8I4X

Cryo-EM structure of 5-subunit Smc5/6


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 8.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


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 31: 1532-1542

  • 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
Structural maintenance of chromosomes protein 51,069Saccharomyces cerevisiae S288CMutation(s): 1 
Gene Names: SMC5
UniProt
Find proteins for Q08204 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Go to UniProtKB:  Q08204
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UniProt GroupQ08204
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Structural maintenance of chromosomes protein 61,104Saccharomyces cerevisiae S288CMutation(s): 1 
Gene Names: SMC6RHC18YLR383WL3502.2
UniProt
Find proteins for Q12749 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Go to UniProtKB:  Q12749
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UniProt GroupQ12749
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
E3 SUMO-protein ligase MMS21267Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: MMS21NSE2YEL019C
EC: 2.3.2
UniProt
Find proteins for P38632 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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UniProt GroupP38632
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Nse6378Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: KRE29
UniProt
Find proteins for P40026 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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  • Reference Sequence
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Non-structural maintenance of chromosome element 5556Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: NSE5YML023C
UniProt
Find proteins for Q03718 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Go to UniProtKB:  Q03718
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UniProt GroupQ03718
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 8.50 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
  • Version 1.2: 2024-10-30
    Changes: Data collection, Database references, Structure summary