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- PDB-8w7c: Activation of mitochondrial Caseinolytic Protease P (ClpP) induce... -

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Basic information

Entry
Database: PDB / ID: 8w7c
TitleActivation of mitochondrial Caseinolytic Protease P (ClpP) induces selective cancer cell lethality
ComponentsATP-dependent Clp protease proteolytic subunit, mitochondrial
KeywordsAPOPTOSIS / XT6 / Mitochondrial / ClpP / Activation
Function / homology
Function and homology information


membrane protein proteolysis / mitochondrial protein catabolic process / endopeptidase Clp / endopeptidase Clp complex / ATP-dependent peptidase activity / protein quality control for misfolded or incompletely synthesized proteins / Mitochondrial protein degradation / proteolysis involved in protein catabolic process / peptidase activity / ATPase binding ...membrane protein proteolysis / mitochondrial protein catabolic process / endopeptidase Clp / endopeptidase Clp complex / ATP-dependent peptidase activity / protein quality control for misfolded or incompletely synthesized proteins / Mitochondrial protein degradation / proteolysis involved in 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)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsJiang, J.-X. / Ding, H. / Lu, M.-L. / Chen, M.-R. / Sun, H.-Y. / Xiao, Y.-B.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Activation of mitochondrial Caseinolytic Protease P (ClpP) induces selective cancer cell lethality
Authors: Jiang, J.-X. / Ding, H. / Lu, M.-L. / Chen, M.-R. / Sun, H.-Y. / Xiao, Y.-B.
History
DepositionAug 30, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Sep 4, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)173,57814
Polymers170,2687
Non-polymers3,3107
Water00
1
A: 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

A: 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

B: ATP-dependent Clp protease proteolytic subunit, mitochondrial
hetero molecules

B: ATP-dependent Clp protease proteolytic subunit, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)347,15728
Polymers340,53614
Non-polymers6,62014
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
crystal symmetry operation3_555x+1/2,y+1/2,z1
crystal symmetry operation4_556-x+1/2,y+1/2,-z+11
Buried area50120 Å2
ΔGint-261 kcal/mol
Surface area83890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)142.245, 153.591, 104.617
Angle α, β, γ (deg.)90.00, 117.96, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 24324.004 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Details: Author stated: The first two amino acid (Gly and Ser) is a linker proteased by SUMO protease. The third amino acid (N0.57 Ser) belongs to disorder region.
Source: (gene. exp.) Homo sapiens (human) / Gene: CLPP / Production host: Escherichia coli (E. coli) / References: UniProt: Q16740, endopeptidase Clp
#2: Chemical
ChemComp-R89 / 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


Mass: 472.890 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C24H20ClF3N4O
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.99 Å3/Da / Density % sol: 58.86 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 200 mM KCl, 100 mM MES, 12%PEG4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 12, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.92→97.344 Å / Num. obs: 77808 / % possible obs: 96.1 % / Redundancy: 3.7 % / CC1/2: 0.982 / Net I/σ(I): 6.3
Reflection shellResolution: 2.92→3.07 Å / Num. unique obs: 41644 / CC1/2: 0.982

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Processing

Software
NameVersionClassification
PHENIX(1.18.2_3874: ???)refinement
autoPROCdata reduction
autoPROCdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→46.2 Å / SU ML: 0.44 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 27.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2599 3914 5.03 %
Rwork0.2397 --
obs0.2407 77808 99.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3→46.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9422 0 231 0 9653
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0049853
X-RAY DIFFRACTIONf_angle_d0.8813361
X-RAY DIFFRACTIONf_dihedral_angle_d20.2313690
X-RAY DIFFRACTIONf_chiral_restr0.0511539
X-RAY DIFFRACTIONf_plane_restr0.0061645
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.040.4221300.43012373X-RAY DIFFRACTION88
3.04-3.070.36941370.37062651X-RAY DIFFRACTION100
3.07-3.110.2891420.32572615X-RAY DIFFRACTION100
3.11-3.160.30671430.29892710X-RAY DIFFRACTION100
3.16-3.20.29231400.29582655X-RAY DIFFRACTION100
3.2-3.250.33781400.2962612X-RAY DIFFRACTION100
3.25-3.30.32091420.30622673X-RAY DIFFRACTION100
3.3-3.350.27141380.3042627X-RAY DIFFRACTION100
3.36-3.410.34451390.3012666X-RAY DIFFRACTION100
3.41-3.470.37591420.27522698X-RAY DIFFRACTION100
3.47-3.540.2751420.26742636X-RAY DIFFRACTION100
3.54-3.610.27451410.26372674X-RAY DIFFRACTION100
3.61-3.690.27281380.28582597X-RAY DIFFRACTION100
3.69-3.780.26461420.25482663X-RAY DIFFRACTION100
3.78-3.870.27011400.2432675X-RAY DIFFRACTION100
3.87-3.980.24261360.24172628X-RAY DIFFRACTION99
3.98-4.090.25321390.22832622X-RAY DIFFRACTION100
4.09-4.230.24291440.21162717X-RAY DIFFRACTION100
4.23-4.380.25061390.20532654X-RAY DIFFRACTION100
4.38-4.550.27441360.21042650X-RAY DIFFRACTION100
4.55-4.760.23141410.20722616X-RAY DIFFRACTION99
4.76-5.010.2171380.20252633X-RAY DIFFRACTION100
5.01-5.320.31221430.22852678X-RAY DIFFRACTION100
5.32-5.730.24981400.23562635X-RAY DIFFRACTION100
5.73-6.310.28061400.24162666X-RAY DIFFRACTION100
6.31-7.220.26331400.21672647X-RAY DIFFRACTION99
7.22-9.080.14221370.18532626X-RAY DIFFRACTION100
9.09-46.20.20511450.19072598X-RAY DIFFRACTION97
Refinement TLS params.Method: refined / Origin x: 22.4173 Å / Origin y: 21.6131 Å / Origin z: 50.5734 Å
111213212223313233
T0.4902 Å20.005 Å20.0548 Å2-0.5475 Å20.0045 Å2--0.5554 Å2
L0.1106 °20.0352 °20.0041 °2-0.3185 °20.0426 °2--0.2101 °2
S-0.007 Å °0.0234 Å °0.0082 Å °-0.0345 Å °0.0025 Å °0.0383 Å °0.0063 Å °0.0127 Å °0.0041 Å °
Refinement TLS groupSelection details: all

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