4JGF | pdb_00004jgf

Crystal Structure of the Cataract-Causing P23T gamma D-Crystallin Mutant

• PDB DOI: https://doi.org/10.2210/pdb4JGF/pdb

• Classification: STRUCTURAL PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2013-03-01 Released: 2013-05-22 
• Deposition Author(s): Ji, F.L., Koharudin, L.M., Jung, J.W., Gronenborn, A.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.284 (Depositor), 0.283 (DCC) 
• R-Value Work: 
  0.228 (Depositor), 0.229 (DCC) 
• R-Value Observed: 
  0.233 (Depositor) 

Literature

Crystal structure of the cataract-causing P23T gamma D-crystallin mutant.

Ji, F., Koharudin, L.M., Jung, J., Gronenborn, A.M.

(2013) Proteins 81: 1493-1498

• PubMed: 23670788 
• DOI: https://doi.org/10.1002/prot.24321
• Primary Citation Related Structures: 
  4JGF


• PubMed Abstract: 
  

  Up to now, efforts to crystallize the cataract-associated P23T mutant of human γD-crystallin have not been successful. Therefore, insights into the light scattering mechanism of this mutant have been exclusively obtained from solution work. Here we present the first crystal structure of the P23T mutant at 2.5 Å resolution. The protein exhibits essentially the same overall structure as seen for the wild-type protein. Based on our structural data, we confirm that no major conformational changes are caused by the mutation, and that solution phase properties of the mutant appear exclusively associated with cataract formation.

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Organizational Affiliation: 
• Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, 15261; School of Life Science and Biotechnology, Dalian University of Technology, Lingong Road, Dalian, 16024, China.

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)

Macromolecule Content 

• Total Structure Weight: 40.81 kDa 
• Atom Count: 2,871 
• Modeled Residue Count: 341 
• Deposited Residue Count: 342 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Gamma-crystallin D	A, B	171	Homo sapiens	Mutation(s): 1  Gene Names: CRYGD, CRYG4
UniProt & NIH Common Fund Data Resources
Find proteins for P07320 (Homo sapiens) Explore P07320  Go to UniProtKB:  P07320
PHAROS:  P07320 GTEx:  ENSG00000118231

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.284 (Depositor), 0.283 (DCC) 
• R-Value Work:  0.228 (Depositor), 0.229 (DCC) 
• R-Value Observed: 0.233 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 37.55	α = 90
b = 101.931	β = 96.54
c = 41.371	γ = 90

Software Package:

Software Name	Purpose
StructureStudio	data collection
PHASER	phasing
REFMAC	refinement
d*TREK	data reduction
d*TREK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-05-22 
Deposition Author(s): Ji, F.L., Koharudin, L.M., Jung, J.W., Gronenborn, A.M.

Revision History  

• Version 1.0: 2013-05-22
  Type: Initial release
  
• Version 1.1: 2013-10-02
  Changes: Database references
• Version 1.2: 2024-02-28
  Changes: Data collection, Database references