7T5P

Cryo-EM structure of human SIMC1-SLF2 complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

The Nse5/6-like SIMC1-SLF2 complex localizes SMC5/6 to viral replication centers.

Oravcova, M.Nie, M.Zilio, N.Maeda, S.Jami-Alahmadi, Y.Lazzerini-Denchi, E.Wohlschlegel, J.A.Ulrich, H.D.Otomo, T.Boddy, M.

(2022) Elife 11

  • DOI: https://doi.org/10.7554/eLife.79676
  • Primary Citation of Related Structures:  
    7T5P

  • PubMed Abstract: 

    The human SMC5/6 complex is a conserved guardian of genome stability and an emerging component of antiviral responses. These disparate functions likely require distinct mechanisms of SMC5/6 regulation. In yeast, Smc5/6 is regulated by its Nse5/6 subunits, but such regulatory subunits for human SMC5/6 are poorly defined. Here, we identify a novel SMC5/6 subunit called SIMC1 that contains SUMO interacting motifs (SIMs) and an Nse5-like domain. We isolated SIMC1 from the proteomic environment of SMC5/6 within polyomavirus large T antigen (LT)-induced subnuclear compartments. SIMC1 uses its SIMs and Nse5-like domain to localize SMC5/6 to polyomavirus replication centers (PyVRCs) at SUMO-rich PML nuclear bodies. SIMC1's Nse5-like domain binds to the putative Nse6 orthologue SLF2 to form an anti-parallel helical dimer resembling the yeast Nse5/6 structure. SIMC1-SLF2 structure-based mutagenesis defines a conserved surface region containing the N-terminus of SIMC1's helical domain that regulates SMC5/6 localization to PyVRCs. Furthermore, SLF1, which recruits SMC5/6 to DNA lesions via its BRCT and ARD motifs, binds SLF2 analogously to SIMC1 and forms a separate Nse5/6-like complex. Thus, two Nse5/6-like complexes with distinct recruitment domains control human SMC5/6 localization.


  • Organizational Affiliation

    Department of Molecular Medicine, The Scripps Research Institute, La Jolla, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
SUMO-interacting motif-containing protein 1589Homo sapiensMutation(s): 2 
Gene Names: SIMC1C5orf25PLEIAD
UniProt & NIH Common Fund Data Resources
Find proteins for Q8NDZ2 (Homo sapiens)
Explore Q8NDZ2 
Go to UniProtKB:  Q8NDZ2
PHAROS:  Q8NDZ2
GTEx:  ENSG00000170085 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8NDZ2
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
SMC5-SMC6 complex localization factor protein 2539Homo sapiensMutation(s): 0 
Gene Names: SLF2C10orf6FAM178A
UniProt & NIH Common Fund Data Resources
Find proteins for Q8IX21 (Homo sapiens)
Explore Q8IX21 
Go to UniProtKB:  Q8IX21
PHAROS:  Q8IX21
GTEx:  ENSG00000119906 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8IX21
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM092740
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM136273

Revision History  (Full details and data files)

  • Version 1.0: 2022-12-07
    Type: Initial release