Biological Assembly 1  

 3D View: Structure | Electron Density

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 30425.63 
• Atom Count: 2004 
• Residue Count: 263 
• Unique protein chains: 2

4JJE

Caspase-3 specific unnatural amino acid peptides

• DOI: 10.2210/pdb4JJE/pdb

• Classification: HYDROLASE/HYDROLASE INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)


• Deposited: 2013-03-07 Released: 2013-06-12 
• Deposition Author(s): Vickers, C.J., Gonzalez-Paez, G.E., Wolan, D.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.481 Å
• R-Value Free: 0.174 
• R-Value Work: 0.150 

Literature

Selective Detection of Caspase-3 versus Caspase-7 Using Activity-Based Probes with Key Unnatural Amino Acids.

Vickers, C.J., Gonzalez-Paez, G.E., Wolan, D.W.

(2013) Acs Chem.Biol. 8: 1558-1566

• PubMed: 23614665 
• DOI: 10.1021/cb400209w
• Primary Citation of Related Structures:  
  4JJ8, 4JJ7


• PubMed Abstract: 
  

Caspases are required for essential biological functions, most notably apoptosis and pyroptosis, but also cytokine production, cell proliferation, and differentiation. One of the most well studied members of this cysteine protease family includes executioner caspase-3, which plays a central role in cell apoptosis and differentiation. Unfortunately, there exists a dearth of chemical tools to selectively monitor caspase-3 activity under complex cellular and in vivo conditions due to its close homology with executioner caspase-7. Commercially available activity-based probes and substrates rely on the canonical DEVD tetrapeptide sequence, which both caspases-3 and -7 recognize with similar affinity, and thus the individual contributions of caspase-3 and/or -7 toward important cellular processes are irresolvable. Here, we analyzed a variety of permutations of the DEVD peptide sequence in order to discover peptides with biased activity and recognition of caspase-3 versus caspases-6, -7, -8, and -9. Through this study, we identify fluorescent and biotinylated probes capable of selective detection of caspase-3 using key unnatural amino acids. Likewise, we determined the X-ray crystal structures of caspases-3, -7, and -8 in complex with our lead peptide inhibitor to elucidate the binding mechanism and active site interactions that promote the selective recognition of caspase-3 over other highly homologous caspase family members.

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Organizational Affiliation: 

Departments of Molecular and Experimental Medicine and Chemical Physiology, The Scripps Research Institute , La Jolla, California 92037, United States.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Caspase-3	A	257	Homo sapiens	Mutation(s): 0  Gene Names: CASP3 (CPP32) EC: 3.4.22.56
Find proteins for P42574 (Homo sapiens) Go to Gene View: CASP3 Go to UniProtKB:  P42574

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
Caspase inhibitor	B	6	N/A	Mutation(s): 0
Protein Feature View is not available: No corresponding UniProt sequence found.

Small Molecules

Biologically Interesting Molecules 1 Unique
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000925	B	ACE-1MH-ASP-B3L-HLX-1U8	Peptide-like / CASPASE inhibitor		--

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.481 Å
• R-Value Free: 0.174 
• R-Value Work: 0.150 
• Space Group: I 2 2 2

Unit Cell:

Length (Å)	Angle (°)
a = 68.110	α = 90.00
b = 84.334	β = 90.00
c = 96.088	γ = 90.00

Software Package:

Software Name	Purpose
HKL-2000	data scaling
SOLVE	phasing
HKL-2000	data reduction
DENZO	data reduction
PHENIX	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2013-03-07 
• Released Date: 2013-06-12 
• Deposition Author(s): Vickers, C.J., Gonzalez-Paez, G.E., Wolan, D.W.

Revision History 

• Version 1.0: 2013-06-12
  Type: Initial release
• Version 1.1: 2014-02-19
  Type: Database references