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Yorodumi- PDB-8w7c: Activation of mitochondrial Caseinolytic Protease P (ClpP) induce... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8w7c | ||||||
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Title | Activation of mitochondrial Caseinolytic Protease P (ClpP) induces selective cancer cell lethality | ||||||
Components | ATP-dependent Clp protease proteolytic subunit, mitochondrial | ||||||
Keywords | APOPTOSIS / 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 | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å | ||||||
Authors | Jiang, J.-X. / Ding, H. / Lu, M.-L. / Chen, M.-R. / Sun, H.-Y. / Xiao, Y.-B. | ||||||
Funding support | 1items
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Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8w7c.cif.gz | 472.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8w7c.ent.gz | 390.8 KB | Display | PDB format |
PDBx/mmJSON format | 8w7c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8w7c_validation.pdf.gz | 2.3 MB | Display | wwPDB validaton report |
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Full document | 8w7c_full_validation.pdf.gz | 2.4 MB | Display | |
Data in XML | 8w7c_validation.xml.gz | 53.6 KB | Display | |
Data in CIF | 8w7c_validation.cif.gz | 64.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w7/8w7c ftp://data.pdbj.org/pub/pdb/validation_reports/w7/8w7c | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | 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 / Mass: 472.890 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C24H20ClF3N4O Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.99 Å3/Da / Density % sol: 58.86 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 200 mM KCl, 100 mM MES, 12%PEG4000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 12, 2023 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 2.92→3.07 Å / Num. unique obs: 41644 / CC1/2: 0.982 |
-Processing
Software |
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Refinement | Method 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
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3→46.2 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 22.4173 Å / Origin y: 21.6131 Å / Origin z: 50.5734 Å
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Refinement TLS group | Selection details: all |