4D2K | pdb_00004d2k

Crystal structure of DREP2 CIDE domain

• PDB DOI: https://doi.org/10.2210/pdb4D2K/pdb

• Classification: APOPTOSIS
• Organism(s): Drosophila melanogaster
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2014-05-12 Released: 2015-05-27 
• Deposition Author(s): Jang, T.H., Park, H.H., Kim, Y.G., Jeong, J.H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.254 (Depositor), 0.263 (DCC) 
• R-Value Work: 
  0.216 (Depositor) 
• R-Value Observed: 
  0.220 (Depositor) 

Starting Model: experimental

Literature

CIDE domains form functionally important higher-order assemblies for DNA fragmentation.

Choi, J.Y., Qiao, Q., Hong, S.H., Kim, C.M., Jeong, J.H., Kim, Y.G., Jung, Y.K., Wu, H., Park, H.H.

(2017) Proc Natl Acad Sci U S A 114: 7361-7366

• PubMed: 28652364 
• DOI: https://doi.org/10.1073/pnas.1705949114
• Primary Citation Related Structures: 
  4D2K, 5XPC


• PubMed Abstract: 
  

  Cell death-inducing DFF45-like effector (CIDE) domains, initially identified in apoptotic nucleases, form a family with diverse functions ranging from cell death to lipid homeostasis. Here we show that the CIDE domains of Drosophila and human apoptotic nucleases Drep2, Drep4, and DFF40 all form head-to-tail helical filaments. Opposing positively and negatively charged interfaces mediate the helical structures, and mutations on these surfaces abolish nuclease activation for apoptotic DNA fragmentation. Conserved filamentous structures are observed in CIDE family members involved in lipid homeostasis, and mutations on the charged interfaces compromise lipid droplet fusion, suggesting that CIDE domains represent a scaffold for higher-order assembly in DNA fragmentation and other biological processes such as lipid homeostasis.

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Organizational Affiliation: 
• School of Chemistry and Biochemistry and Graduate School of Biochemistry, Yeungnam University, Gyeongsan 712-749, South Korea.
Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115.
Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115.
School of Biological Science, Seoul National University, Seoul 151-747, South Korea.
Pohang Accelerator Laboratory, Pohang University of Science and Technology, Pohang 790-784, South Korea.
Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115; [e-mail] [e-mail].
School of Chemistry and Biochemistry and Graduate School of Biochemistry, Yeungnam University, Gyeongsan 712-749, South Korea; [e-mail] [e-mail].

Biological Assembly 1  

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

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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

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

Biological assembly 4 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 40.25 kDa 
• Atom Count: 2,635 
• Modeled Residue Count: 321 
• Deposited Residue Count: 348 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DREP2	A, B, C, D	87	Drosophila melanogaster	Mutation(s): 0
UniProt
Find proteins for Q7K304 (Drosophila melanogaster) Explore Q7K304  Go to UniProtKB:  Q7K304

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.254 (Depositor), 0.263 (DCC) 
• R-Value Work:  0.216 (Depositor) 
• R-Value Observed: 0.220 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.283	α = 90
b = 88.708	β = 90
c = 113.372	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-05-27 
Deposition Author(s): Jang, T.H., Park, H.H., Kim, Y.G., Jeong, J.H.

Revision History  

• Version 1.0: 2015-05-27
  Type: Initial release
  
• Version 1.1: 2017-06-28
  Changes: Database references
• Version 1.2: 2017-07-12
  Changes: Database references
• Version 1.3: 2017-08-02
  Changes: Database references
• Version 1.4: 2023-12-20
  Changes: Data collection, Database references, Other, Refinement description