8W7C | pdb_00008w7c

Activation of mitochondrial Caseinolytic Protease P (ClpP) induces selective cancer cell lethality

• PDB DOI: https://doi.org/10.2210/pdb8W7C/pdb

• Classification: APOPTOSIS
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2023-08-30 Released: 2024-09-04 
• Deposition Author(s): Jiang, J.-X., Ding, H., Lu, M.-L., Chen, M.-R., Sun, H.-Y., Xiao, Y.-B.
• Funding Organization(s): Not funded

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 
  0.260 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.240 (Depositor), 0.240 (DCC) 
• R-Value Observed: 
  0.241 (Depositor) 

Starting Model: experimental

Literature

Activation of mitochondrial Caseinolytic Protease P (ClpP) induces selective cancer cell lethality

Jiang, J.-X., Ding, H., Lu, M.-L., Chen, M.-R., Sun, H.-Y., Xiao, Y.-B.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D7  (Explore in 3D)
Global Stoichiometry: Homo 14-mer - A14 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 173.58 kDa 
• Atom Count: 9,669 
• Modeled Residue Count: 1,219 
• Deposited Residue Count: 1,561 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP-dependent Clp protease proteolytic subunit, mitochondrial	A, B, C, D, E, F, G	223	Homo sapiens	Mutation(s): 0  Gene Names: CLPP EC: 3.4.21.92
UniProt & NIH Common Fund Data Resources
Find proteins for Q16740 (Homo sapiens) Explore Q16740  Go to UniProtKB:  Q16740
PHAROS:  Q16740 GTEx:  ENSG00000125656

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
R89	H [auth A], I [auth B], J [auth C], K [auth D], L [auth E], M [auth F], N [auth G]	11-[(3-chlorophenyl)methyl]-7-[[4-(trifluoromethyl)phenyl]methyl]-2,5,7,11-tetrazatricyclo[7.4.0.0^{2,6}]trideca-1(9),3,5-trien-8-one C24 H20 Cl F3 N4 O YLOGPPCKNRATOS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free:  0.260 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.240 (Depositor), 0.240 (DCC) 
• R-Value Observed: 0.241 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 142.245	α = 90
b = 153.591	β = 117.96
c = 104.617	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
autoPROC	data reduction
autoPROC	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-09-04 
Deposition Author(s): Jiang, J.-X., Ding, H., Lu, M.-L., Chen, M.-R., Sun, H.-Y., Xiao, Y.-B.

---

Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2024-09-04
  Type: Initial release