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PDBsum entry 3bwe

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protein ligands Protein-protein interface(s) links
Chaperone PDB id
3bwe
Jmol PyMol
Contents
Protein chain
(+ 1 more) 188 a.a. *
Ligands
PO4 ×7
Waters ×283
* Residue conservation analysis
PDB id:
3bwe
Name: Chaperone
Title: Crystal structure of aggregated form of dj1
Structure: Protein dj-1. Chain: a, b, c, d, e, f, g. Synonym: oncogene dj1, parkinson disease protein 7. Engineered: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Gene: park7. Expressed in: escherichia coli. Expression_system_taxid: 562
Resolution:
2.40Å     R-factor:   0.232     R-free:   0.282
Authors: S.S.Cha
Key ref:
S.S.Cha et al. (2008). Crystal structure of filamentous aggregates of human DJ-1 formed in an inorganic phosphate-dependent manner. J Biol Chem, 283, 34069-34075. PubMed id: 18922803 DOI: 10.1074/jbc.M804243200
Date:
09-Jan-08     Release date:   14-Oct-08    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q99497  (PARK7_HUMAN) -  Protein DJ-1
Seq:
Struc:
189 a.a.
188 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cell body   20 terms 
  Biological process     mitochondrion organization   93 terms 
  Biochemical function     protein binding     33 terms  

 

 
DOI no: 10.1074/jbc.M804243200 J Biol Chem 283:34069-34075 (2008)
PubMed id: 18922803  
 
 
Crystal structure of filamentous aggregates of human DJ-1 formed in an inorganic phosphate-dependent manner.
S.S.Cha, H.I.Jung, H.Jeon, Y.J.An, I.K.Kim, S.Yun, H.J.Ahn, K.C.Chung, S.H.Lee, P.G.Suh, S.O.Kang.
 
  ABSTRACT  
 
Mutations in the DJ-1 gene have been implicated in the autosomal recessive early onset parkinsonism. DJ-1 is a soluble dimeric protein with critical roles in response to oxidative stress and in neuronal maintenance. However, several lines of evidence suggest the existence of a nonfunctional aggregated form of DJ-1 in the brain of patients with some neurodegenerative diseases. Here, we show that inorganic phosphate, an important anion that exhibits elevated levels in patients with Parkinson disease, transforms DJ-1 into filamentous aggregates. According to the 2.4-A crystal structure, DJ-1 dimers are linearly stacked through P(i)-mediated interactions to form protofilaments, which are then bundled into a filamentous assembly.
 
  Selected figure(s)  
 
Figure 3.
Structure of DJ-1. A, ribbon diagram of a DJ-1 dimer in the reference orientation. I[x]L and I[x]R stand for the left and right monomers of an I[x] dimer in this orientation, respectively. To distinguish monomers in the dimer, I[x]L is covered with transparent surface. The 2-fold axis is vertical to the figure. Green dots represent sites involved in lateral interactions, sticks represent residues implicated in the F contacts, and red spheres represent P[i]. The vertical line with arrows at both ends represents the protofilament axis, that is, the rotational axis. B, ribbon drawing of a protofilament. I[1–6]L and I[1–6]R monomers are shown in pink and lime, respectively. For emphasis on the identity between I[0] and I[7] dimers, the two dimers are differently colored; the left and right monomers of I[0] and I[7] dimers are in yellow and magenta, respectively. The long line shows one longitudinal repeat unit of a protofilament. Green ellipses indicate the location of grooves involved in the lateral interactions between protofilaments, and curved green lines show the prominence regions. P[i]s are shown as blue spheres. The boxed region is the F interface between I[0] and I[1] dimers. The 2-fold axis of the F interface is vertical to the figure. C, the final 2F[o] - F[c] electron density map, contoured at 1 σ, showing Arg^48 and an inorganic phosphate. D, front view of the boxed region of B. Residues implicated in the F contacts are labeled and represented by sticks. Oxygen, nitrogen, and sulfur atoms are shown in red, blue, and yellow, respectively. The color scheme for carbon atoms is identical to that in Fig. 1B. Polar interactions between atoms are shown as dashed white lines. E, side view of the boxed region of B. The color scheme for carbon atoms is identical to that in Fig. 1B.
Figure 4.
Lateral arrangements among protofilaments. A, top, schematic drawing of the top view. Each circle represents one protofilament, and red lines show the contacts between protofilaments. Bottom, packing model of seven protofilaments simulated in QUANTA. The green ellipsoids show that the central protofilament in red makes no contact with two neighboring protofilaments. B, left panel, surface representation showing a lateral contact between the central protofilament in red and the blue protofilament in A. The three long lines indicate the longitudinal repeat units of protofilaments, and the four short arrows represent the protofilament axes. The green box covers the only contact between the longitudinal repeat unit of the central protofilament and the adjacent protofilament in blue. There are no lateral interactions in the green circle, although slight contacts between protofilaments are seen because of the figure orientation. Right panel, the close-up view of the region covered by the green box in the left figure. The surfaces are transparently represented to show the interior. The residues implicated in the lateral interactions are represented by sticks and labeled. Oxygen and nitrogen are shown in red and blue, respectively. Polar interactions between atoms are shown as dashed black lines.
 
  The above figures are reprinted from an Open Access publication published by the ASBMB: J Biol Chem (2008, 283, 34069-34075) copyright 2008.  
  Figures were selected by an automated process.  

 

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