Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 67.62 kDa 
• Atom Count: 4423 
• Residue Count: 540 
• Unique protein chains: 1

3E4C

Procaspase-1 zymogen domain crystal structure

• DOI: 10.2210/pdb3E4C/pdb

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


• Deposited: 2008-08-11 Released: 2008-12-30 
• Deposition Author(s): Elliott, J.M., Rouge, L., Wiesmann, C., Scheer, J.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 0.263 
• R-Value Work: 0.200 
• R-Value Observed: 0.204 

Literature

Crystal structure of procaspase-1 zymogen domain reveals insight into inflammatory caspase autoactivation

Elliott, J.M., Rouge, L., Wiesmann, C., Scheer, J.M.

(2009) J Biol Chem 284: 6546-6553

• PubMed: 19117953 
• DOI: 10.1074/jbc.M806121200
• Primary Citation of Related Structures:  
  3E4C


• PubMed Abstract: 
  

One key event in inflammatory signaling is the activation of the initiator caspase, procaspase-1. Presented here is the crystal structure of the procaspase-1 zymogen without its caspase recruitment domain solved to 2.05 A. Although the isolated domain is monomeric in solution, the protein appeared dimeric in crystals. The loop arrangements in the dimer provide insight into the first autoproteolytic events that occur during activation by oligomerization. Additionally, in contrast to other caspases, we demonstrate that autoproteolysis at the second cleavage site, Asp316, is necessary for conversion to a stable dimer in solution. Critical elements of secondary structure are revealed in the crystal structure that explain why a dimeric protein is favored after proteolysis at this aspartic acid. Dimer stabilization is concurrent with a 130-fold increase in kcat, the sole contributing kinetic factor to an activated and efficient mediator of inflammation.

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Organizational Affiliation: 

Department of Protein Chemistry, Genentech, Inc., South San Francisco, California 94080, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Caspase-1	A, B	302	Homo sapiens	Mutation(s): 1  Gene Names: CASP1, IL1BC, IL1BCE EC: 3.4.22.36
Find proteins for P29466 (Homo sapiens) Explore P29466  Go to UniProtKB:  P29466
NIH Common Fund Data Resources
PHAROS:  P29466 GTEx:  ENSG00000137752

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG	B	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 0.263 
• R-Value Work: 0.200 
• R-Value Observed: 0.204 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.1	α = 105.95
b = 58.004	β = 119.6
c = 60.12	γ = 92.77

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2008-08-11 
• Released Date: 2008-12-30 
Deposition Author(s): Elliott, J.M., Rouge, L., Wiesmann, C., Scheer, J.M.

Revision History 

• Version 1.0: 2008-12-30
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Refinement description, Version format compliance
• Version 1.2: 2020-09-09
  Changes: Database references, Derived calculations, Structure summary