9EE7 | pdb_00009ee7

Folded domains of Xrs2 from S.cerevisiae

• PDB DOI: https://doi.org/10.2210/pdb9EE7/pdb

• Classification: PROTEIN BINDING
• Organism(s): Saccharomyces cerevisiae
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-11-18 Released: 2025-09-10 
• Deposition Author(s): Vigneswaran, A., Shi, K., Evans, R., Aihara, H., Latham, M.P.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.38 Å
• R-Value Free: 
  0.311 (Depositor), 0.311 (DCC) 
• R-Value Work: 
  0.298 (Depositor), 0.298 (DCC) 
• R-Value Observed: 
  0.299 (Depositor) 

Starting Model: in silico

Literature

Crystal structure of the folded domains of Xrs2 from Saccharomyces cerevisiae.

Vigneswaran, A., Shi, K., Aihara, H., Evans 3rd, R.L., Latham, M.P.

(2025) Acta Crystallogr F Struct Biol Commun 81: 365-373

• PubMed: 40767353 
• DOI: https://doi.org/10.1107/S2053230X25006867
• Primary Citation of Related Structures:  
  9EE7


• PubMed Abstract: 
  

  The MRE11-RAD50-NBS1/Xrs2 (MRN/X) protein complex acts as a first responder in DNA double-strand break repair and telomere-length maintenance, yet the structural architecture of the yeast ortholog Xrs2 has remained unresolved. In this study, we present the first structure of the folded N-terminal region of Xrs2 from Saccharomyces cerevisiae, resolved at 2.38 Å using X-ray crystallography. Like the previously determined crystal structures of Schizosaccharomyces pombe Nbs1, the folded structure of S. cerevisiae Xrs2 adopts an extended three-domain organization at its N-terminus. Electrostatic analysis reveals two distinct charged patches: a positively charged patch on the FHA domain and a negatively charged patch in the cleft between the FHA and BRCT1 domains. This charge segregation is likely to play a role in mediating interactions with various ligands.

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Organizational Affiliation: 
• Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 37.17 kDa 
• Atom Count: 2,182 
• Modeled Residue Count: 300 
• Deposited Residue Count: 325 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA repair protein XRS2	A	325	Saccharomyces cerevisiae	Mutation(s): 0  Gene Names: XRS2, YDR369C, D9481.13
UniProt
Find proteins for P33301 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P33301  Go to UniProtKB:  P33301

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.38 Å
• R-Value Free:  0.311 (Depositor), 0.311 (DCC) 
• R-Value Work:  0.298 (Depositor), 0.298 (DCC) 
• R-Value Observed: 0.299 (Depositor) 

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.843	α = 90
b = 84.843	β = 90
c = 316.716	γ = 120

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-09-10 
Deposition Author(s): Vigneswaran, A., Shi, K., Evans, R., Aihara, H., Latham, M.P.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R35GM128906

Revision History  

• Version 1.0: 2025-09-10
  Type: Initial release