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 9K7Q | pdb_00009k7q

Parkinson disease protein 7 (DJ-1) and Alpha-synuclein (Alpha-syn) complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.58 Å
  • R-Value Free: 
    0.222 (Depositor), 0.290 (DCC) 
  • R-Value Work: 
    0.145 (Depositor), 0.193 (DCC) 
  • R-Value Observed: 
    0.149 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 9K7Q

This is version 1.1 of the entry. See complete history. 

Literature

Structural basis of alpha-synuclein and DJ-1 complex.

Kim, H.J., Kim, D.H., Han, C.W., Jeong, M.S., Jang, S.B.

(2026) Int J Biol Macromol 379: 154021-154021

  • DOI: https://doi.org/10.1016/j.ijbiomac.2026.154021
  • Primary Citation Related Structures: 
    9K7Q

  • PubMed Abstract: 

    The structure of α-synuclein is predominantly α-helical when bound to cellular membranes. However, under pathological or destabilizing conditions, this α-helical structure transitions into β-sheet-rich conformations, promoting protein aggregation and formation of Lewy bodies (LBs) in neurodegenerative disorders such as Parkinson's disease dementia (PDD), dementia with Lewy bodies (DLB), multiple system atrophy (MSA), and Alzheimer's disease (AD). DJ-1 is a multifunctional brain protein acting as a chaperone or protease under oxidative stress and associating with abnormal protein aggregates. Although previous studies suggested DJ-1 inhibits α-synuclein aggregation, the structural basis remained elusive. Here, we elucidate the direct interaction between α-synuclein and DJ-1 using size-exclusion chromatography (SEC), fluorescence spectroscopy, and multi-angle light scattering (MALS), and determined their crystal structure by X-ray diffraction. The interaction interface was mapped to residues Q24, E28, A29, and N65 of α-synuclein and K148, N173, and Q180 of DJ-1, with Q180 forming strong hydrogen bonds (2.60-2.97 Å) with α-synuclein. Transmission electron microscopy (TEM) demonstrated DJ-1 suppresses α-synuclein fibril formation. Based on the structure, we designed a DJ-1-derived peptide (173-180) that significantly inhibited α-synuclein aggregation in TEM and ELISA assays, suggesting its potential as a therapeutic candidate for α-synucleinopathies.


  • Organizational Affiliation: 
    • Institute of Systems Biology, Pusan National University, Jangjeon-dong, Geumjeong-gu, Busan, 46241, Republic of Korea.

Macromolecule Content 

  • Total Structure Weight: 127.13 kDa 
  • Atom Count: 8,885 
  • Modeled Residue Count: 1,214 
  • Deposited Residue Count: 1,214 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Parkinson disease protein 7187Homo sapiensMutation(s): 0 
Gene Names: PARK7
EC: 3.1.2 (PDB Primary Data), 3.5.1 (PDB Primary Data), 3.5.1.124 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for Q99497 (Homo sapiens)
Explore Q99497 
Go to UniProtKB:  Q99497
GTEx:  ENSG00000116288 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ99497
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Alpha-synucleinG [auth M]92Homo sapiensMutation(s): 0 
Gene Names: SNCA, NACP, PARK1
UniProt & NIH Common Fund Data Resources
Find proteins for P37840 (Homo sapiens)
Explore P37840 
Go to UniProtKB:  P37840
GTEx:  ENSG00000145335 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP37840
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.58 Å
  • R-Value Free:  0.222 (Depositor), 0.290 (DCC) 
  • R-Value Work:  0.145 (Depositor), 0.193 (DCC) 
  • R-Value Observed: 0.149 (Depositor) 
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 75.285α = 89.89
b = 75.274β = 89.92
c = 75.39γ = 60.04
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata scaling
HKL-2000data reduction

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2025-10-29
    Type: Initial release
  • Version 1.1: 2026-11-11
    Changes: Database references