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 (software)

Macromolecule Content

• Total Structure Weight: 62.82 kDa 
• Atom Count: 3857 
• Residue Count: 475 
• Unique protein chains: 3

3IBC

Crystal Structure of Caspase-7 incomplex with Acetyl-YVAD-CHO

• DOI: 10.2210/pdb3IBC/pdb

• Classification: hydrolase, apoptosis
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-07-15 Released: 2009-09-01 
• Deposition Author(s): Agniswamy, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.75 Å
• R-Value Free: 0.242 
• R-Value Work: 0.203 
• R-Value Observed: 0.218 

Literature

Conformational similarity in the activation of caspase-3 and -7 revealed by the unliganded and inhibited structures of caspase-7.

Agniswamy, J., Fang, B., Weber, I.T.

(2009) Apoptosis 14: 1135-1144

• PubMed: 19655253 
• DOI: 10.1007/s10495-009-0388-9
• Primary Citation of Related Structures:  
  3IBF, 3IBC


• PubMed Abstract: 
  

Caspase-mediated apoptosis has important roles in normal cell differentiation and aging and in many diseases including cancer, neuromuscular disorders and neurodegenerative diseases. Therefore, modulation of caspase activity and conformational states is of therapeutic importance. We report crystal structures of a new unliganded conformation of caspase-7 and the inhibited caspase-7 with the tetrapeptide Ac-YVAD-Cho. Different conformational states and mechanisms for substrate recognition have been proposed based on unliganded structures of the redundant apoptotic executioner caspase-3 and -7. The current study shows that the executioner caspase-3 and -7 have similar conformations for the unliganded active site as well as the inhibitor-bound active site. The new unliganded caspase-7 structure exhibits the tyrosine flipping mechanism in which the Tyr230 has rotated to block entry to the S2 binding site similar to the active site conformation of unliganded caspase-3. The inhibited structure of caspase-7/YVAD shows that the P4 Tyr binds the S4 region specific to polar residues at the expense of a main chain hydrogen bond between the P4 amide and carbonyl oxygen of caspase-7 Gln 276, which is similar to the caspase-3 complex. This new knowledge of the structures and conformational states of unliganded and inhibited caspases will be important for the design of drugs to modulate caspase activity and apoptosis.

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Organizational Affiliation: 

Department of Biology, Georgia State University, Atlanta, GA 30303, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Caspase-7	A, C	173	Homo sapiens	Mutation(s): 0  Gene Names: CASP7, MCH3 EC: 3.4.22.60
Find proteins for P55210 (Homo sapiens) Explore P55210  Go to UniProtKB:  P55210
NIH Common Fund Data Resources
PHAROS:  P55210 GTEx:  ENSG00000165806

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Caspase-7	B, D	97	Homo sapiens	Mutation(s): 0  Gene Names: CASP7, MCH3 EC: 3.4.22.60
Find proteins for P55210 (Homo sapiens) Explore P55210  Go to UniProtKB:  P55210
NIH Common Fund Data Resources
PHAROS:  P55210 GTEx:  ENSG00000165806

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Acetyl-YVAD-CHO	E, F	5	N/A	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.75 Å
• R-Value Free: 0.242 
• R-Value Work: 0.203 
• R-Value Observed: 0.218 
• Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 88.248	α = 90
b = 88.248	β = 90
c = 188.15	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2009-07-15 
• Released Date: 2009-09-01 
Deposition Author(s): Agniswamy, J.

Revision History 

• Version 1.0: 2009-09-01
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance