7DG2

Nse1-Nse3-Nse4 complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.191 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structure Basis for Shaping the Nse4 Protein by the Nse1 and Nse3 Dimer within the Smc5/6 Complex.

Jo, A.Li, S.Shin, J.W.Zhao, X.Cho, Y.

(2021) J Mol Biol 433: 166910-166910

  • DOI: https://doi.org/10.1016/j.jmb.2021.166910
  • Primary Citation of Related Structures:  
    7DG2

  • PubMed Abstract: 

    The Smc5/6 complex facilitates chromosome replication and DNA break repair. Within this complex, a subcomplex composed of Nse1, Nse3 and Nse4 is thought to play multiple roles through DNA binding and regulating ATP-dependent activities of the complex. However, how the Nse1-Nse3-Nse4 subcomplex carries out these multiple functions remain unclear. To address this question, we determine the crystal structure of the Xenopus laevis Nse1-Nse3-Nse4 subcomplex at 1.7 Å resolution and examine how it interacts with DNA. Our structural analyses show that the Nse1-Nse3 dimer adopts a closed conformation and forms three interfaces with a segment of Nse4, forcing it into a Z-shaped conformation. The Nse1-Nse3-Nse4 structure provides an explanation for how the lung disease immunodeficiency and chromosome breakage syndrome-causing mutations could dislodge Nse4 from Nse1-Nse3. Our DNA binding and mutational analyses reveal that the N-terminal and the middle region of Nse4 contribute to DNA interaction and cell viability. Integrating our data with previous crosslink mass spectrometry data, we propose potential roles of the Nse1-Nse3-Nse4 complex in binding DNA within the Smc5/6 complex.


  • Organizational Affiliation

    Department of Life Science, Pohang University of Science and Technology, Pohang, Republic of Korea.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Non-structural maintenance of chromosomes element 1 homolog247Xenopus laevisMutation(s): 0 
Gene Names: nsmce1
EC: 2.3.2.27
UniProt
Find proteins for Q6PAF4 (Xenopus laevis)
Explore Q6PAF4 
Go to UniProtKB:  Q6PAF4
Entity Groups  
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UniProt GroupQ6PAF4
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
MAGE domain-containing proteinB [auth C]217Xenopus laevisMutation(s): 0 
Gene Names: XELAEV_18029664mg
UniProt
Find proteins for A0A1L8G3Z0 (Xenopus laevis)
Explore A0A1L8G3Z0 
Go to UniProtKB:  A0A1L8G3Z0
Entity Groups  
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UniProt GroupA0A1L8G3Z0
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Non-structural maintenance of chromosomes element 4C [auth D]79Xenopus laevisMutation(s): 0 
Gene Names: nsmce4a.LLOC100158435nsmce4a
UniProt
Find proteins for B1WBD6 (Xenopus laevis)
Explore B1WBD6 
Go to UniProtKB:  B1WBD6
Entity Groups  
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UniProt GroupB1WBD6
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.191 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.486α = 90
b = 66.161β = 90
c = 168.367γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Released Date: 2021-05-26 
  • Deposition Author(s): Cho, Y., Jo, A.

Revision History  (Full details and data files)

  • Version 1.0: 2021-05-26
    Type: Initial release
  • Version 1.1: 2023-11-29
    Changes: Data collection, Database references, Refinement description