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- PDB-9xyh: Human mitochondrial ClpP in complex with OICR-18704 in the heptam... -

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Basic information

Entry
Database: PDB / ID: 9xyh
TitleHuman mitochondrial ClpP in complex with OICR-18704 in the heptameric state
ComponentsATP-dependent Clp protease proteolytic subunit, mitochondrial
KeywordsHYDROLASE / Protease / Proteolysis / Complex with inhibitor
Function / homology
Function and homology information


membrane protein proteolysis / mitochondrial protein catabolic process / endopeptidase Clp complex / endopeptidase Clp / ATP-dependent peptidase activity / protein quality control for misfolded or incompletely synthesized proteins / Mitochondrial protein degradation / protein catabolic process / peptidase activity / ATPase binding ...membrane protein proteolysis / mitochondrial protein catabolic process / endopeptidase Clp complex / endopeptidase Clp / ATP-dependent peptidase activity / protein quality control for misfolded or incompletely synthesized proteins / Mitochondrial protein degradation / protein catabolic process / peptidase activity / ATPase binding / endopeptidase activity / mitochondrial matrix / serine-type endopeptidase activity / mitochondrion / proteolysis / identical protein binding
Similarity search - Function
ClpP, Ser active site / Endopeptidase Clp serine active site. / ClpP, histidine active site / Endopeptidase Clp histidine active site. / ATP-dependent Clp protease proteolytic subunit / Clp protease proteolytic subunit /Translocation-enhancing protein TepA / Clp protease / ClpP/crotonase-like domain superfamily
Similarity search - Domain/homology
: / ATP-dependent Clp protease proteolytic subunit, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsUday, A.B. / Zeytuni, N. / Goncalves, M. / Vahidi, S.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)PJT-191940 Canada
CitationJournal: Nat Commun / Year: 2026
Title: Allosteric inhibition of human mitochondrial ClpP by hijacking the dordaviprone (ONC201) binding site
Authors: 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. / ...Authors: 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.
History
DepositionAug 26, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 14, 2026Provider: repository / Type: Initial release
Revision 1.0Oct 14, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ATP-dependent Clp protease proteolytic subunit, mitochondrial
B: ATP-dependent Clp protease proteolytic subunit, mitochondrial
C: ATP-dependent Clp protease proteolytic subunit, mitochondrial
D: ATP-dependent Clp protease proteolytic subunit, mitochondrial
E: ATP-dependent Clp protease proteolytic subunit, mitochondrial
F: ATP-dependent Clp protease proteolytic subunit, mitochondrial
G: ATP-dependent Clp protease proteolytic subunit, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)170,2619
Polymers169,2597
Non-polymers1,0022
Water23413
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
ATP-dependent Clp protease proteolytic subunit, mitochondrial / Endopeptidase Clp


Mass: 24179.875 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CLPP / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q16740, endopeptidase Clp
#2: Chemical ChemComp-A1CRQ / 4-[4-({7-chloro-3-[(1S)-1-cyanoethyl]-4-oxo-3,4-dihydroquinazolin-2-yl}methyl)piperazin-1-yl]-2-(trifluoromethyl)benzonitrile


Mass: 500.903 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H20ClF3N6O / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 13 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Human mitochondrial ClpP in complex with allosteric inhibitor OICR-18704
Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 7.8
Buffer component
IDConc.NameFormulaBuffer-ID
150 mMTrisC4H11NO31
2100 mMPottassium chlorideKCl1
310 mMMagnesium chlorideMgCl21
41 mMDithiothreitolC4H10O2S21
SpecimenConc.: 15 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.7.0particle selection
2PHENIX1.21.2_5419model refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 306338 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 41.22 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00229245
ELECTRON MICROSCOPYf_angle_d0.516912503
ELECTRON MICROSCOPYf_chiral_restr0.04041426
ELECTRON MICROSCOPYf_plane_restr0.00411577
ELECTRON MICROSCOPYf_dihedral_angle_d5.01561282

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