4XLG

C. glabrata Slx1 in complex with Slx4CCD.

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.78 Å
  • R-Value Free: 0.182 
  • R-Value Work: 0.158 
  • R-Value Observed: 0.159 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history. 


Literature

Structural and Mechanistic Analysis of the Slx1-Slx4 Endonuclease.

Gaur, V., Wyatt, H.D., Komorowska, W., Szczepanowski, R.H., de Sanctis, D., Gorecka, K.M., West, S.C., Nowotny, M.

(2015) Cell Rep 10: 1467-1476

  • DOI: 10.1016/j.celrep.2015.02.019
  • Structures With Same Primary Citation

  • PubMed Abstract: 

    • The SLX1-SLX4 endonuclease required for homologous recombination and DNA repair in eukaryotic cells cleaves a variety of branched DNA structures. The nuclease subunit SLX1 is activated by association with a scaffolding protein SLX4. At the present ti ...

    The SLX1-SLX4 endonuclease required for homologous recombination and DNA repair in eukaryotic cells cleaves a variety of branched DNA structures. The nuclease subunit SLX1 is activated by association with a scaffolding protein SLX4. At the present time, little is known about the structure of SLX1-SLX4 or its mechanism of action. Here, we report the structural insights into SLX1-SLX4 by detailing the crystal structure of Candida glabrata (Cg) Slx1 alone and in combination with the C-terminal region of Slx4. The structure of Slx1 reveals a compact arrangement of the GIY-YIG nuclease and RING domains, which is reinforced by a long α helix. Slx1 forms a stable homodimer that blocks its active site. Slx1-Slx4 interaction is mutually exclusive with Slx1 homodimerization, suggesting a mechanism for Slx1 activation by Slx4.

    Organizational Affiliation: 

    Laboratory of Protein Structure, International Institute of Molecular and Cell Biology, 4 Księcia Trojdena Street, 02-109 Warsaw, Poland. Electronic address: mnowotny@iimcb.gov.pl.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Structure-specific endonuclease subunit SLX4
B
80[Candida] glabrata CBS 138Mutation(s): 0 
Gene Names: SLX4, CAGL0M04389g
Find proteins for Q6FJQ6 (Candida glabrata (strain ATCC 2001 / CBS 138 / JCM 3761 / NBRC 0622 / NRRL Y-65))
Go to UniProtKB:  Q6FJQ6

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Structure-specific endonuclease subunit SLX1
A
312[Candida] glabrata CBS 138Mutation(s): 1 
Gene Names: SLX1, CAGL0K06941g
EC: 3.1
Find proteins for Q6FML9 (Candida glabrata (strain ATCC 2001 / CBS 138 / JCM 3761 / NBRC 0622 / NRRL Y-65))
Go to UniProtKB:  Q6FML9
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N		 Ligand Interaction
CL
Query on CL
Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.78 Å
  • R-Value Free: 0.182 
  • R-Value Work: 0.158 
  • R-Value Observed: 0.159 
  • Space Group: P 63
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 135.79α = 90
b = 135.79β = 90
c = 56.71γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
PHASERphasing
XSCALEdata scaling

Structure Validation

View Full Validation Report


View more in-depth experimental data

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Wellcome TrustUnited Kingdom98022

Revision History 

  • Version 1.0: 2015-03-25
    Type: Initial release
  • Version 1.1: 2015-05-20
    Changes: Database references