4XM5 | pdb_00004xm5

C. glabrata Slx1.

• PDB DOI: https://doi.org/10.2210/pdb4XM5/pdb

• Classification: HYDROLASE
• Organism(s): Nakaseomyces glabratus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2015-01-14 Released: 2015-03-25 
• Deposition Author(s): Gaur, V., Wyatt, H.D.M., Komorowska, W., Szczepanowski, R.H., de Sanctis, D., Gorecka, K.M., West, S.C., Nowotny, M.
• Funding Organization(s): Wellcome Trust

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.34 Å
• R-Value Free: 
  0.251 (Depositor), 0.254 (DCC) 
• R-Value Work: 
  0.191 (Depositor), 0.197 (DCC) 
• R-Value Observed: 
  0.197 (Depositor) 

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

• PubMed: 25753413 
• DOI: https://doi.org/10.1016/j.celrep.2015.02.019
• Primary Citation 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. 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.

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Organizational Affiliation: 
• Laboratory of Protein Structure, International Institute of Molecular and Cell Biology, 4 Księcia Trojdena Street, 02-109 Warsaw, Poland.
London Research Institute, Cancer Research UK, Clare Hall Laboratories, Blanche Lane, South Mimms, Herts EN6 3LD, UK.
Biophysics Core Facility, International Institute of Molecular and Cell Biology, 4 Księcia Trojdena Street, 02-109 Warsaw, Poland.
European Synchrotron Radiation Facility (ESRF), 71 Avenue des Martyrs, CS 40220, 38043 Grenoble Cédex 9, France.
Laboratory of Protein Structure, International Institute of Molecular and Cell Biology, 4 Księcia Trojdena Street, 02-109 Warsaw, Poland. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 36.65 kDa 
• Atom Count: 2,207 
• Modeled Residue Count: 267 
• Deposited Residue Count: 312 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Structure-specific endonuclease subunit SLX1	A	312	Nakaseomyces glabratus	Mutation(s): 0  Gene Names: SLX1, CAGL0K06941g EC: 3.1
UniProt
Find proteins for Q6FML9 (Candida glabrata (strain ATCC 2001 / BCRC 20586 / JCM 3761 / NBRC 0622 / NRRL Y-65 / CBS 138)) Explore Q6FML9  Go to UniProtKB:  Q6FML9

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	B [auth A], C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CL	D [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.34 Å
• R-Value Free:  0.251 (Depositor), 0.254 (DCC) 
• R-Value Work:  0.191 (Depositor), 0.197 (DCC) 
• R-Value Observed: 0.197 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.486	α = 90
b = 57.486	β = 90
c = 183.642	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHENIX	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2015-03-25 
Deposition Author(s): Gaur, V., Wyatt, H.D.M., Komorowska, W., Szczepanowski, R.H., de Sanctis, D., Gorecka, K.M., West, S.C., Nowotny, M.

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Funding Organization	Location	Grant Number
Wellcome Trust	United Kingdom	98022

Revision History  

• Version 1.0: 2015-03-25
  Type: Initial release
  
• Version 1.1: 2015-05-20
  Changes: Database references
• Version 1.2: 2024-05-08
  Changes: Data collection, Database references