2D2Z | pdb_00002d2z

Crystal structure of Soluble Form Of CLIC4

• PDB DOI: https://doi.org/10.2210/pdb2D2Z/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2005-09-21 Released: 2006-05-16 
• Deposition Author(s): Li, Y.F., Li, D.F., Wang, D.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.262 (Depositor), 0.254 (DCC) 
• R-Value Work: 
  0.216 (Depositor), 0.212 (DCC) 
• R-Value Observed: 
  0.216 (Depositor) 

Literature

Trimeric structure of the wild soluble chloride intracellular ion channel CLIC4 observed in crystals

Li, Y.F., Li, D.F., Zeng, Z.H., Wang, D.C.

(2006) Biochem Biophys Res Commun 343: 1272-1278

• PubMed: 16581025 
• DOI: https://doi.org/10.1016/j.bbrc.2006.03.099
• Primary Citation Related Structures: 
  2D2Z


• PubMed Abstract: 
  

  The crystal structure of a wild type of the human soluble chloride intracellular ion channel CLIC4 (wCLIC4) has been determined at a resolution of 2.2A. The structure shows a homotrimer in an asymmetric unit, which is first observed in CLICs. The assembly of the trimer takes a unique triple interaction mode between three monomers with a hydrogen-bond network and hydrophobic contacts. Through such complicated interactions, the homotrimer of wCLIC4 is firmly stabilized. The structure shows an oligomeric mode with a unique assembly mechanism by which the oligomerization of CLIC4 can be performed without any intramolecular disulfide bond formation. It indicated a possibility that CLIC4 may take a unique structural organization distinct from CLIC1 for docking with lipid bilayers. In addition, the structure shows distinct conformational states of the h2 region for respective monomers of the trimer, which reveal an intrinsic conformational susceptibility for this significant region in the structural transition.

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Organizational Affiliation: 
• National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, People's Republic of China.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly 3  

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

Biological assembly 3 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 89.64 kDa 
• Atom Count: 6,238 
• Modeled Residue Count: 694 
• Deposited Residue Count: 783 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Chloride intracellular channel protein 4	A, B, C	261	Homo sapiens	Mutation(s): 0  EC: 1.8
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y696 (Homo sapiens) Explore Q9Y696  Go to UniProtKB:  Q9Y696
PHAROS:  Q9Y696 GTEx:  ENSG00000169504

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.262 (Depositor), 0.254 (DCC) 
• R-Value Work:  0.216 (Depositor), 0.212 (DCC) 
• R-Value Observed: 0.216 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.19	α = 90
b = 86.05	β = 112.99
c = 73.38	γ = 90

Software Package:

Software Name	Purpose
crystal	data collection
SCALA	data scaling
CCP4	model building
CNS	refinement
CrystalClear	data reduction
CCP4	data scaling
CCP4	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-05-16 
Deposition Author(s): Li, Y.F., Li, D.F., Wang, D.C.

Revision History  

• Version 1.0: 2006-05-16
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-11
  Changes: Refinement description
• Version 1.4: 2024-03-13
  Changes: Data collection, Database references