Biological Assembly 1  

 3D View: Structure | 1D-3D View | Validation Report | 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: 42.96 kDa 
• Atom Count: 3145 
• Modelled Residue Count: 374 
• Deposited Residue Count: 375 
• Unique protein chains: 3

1NX0

Structure of Calpain Domain 6 in Complex with Calpastatin DIC

• PDB DOI: 10.2210/pdb1NX0/pdb

• Classification: HYDROLASE/HYDROLASE INHIBITOR
• Organism(s): Sus scrofa
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2003-02-07 Released: 2003-08-19 
• Deposition Author(s): Todd, B., Moore, D., Deivanayagam, C.C.S., Lin, G.-D., Chattopadhyay, D., Maki, M., Wang, K.K.W., Narayana, S.V.L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.261 
• R-Value Work: 0.218 
• R-Value Observed: 0.218 

Literature

A structural model for the inhibition of calpain by calpastatin: crystal structures of the native domain VI of calpain and its complexes with calpastatin peptide and a small molecule inhibitor.

Todd, B., Moore, D., Deivanayagam, C.C.S., Lin, G.-D., Chattopadhyay, D., Maki, M., Wang, K.K.W., Narayana, S.V.L.

(2003) J Mol Biol 328: 131-146

• PubMed: 12684003 
• DOI: 10.1016/s0022-2836(03)00274-2
• Primary Citation of Related Structures:  
  1NX0, 1NX1, 1NX2, 1NX3


• PubMed Abstract: 
  

The Ca(2+)-dependent cysteine protease calpain along with its endogenous inhibitor calpastatin is widely distributed. The interactions between calpain and calpastatin have been studied to better understand the nature of calpain inhibition by calpastatin, which can aid the design of small molecule inhibitors to calpain. Here we present the crystal structure of a complex between a calpastatin peptide and the calcium-binding domain VI of calpain. DIC19 is a 19 residue peptide, which corresponds to one of the three interacting domains of calpastatin, which is known to interact with domain VI of calpain. We present two crystal structures of DIC19 bound to domain VI of calpain, determined by molecular replacement methods to 2.5A and 2.2A resolution. In the process of crystallizing the inhibitor complex, a new native crystal form was identified which had the homodimer 2-fold axis along a crystallographic axis as opposed to the previously observed dimer in the asymmetric unit. The crystal structures of the native domain VI and its inhibitor PD150606 (3-(4-iodophenyl)-2-mercapto-(Z)-2-propenoic acid) complex were determined with the help of molecular replacement methods to 2.0A and 2.3A resolution, respectively. In addition, we built a homology model for the complex between domain IV and DIA19 peptide of calpastatin. Finally, we present a model for the calpastatin-inhibited calpain.

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Organizational Affiliation: 

Center for Biophysical Sciences and Engineering, University of Alabama at Birmingham, Birmingham, AL 35294, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Calcium-dependent protease, small subunit	A, B	173	Sus scrofa	Mutation(s): 0  Gene Names: CAPNS1 OR CAPN4, CAPNS1, CAPN4
UniProt
Find proteins for P04574 (Sus scrofa) Explore P04574  Go to UniProtKB:  P04574

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Calpastatin	C, D	12	Sus scrofa	Mutation(s): 0  Gene Names: CAST
UniProt
Find proteins for P12675 (Sus scrofa) Explore P12675  Go to UniProtKB:  P12675

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Small molecule inhibitor	E	5	N/A	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	F [auth A], G [auth A], H [auth A], I [auth B], J [auth B], K [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.261 
• R-Value Work: 0.218 
• R-Value Observed: 0.218 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.78	α = 90
b = 83.3	β = 90
c = 92.15	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2003-02-07 
• Released Date: 2003-08-19 
Deposition Author(s): Todd, B., Moore, D., Deivanayagam, C.C.S., Lin, G.-D., Chattopadhyay, D., Maki, M., Wang, K.K.W., Narayana, S.V.L.

Revision History  

• Version 1.0: 2003-08-19
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance
• Version 1.3: 2012-05-02
  Changes: Structure summary