Biological Assembly 1  

 3D View: Structure | Electron Density

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Hetero 4-mer - A2B2 

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

Macromolecule Content

• Total Structure Weight: 30.10 kDa 
• Atom Count: 2108 
• Residue Count: 246 
• Unique protein chains: 2

1SC4

Crystal structure of the human caspase-1 C285A mutant after removal of malonate

• DOI: 10.2210/pdb1SC4/pdb

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


• Deposited: 2004-02-11 Released: 2004-08-10 
• Deposition Author(s): Romanowski, M.J., Scheer, J.M., O'Brien, T., McDowell, R.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.258 
• R-Value Work: 0.221 
• R-Value Observed: 0.223 

Literature

Crystal structures of a ligand-free and malonate-bound human caspase-1: implications for the mechanism of substrate binding.

Romanowski, M.J., Scheer, J.M., O'Brien, T., McDowell, R.S.

(2004) Structure 12: 1361-1371

• PubMed: 15296730 
• DOI: 10.1016/j.str.2004.05.010
• Primary Citation of Related Structures:  
  1SC4, 1SC3, 1SC1


• PubMed Abstract: 
  

Caspase-1, a mediator of the posttranslational processing of IL-1beta and IL-18, requires an aspartic acid in the P1 position of its substrates. The mechanisms of caspase-1 activation remain poorly understood despite numerous structures of the enzyme complexed with aspartate-based inhibitors. Here we report a crystal structure of ligand-free caspase-1 that displays dramatic rearrangements of loops defining the active site to generate a closed conformation that is incompatible with substrate binding. A structure of the enzyme complexed with malonate shows the protein in its open (active-site ligand-bound) conformation in which malonate reproduces the hydrogen bonding network observed in structures with covalent inhibitors. These results illustrate the essential function of the obligatory aspartate recognition element that opens the active site of caspase-1 to substrates and may be the determinant responsible for the conformational changes between ligand-free and -bound forms of the enzyme, and suggest a new approach for identifying novel aspartic acid mimetics.

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Organizational Affiliation: 

Department of Structural Biology, Sunesis Pharmaceuticals, Inc., 341 Oyster Point Boulevard, South San Francisco, California 94080, USA. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Interleukin-1 beta convertase	A	178	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

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Interleukin-1 beta convertase	B	88	Homo sapiens	Mutation(s): 0  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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.258 
• R-Value Work: 0.221 
• R-Value Observed: 0.223 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.982	α = 90
b = 62.982	β = 90
c = 143.158	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
CrystalClear	data reduction
d*TREK	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2004-02-11 
• Released Date: 2004-08-10 
Deposition Author(s): Romanowski, M.J., Scheer, J.M., O'Brien, T., McDowell, R.S.

Revision History 

• Version 1.0: 2004-08-10
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance