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: 63.01 kDa 
• Atom Count: 3943 
• Residue Count: 482 
• Unique protein chains: 3

3EDR

The crystal structure of caspase-7 in complex with Acetyl-LDESD-CHO

• DOI: 10.2210/pdb3EDR/pdb

• Classification: HYDROLASE/HYDROLASE INHIBITOR
• Organism(s): Homo sapiens, Saccharomyces cerevisiae S288C
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-09-03 Released: 2008-10-28 
• Deposition Author(s): Agniswamy, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.45 Å
• R-Value Free: 0.248 
• R-Value Work: 0.201 
• R-Value Observed: 0.231 

Literature

Structural basis for executioner caspase recognition of P5 position in substrates.

Fu, G., Chumanevich, A.A., Agniswamy, J., Fang, B., Harrison, R.W., Weber, I.T.

(2008) Apoptosis 13: 1291-1302

• PubMed: 18780184 
• DOI: 10.1007/s10495-008-0259-9
• Primary Citation of Related Structures:  
  3EDQ, 3EDR


• PubMed Abstract: 
  

Caspase-3, -6 and -7 cleave many proteins at specific sites to induce apoptosis. Their recognition of the P5 position in substrates has been investigated by kinetics, modeling and crystallography. Caspase-3 and -6 recognize P5 in pentapeptides as shown by enzyme activity data and interactions observed in the crystal structure of caspase-3/LDESD and in a model for caspase-6. In caspase-3 the P5 main-chain was anchored by interactions with Ser209 in loop-3 and the P5 Leu side-chain interacted with Phe250 and Phe252 in loop-4 consistent with 50% increased hydrolysis of LDEVD relative to DEVD. Caspase-6 formed similar interactions and showed a preference for polar P5 in QDEVD likely due to interactions with polar Lys265 and hydrophobic Phe263 in loop-4. Caspase-7 exhibited no preference for P5 residue in agreement with the absence of P5 interactions in the caspase-7/LDESD crystal structure. Initiator caspase-8, with Pro in the P5-anchoring position and no loop-4, had only 20% activity on tested pentapeptides relative to DEVD. Therefore, caspases-3 and -6 bind P5 using critical loop-3 anchoring Ser/Thr and loop-4 side-chain interactions, while caspase-7 and -8 lack P5-binding residues.

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Organizational Affiliation: 

Department of Biology, Molecular Basis of Disease Program, 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
Inhibitor Ac-ldesd-cho peptide	E, F	6	Saccharomyces cerevisiae S288C	Mutation(s): 0  Gene Names: YKR018C
Find proteins for P36114 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P36114  Go to UniProtKB:  P36114

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 3
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000241	E, F	N-acetyl-L-leucyl-L-alpha-aspartyl-L-alpha-glutamyl-L-seryl-L-aspartic aldehyde	Peptide-like /  Inhibitor		--

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.45 Å
• R-Value Free: 0.248 
• R-Value Work: 0.201 
• R-Value Observed: 0.231 
• Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 88.637	α = 90
b = 88.637	β = 90
c = 187.708	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: 2008-09-03 
• Released Date: 2008-10-28 
Deposition Author(s): Agniswamy, J.

Revision History 

• Version 1.0: 2008-10-28
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance
• Version 1.2: 2013-02-27
  Changes: Other