5XW4 | pdb_00005xw4

Crystal structure of budding yeast Cdc14p (wild type) in the apo state

• PDB DOI: https://doi.org/10.2210/pdb5XW4/pdb

• Classification: CELL CYCLE
• Organism(s): Saccharomyces cerevisiae S288C
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2017-06-29 Released: 2017-08-09 
• Deposition Author(s): Kobayashi, J., Matsuura, Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 
  0.203 (Depositor), 0.205 (DCC) 
• R-Value Work: 
  0.178 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.179 (Depositor) 

Starting Model: experimental

Literature

Structure and dimerization of the catalytic domain of the protein phosphatase Cdc14p, a key regulator of mitotic exit in Saccharomyces cerevisiae

Kobayashi, J., Matsuura, Y.

(2017) Protein Sci 26: 2105-2112

• PubMed: 28758351 
• DOI: https://doi.org/10.1002/pro.3244
• Primary Citation Related Structures: 
  5XW4, 5XW5


• PubMed Abstract: 
  

  In the budding yeast Saccharomyces cerevisiae, the protein phosphatase Cdc14p orchestrates various events essential for mitotic exit. We have determined the X-ray crystal structures at 1.85 Å resolution of the catalytic domain of Cdc14p in both the apo state, and as a complex with S160-phosphorylated Swi6p peptide. Each asymmetric unit contains two Cdc14p chains arranged in an intimately associated homodimer, consistent with its oligomeric state in solution. The dimerization interface is located on the backside of the substrate-binding cleft. Structure-based mutational analyses indicate that the dimerization of Cdc14p is required for normal growth of yeast cells.

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Organizational Affiliation: 
• Division of Biological Science, Nagoya University, Japan.
Structural Biology Research Center, Graduate School of Science, Nagoya University, Japan.

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)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 95.28 kDa 
• Atom Count: 6,526 
• Modeled Residue Count: 737 
• Deposited Residue Count: 830 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tyrosine-protein phosphatase CDC14	A, B	415	Saccharomyces cerevisiae S288C	Mutation(s): 0  Gene Names: CDC14, OAF3, YFR028C EC: 3.1.3.48
UniProt
Find proteins for Q00684 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q00684  Go to UniProtKB:  Q00684

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free:  0.203 (Depositor), 0.205 (DCC) 
• R-Value Work:  0.178 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.179 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.85	α = 90
b = 95.13	β = 90
c = 137.76	γ = 90

Software Package:

Software Name	Purpose
Aimless	data scaling
MOLREP	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
iMOSFLM	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-08-09 
Deposition Author(s): Kobayashi, J., Matsuura, Y.

Revision History  

• Version 1.0: 2017-08-09
  Type: Initial release
  
• Version 1.1: 2017-10-25
  Changes: Database references
• Version 1.2: 2023-11-22
  Changes: Data collection, Database references, Refinement description