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Yorodumi- PDB-4zvp: Caspase-7 Variant 2 (V2) with reprogrammed substrate specificity ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4zvp | ||||||
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Title | Caspase-7 Variant 2 (V2) with reprogrammed substrate specificity due to Y230V/W232M/Q276C substitutions bound to DEVD inhibitor. | ||||||
Components |
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Keywords | HYDROLASE/HYDROLASE INHIBITOR / Directed Evolution / Protease / Peptide Inhibitor / Designed Active Site Specificity / HYDROLASE-HYDROLASE INHIBITOR complex | ||||||
Function / homology | Function and homology information caspase-7 / lymphocyte apoptotic process / positive regulation of plasma membrane repair / cellular response to staurosporine / cysteine-type endopeptidase activity involved in execution phase of apoptosis / SMAC, XIAP-regulated apoptotic response / Activation of caspases through apoptosome-mediated cleavage / cysteine-type endopeptidase activity involved in apoptotic process / SMAC (DIABLO) binds to IAPs / SMAC(DIABLO)-mediated dissociation of IAP:caspase complexes ...caspase-7 / lymphocyte apoptotic process / positive regulation of plasma membrane repair / cellular response to staurosporine / cysteine-type endopeptidase activity involved in execution phase of apoptosis / SMAC, XIAP-regulated apoptotic response / Activation of caspases through apoptosome-mediated cleavage / cysteine-type endopeptidase activity involved in apoptotic process / SMAC (DIABLO) binds to IAPs / SMAC(DIABLO)-mediated dissociation of IAP:caspase complexes / fibroblast apoptotic process / execution phase of apoptosis / Apoptotic cleavage of cellular proteins / protein maturation / Caspase-mediated cleavage of cytoskeletal proteins / response to UV / cysteine-type peptidase activity / striated muscle cell differentiation / protein catabolic process / protein processing / positive regulation of neuron apoptotic process / peptidase activity / heart development / cellular response to lipopolysaccharide / neuron apoptotic process / aspartic-type endopeptidase activity / defense response to bacterium / cysteine-type endopeptidase activity / apoptotic process / proteolysis / RNA binding / extracellular space / nucleoplasm / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Hill, M.E. / MacPherson, D.J. / Hardy, J.A. | ||||||
Funding support | United States, 1items
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Citation | Journal: Acs Chem.Biol. / Year: 2016 Title: Reprogramming Caspase-7 Specificity by Regio-Specific Mutations and Selection Provides Alternate Solutions for Substrate Recognition. Authors: Hill, M.E. / MacPherson, D.J. / Wu, P. / Julien, O. / Wells, J.A. / Hardy, J.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4zvp.cif.gz | 112.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4zvp.ent.gz | 83.4 KB | Display | PDB format |
PDBx/mmJSON format | 4zvp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4zvp_validation.pdf.gz | 462.8 KB | Display | wwPDB validaton report |
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Full document | 4zvp_full_validation.pdf.gz | 464.6 KB | Display | |
Data in XML | 4zvp_validation.xml.gz | 18.7 KB | Display | |
Data in CIF | 4zvp_validation.cif.gz | 25.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zv/4zvp ftp://data.pdbj.org/pub/pdb/validation_reports/zv/4zvp | HTTPS FTP |
-Related structure data
Related structure data | 4zvoC 4zvqC 4zvrC 4zvsC 4zvtC 4zvuC 3edrS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / End auth comp-ID: GLN / End label comp-ID: GLN
NCS ensembles :
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-Components
#1: Protein | Mass: 22189.203 Da / Num. of mol.: 2 / Fragment: UNP residues 34-231 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CASP7, MCH3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P55210, caspase-7 #2: Protein | Mass: 13079.757 Da / Num. of mol.: 2 / Fragment: UNP residues 232-336 / Mutation: Y230V/W232M/Q276C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CASP7, MCH3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P55210, caspase-7 #3: Protein/peptide | Mass: 486.473 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #4: Water | ChemComp-HOH / | |
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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: 2.94 Å3/Da / Density % sol: 58.16 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 300 mM diammonium citrate, 14% PEG 3350, 10 mM GuHCl, 20% glycerol |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97919 Å | |||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 29, 2014 | |||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97919 Å / Relative weight: 1 | |||||||||||||||||||||||||||
Reflection | Resolution: 2.5→93.79 Å / Num. obs: 29117 / % possible obs: 100 % / Redundancy: 7.5 % / Biso Wilson estimate: 45.27 Å2 / CC1/2: 0.991 / Rpim(I) all: 0.058 / Rsym value: 0.142 / Net I/σ(I): 8.4 / Num. measured all: 217941 / Scaling rejects: 37 | |||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3EDR Resolution: 2.5→69.769 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.26 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 108.29 Å2 / Biso mean: 45.4659 Å2 / Biso min: 26.47 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.5→69.769 Å
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Refine LS restraints |
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Refine LS restraints NCS |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10
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