8XQK | pdb_00008xqk

The Crystal Structure of Apaf from Biortus.

• PDB DOI: https://doi.org/10.2210/pdb8XQK/pdb

• Classification: APOPTOSIS
• Organism(s): Homo sapiens
• Expression System: prokaryote coculture
• Mutation(s): No 


• Deposited: 2024-01-05 Released: 2024-03-06 
• Deposition Author(s): Wang, F., Cheng, W., Lv, Z., Ju, C., Ni, C.
• Funding Organization(s): Not funded

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.85 Å
• R-Value Free: 
  0.283 (Depositor), 0.290 (DCC) 
• R-Value Work: 
  0.225 (Depositor), 0.230 (DCC) 

Starting Model: experimental

Literature

The Crystal Structure of Apaf from Biortus.

Wang, F., Cheng, W., Lv, Z., Ju, C., Ni, C.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 4 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 45.1 kDa 
• Atom Count: 3,222 
• Modeled Residue Count: 381 
• Deposited Residue Count: 392 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Apoptotic protease-activating factor 1	A, B, C, D	98	Homo sapiens	Mutation(s): 0  Gene Names: APAF1, KIAA0413
UniProt & NIH Common Fund Data Resources
Find proteins for O14727 (Homo sapiens) Explore O14727  Go to UniProtKB:  O14727
PHAROS:  O14727 GTEx:  ENSG00000120868

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4 (Subject of Investigation/LOI)	E [auth A], F [auth B], G [auth B], H [auth C], I [auth D]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.85 Å
• R-Value Free:  0.283 (Depositor), 0.290 (DCC) 
• R-Value Work:  0.225 (Depositor), 0.230 (DCC) 

Space Group: P 2 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 31.641	α = 90
b = 75.336	β = 90
c = 161.067	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-03-06 
Deposition Author(s): Wang, F., Cheng, W., Lv, Z., Ju, C., Ni, C.

---

Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2024-03-06
  Type: Initial release