structural understanding of Smc5/6 hinders the elucidation of its diverse functions. Here, we report cryo-EM structures of the budding yeast Smc5/6 complex in eight-subunit, six-subunit and five-subunit states. Structural maps throughout the entire length of these complexes reveal modularity and key elements in complex assembly. We show that the non-SMC element (Nse)2 subunit supports the overall shape of the complex and uses a wedge motif to aid the stability and function of the complex. The Nse6 subunit features a flexible hook region for attachment to the Smc5 and Smc6 arm regions, contributing to the DNA repair roles of the complex. Our results also suggest a structural basis for the opposite effects of the Nse1-3-4 and Nse5-6 subcomplexes in regulating Smc5/6 ATPase activity. Collectively, our integrated structural and functional data provide a framework for understanding Smc5/6 assembly and function.


  • Organizational Affiliation

    The Center for Microbes, Development and Health, CAS Key Laboratory of Molecular Virology and Immunology, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences,University of Chinese Academy of Sciences, Shanghai, China.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
SMC6 isoform 1A [auth B]1,114Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: SMC6
UniProt
Find proteins for A0A8H4BXH7 (Saccharomyces cerevisiae)
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UniProt GroupA0A8H4BXH7
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Structural maintenance of chromosomes protein 5B [auth A]1,093Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: SMC5
UniProt
Find proteins for A0A6V8S000 (Saccharomyces cerevisiae)
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UniProt GroupA0A6V8S000
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
MMS21 isoform 1267Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: MMS21
UniProt
Find proteins for A0A8H8ULJ5 (Saccharomyces cerevisiae)
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UniProt GroupA0A8H8ULJ5
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Non-structural maintenance of chromosomes element 1 homologD [auth F]336Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: NSE1
UniProt
Find proteins for A0A8H4F9V3 (Saccharomyces cerevisiae)
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UniProt GroupA0A8H4F9V3
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
NSE3 isoform 1E [auth G]303Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: NSE3
UniProt
Find proteins for A0A8H8UNJ0 (Saccharomyces cerevisiae)
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UniProt GroupA0A8H8UNJ0
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Non-structural maintenance of chromosomes element 4F [auth H]402Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: NSE4
UniProt
Find proteins for A0A6L0Z6W9 (Saccharomyces cerevisiae)
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UniProt GroupA0A6L0Z6W9
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 6.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other government--

Revision History  (Full details and data files)

  • Version 1.0: 2024-06-26
    Type: Initial release
  • Version 1.1: 2024-07-03
    Changes: Data collection, Database references