9XYJ | pdb_00009xyj

Human mitochondrial ClpP V62A variant

• PDB DOI: https://doi.org/10.2210/pdb9XYJ/pdb
• EM Map EMD-72339: EMDB EMDataResource

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2025-08-26 Released: 2026-10-14 
• Deposition Author(s): Uday, A.B., Zeytuni, N., Goncalves, M., Vahidi, S.
• Funding Organization(s): Canadian Institutes of Health Research (CIHR)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.20 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Allosteric inhibition of human mitochondrial ClpP by hijacking the dordaviprone (ONC201) binding site

Goncalves, M.M., Uday, A.B., Watson, I.D.G., Chau, A.M., Kalhor-Monfared, S., Wan, B., Kiyota, T., Currie, S.Q.W., Jitkova, Y., Feng, Y., Diamandas, M., Ling, D., Ma, M., Mancini, R.S., Wang, Z., Casas-Selves, M., Joshi, D., Mohammed, M., Subramaniam, R., Fernandes, E.L., Yan, Y., Pomroy, N., Hurren, R., Gronda, M., Velyvis, A., Yudin, A.K., Reed, M.A., Prive, G., Aman, A., Isaac, M., Marcellus, R., Uehling, D., Schimmer, A.D., Zeytuni, N., Vahidi, S.

(2026) Nat Commun 

• DOI: https://doi.org/10.1038/s41467-026-78140-5

Biological Assembly 1  

Global Symmetry: Cyclic - C7  (Explore in 3D)
Global Stoichiometry: Homo 7-mer - A7 

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

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 169.06 kDa 
• Atom Count: 8,953 
• Modeled Residue Count: 1,146 
• Deposited Residue Count: 1,547 
• 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	221	Homo sapiens	Mutation(s): 1  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

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.20 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.21.2_5419
RECONSTRUCTION	cryoSPARC

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-10-14 
Deposition Author(s): Uday, A.B., Zeytuni, N., Goncalves, M., Vahidi, S.

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Funding Organization	Location	Grant Number
Canadian Institutes of Health Research (CIHR)	Canada	PJT-191940

Revision History  

• Version 1.0: 2026-10-14
  Type: Initial release