4ZDT

Crystal structure of the RING finger domain of Slx1 in complex with the C-terminal domain of Slx4


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.216 

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Literature

Crystal structure and SUMO binding of Slx1-Slx4 complex

Lian, F.M.Xie, S.Qian, C.M.

(2016) Sci Rep 6: 19331-19331

  • DOI: https://doi.org/10.1038/srep19331
  • Primary Citation of Related Structures:  
    4ZDT

  • PubMed Abstract: 

    The SLX1-SLX4 complex is a structure-specific endonuclease that cleaves branched DNA structures and plays significant roles in DNA recombination and repair in eukaryotic cells. The heterodimeric interaction between SLX1 and SLX4 is essential for the endonuclease activity of SLX1. Here, we present the crystal structure of Slx1 C-terminal zinc finger domain in complex with the C-terminal helix-turn-helix domain of Slx4 from Schizosaccharomyces pombe at 2.0 Å resolution. The structure reveals a conserved binding mechanism underling the Slx1-Slx4 interaction. Structural and sequence analyses indicate Slx1 C-terminal domain is actually an atypical C4HC3-type RING finger which normally possesses E3 ubiquitin ligase activity, but here is absolutely required for Slx1 interaction with Slx4. Furthermore, we found the C-terminal tail of S. pombe Slx1 contains a SUMO-interacting motif and can recognize Pmt3 (S. pombe SUMO), suggesting that Slx1-Slx4 complex could be recruited by SUMOylated protein targets to take part in replication associated DNA repair processes.


  • Organizational Affiliation

    School of Biomedical Sciences, The University of Hong Kong, Hong Kong, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Structure-specific endonuclease subunit slx1
A, C
73Schizosaccharomyces pombe 972h-Mutation(s): 0 
Gene Names: slx1SPAP27G11.15
EC: 3.1
UniProt
Find proteins for Q9P7M3 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Explore Q9P7M3 
Go to UniProtKB:  Q9P7M3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9P7M3
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Structure-specific endonuclease subunit slx4
B, D
71Schizosaccharomyces pombe 972h-Mutation(s): 0 
Gene Names: slx4SPAC688.06c
UniProt
Find proteins for Q9P6M0 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Explore Q9P6M0 
Go to UniProtKB:  Q9P6M0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9P6M0
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
N [auth D]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL
Query on GOL

Download Ideal Coordinates CCD File 
G [auth B],
H [auth B],
I [auth B],
L [auth D],
M [auth D]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
E [auth A],
F [auth A],
J [auth C],
K [auth C]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.216 
  • Space Group: P 41
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 85.233α = 90
b = 85.233β = 90
c = 74.835γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
SCALEPACKdata reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Hong Kong Research Grants CouncilHong Kong--

Revision History  (Full details and data files)

  • Version 1.0: 2016-02-03
    Type: Initial release
  • Version 1.1: 2024-03-20
    Changes: Data collection, Database references, Derived calculations