8I4V

Cryo-EM structure of 5-subunit Smc5/6 arm region


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 5.97 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 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 

  • 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))
Explore Q08204 
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 61,114Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SMC6
UniProt
Find proteins for Q12749 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q12749 
Go to UniProtKB:  Q12749
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UniProt GroupQ12749
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
E3 SUMO-protein ligase MMS21251Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: NSE2
EC: 2.3.2
UniProt
Find proteins for P38632 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P38632 
Go to UniProtKB:  P38632
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UniProt GroupP38632
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
DNA repair protein KRE2964Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: KRE29YER038C
UniProt
Find proteins for P40026 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P40026 
Go to UniProtKB:  P40026
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UniProt GroupP40026
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 5.97 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