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
  • Primary Citation of Related Structures:  
    4XLG, 4XM5

  • 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 time, little is known about the structure of SLX1-SLX4 or its mechanism of action ...

    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
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Structure-specific endonuclease subunit SLX4A [auth B]80[Candida] glabrata CBS 138Mutation(s): 0 
Gene Names: SLX4, CAGL0M04389g
UniProt
Find proteins for Q6FJQ6 (Candida glabrata (strain ATCC 2001 / CBS 138 / JCM 3761 / NBRC 0622 / NRRL Y-65))
Explore Q6FJQ6 
Go to UniProtKB:  Q6FJQ6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6FJQ6
Protein Feature View
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  • Reference Sequence
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(by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Structure-specific endonuclease subunit SLX1B [auth A]312[Candida] glabrata CBS 138Mutation(s): 1 
Gene Names: SLX1, CAGL0K06941g
EC: 3.1
UniProt
Find proteins for Q6FML9 (Candida glabrata (strain ATCC 2001 / CBS 138 / JCM 3761 / NBRC 0622 / NRRL Y-65))
Explore Q6FML9 
Go to UniProtKB:  Q6FML9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6FML9
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN
Download Ideal Coordinates CCD File 
C [auth A],
D [auth A]		ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N		 Ligand Interaction
CL
Query on CL
Download Ideal Coordinates CCD File 
E [auth A],
F [auth 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

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Wellcome TrustUnited Kingdom98022

Revision History  (Full details and data files)

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