4P35

Crystal structure of DJ-1 with Zinc(II) bound (crystal I)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.171 
  • R-Value Work: 0.142 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Thermodynamic and Structural Characterization of the Specific Binding of Zn(II) to Human Protein DJ-1.

Tashiro, S.Caaveiro, J.M.Wu, C.X.Hoang, Q.Q.Tsumoto, K.

(2014) Biochemistry 53: 2218-2220

  • DOI: 10.1021/bi500294h
  • Primary Citation of Related Structures:  
  • Also Cited By: 6AFL, 6AFJ, 6AFI, 6AFH, 6AFG, 6AFF, 6AFE, 6AFD, 6AFC, 6AFB, 6AFA, 6AF9, 6AF7, 6AF5

  • PubMed Abstract: 
  • Mutations of DJ-1 cause familial Parkinson's disease (PD), although the role of DJ-1 in PD remains unresolved. Very recent reports have shown that DJ-1 interacts with copper ions. This evidence opens new avenues to understanding the function of DJ-1 ...

    Mutations of DJ-1 cause familial Parkinson's disease (PD), although the role of DJ-1 in PD remains unresolved. Very recent reports have shown that DJ-1 interacts with copper ions. This evidence opens new avenues to understanding the function of DJ-1 and its role in PD. Herein, we report that Zn(II) binds to DJ-1 with great selectivity among the other metals examined: Mn(II), Fe(II), Co(II), Ni(II), and Cu(II). High-resolution X-ray crystallography (1.18 Å resolution) shows Zn(II) is coordinated to the protein by the key residues Cys106 and Glu18. These results suggest that DJ-1 may be regulated and/or stabilized by Zn(II).


    Organizational Affiliation

    Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo , Kashiwa 277-8562, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Protein DJ-1
A
189Homo sapiensMutation(s): 0 
Gene Names: PARK7
EC: 3.1.2.-, 3.5.1.-, 3.5.1.124
Find proteins for Q99497 (Homo sapiens)
Go to Gene View: PARK7
Go to UniProtKB:  Q99497
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download SDF File 
Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
GOL
Query on GOL

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Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.171 
  • R-Value Work: 0.142 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 75.130α = 90.00
b = 75.130β = 90.00
c = 75.540γ = 120.00
Software Package:
Software NamePurpose
PHASERphasing
REFMACrefinement
SCALAdata scaling
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-04-09
    Type: Initial release
  • Version 1.1: 2014-05-14
    Type: Database references
  • Version 1.2: 2014-07-23
    Type: Structure summary
  • Version 1.3: 2015-09-23
    Type: Other
  • Version 1.4: 2017-11-22
    Type: Data collection, Derived calculations, Refinement description