Biological Assembly 1  

 3D View: Structure

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Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 10640.21 
• Atom Count: 743 
• Residue Count: 92 
• Unique protein chains: 1

2YGS

CARD DOMAIN FROM APAF-1

• DOI: 10.2210/pdb2YGS/pdb

• Classification: APOPTOSIS
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)


• Deposited: 1999-05-08 Released: 2000-04-19 
• Deposition Author(s): Shi, Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.6 Å
• R-Value Free: 0.236 
• R-Value Work: 0.198 

Literature

Structural basis of procaspase-9 recruitment by the apoptotic protease-activating factor 1.

Qin, H., Srinivasula, S.M., Wu, G., Fernandes-Alnemri, T., Alnemri, E.S., Shi, Y.

(1999) Nature 399: 549-557

• PubMed: 10376594 
• DOI: 10.1038/21124
• Primary Citation of Related Structures:  
  3YGS


• PubMed Abstract: 
  

Caspase-9-mediated apoptosis (programmed cell death) plays a central role in the development and homeostasis of all multicellular organisms. Mature caspase-9 is derived from its procaspase precursor as a result of recruitment by the activating factor Apaf-1. The crystal structures of the caspase-recruitment domain of Apaf-1 by itself and in complex with the prodomain of procaspase-9 have been determined at 1.6 and 2.5 A resolution, respectively. These structures and other evidence reveal that each molecule of Apaf-1 interacts with a molecule of procaspase-9 through two highly charged and complementary surfaces formed by non-conserved residues; these surfaces determine recognition specificity through networks of intermolecular hydrogen bonds and van der Waals interactions. Mutation of the important interface residues in procaspase-9 or Apaf-1 prevents or reduces activation of procaspase-9 in a cell-free system. Wild-type, but not mutant, prodomains of caspase-9 completely inhibit catalytic processing of procaspase-9. Furthermore, analysis of homologues from Caenorhabditis elegans indicates that recruitment of CED-3 by CED-4 is probably mediated by the same set of conserved structural motifs, with a corresponding change in the specificity-determining residues.

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Organizational Affiliation: 

Department of Chemistry, Princeton University, New Jersey 08544, USA.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
APOPTOTIC PROTEASE ACTIVATING FACTOR 1	A	92	Homo sapiens	Mutation(s): 0  Gene Names: APAF1 (KIAA0413)
Find proteins for O14727 (Homo sapiens) Go to Gene View: APAF1 Go to UniProtKB:  O14727

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.6 Å
• R-Value Free: 0.236 
• R-Value Work: 0.198 
• Space Group: C 1 2 1

Unit Cell:

Length (Å)	Angle (°)
a = 56.700	α = 90.00
b = 36.000	β = 118.20
c = 47.900	γ = 90.00

Software Package:

Software Name	Purpose
X-PLOR	phasing
X-PLOR	model building
X-PLOR	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1999-05-08 
• Released Date: 2000-04-19 
• Deposition Author(s): Shi, Y.

Revision History 

• Version 1.0: 2000-04-19
  Type: Initial release
• Version 1.1: 2008-04-26
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Version format compliance