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Open data
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Basic information
Entry | Database: PDB / ID: 6bdt | ||||||
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Title | Crystal Structure of Human Calpain-3 Protease Core Mutant-C129S | ||||||
![]() | Calpain-3 | ||||||
![]() | HYDROLASE / Calcium binding / Cysteine protease / Calpain / P94 | ||||||
Function / homology | ![]() calpain-3 / positive regulation of satellite cell activation involved in skeletal muscle regeneration / ligase regulator activity / calcium-dependent self proteolysis / G1 to G0 transition involved in cell differentiation / regulation of myoblast differentiation / cellular response to salt stress / myofibril assembly / muscle structure development / calcium-dependent cysteine-type endopeptidase activity ...calpain-3 / positive regulation of satellite cell activation involved in skeletal muscle regeneration / ligase regulator activity / calcium-dependent self proteolysis / G1 to G0 transition involved in cell differentiation / regulation of myoblast differentiation / cellular response to salt stress / myofibril assembly / muscle structure development / calcium-dependent cysteine-type endopeptidase activity / sodium ion binding / self proteolysis / regulation of catalytic activity / negative regulation of protein sumoylation / protein localization to membrane / regulation of canonical NF-kappaB signal transduction / response to muscle activity / muscle organ development / structural constituent of muscle / muscle cell cellular homeostasis / myofibril / sarcomere organization / positive regulation of proteolysis / catalytic activity / cysteine-type peptidase activity / titin binding / T-tubule / cellular response to calcium ion / Degradation of the extracellular matrix / positive regulation of release of sequestered calcium ion into cytosol / protein destabilization / protein catabolic process / Z disc / response to calcium ion / peptidase activity / positive regulation of NF-kappaB transcription factor activity / protein-containing complex assembly / molecular adaptor activity / negative regulation of DNA-templated transcription / apoptotic process / calcium ion binding / nucleolus / negative regulation of apoptotic process / positive regulation of DNA-templated transcription / protein-containing complex / proteolysis / identical protein binding / nucleus / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Ye, Q. / Campbell, R.L. / Davies, P.L. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structures of human calpain-3 protease core with and without bound inhibitor reveal mechanisms of calpain activation. Authors: Ye, Q. / Campbell, R.L. / Davies, P.L. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 273.5 KB | Display | ![]() |
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PDB format | ![]() | 217.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 471.4 KB | Display | ![]() |
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Full document | ![]() | 488.5 KB | Display | |
Data in XML | ![]() | 45.2 KB | Display | |
Data in CIF | ![]() | 61.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6bgpC ![]() 6bjdC ![]() 6bkjC ![]() 1mdwS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Beg auth comp-ID: GLU / Beg label comp-ID: GLU / Refine code: _
NCS ensembles :
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Components
#1: Protein | Mass: 44440.109 Da / Num. of mol.: 4 / Mutation: C129S Source method: isolated from a genetically manipulated source Details: Muscle-specific calcium-activated neutral protease 3 Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-CA / #3: Chemical | ChemComp-CL / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2 Å3/Da / Density % sol: 38.37 % |
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Crystal grow | Temperature: 295.15 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: PEG 8000, MES, calcium chloride |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 3, 2014 / Details: Oxford Danfysik toroidal focusing mirror |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0781 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→50 Å / Num. obs: 62975 / % possible obs: 97.9 % / Redundancy: 14.2 % / CC1/2: 0.997 / Rrim(I) all: 0.21 / Χ2: 1.09 / Net I/σ(I): 11.22 |
Reflection shell | Resolution: 2.3→2.32 Å / Redundancy: 13.89 % / Mean I/σ(I) obs: 2.16 / Num. unique obs: 33695 / CC1/2: 0.8 / Rrim(I) all: 1.3 / Χ2: 0.98 / % possible all: 96.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1MDW Resolution: 2.3→17.99 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.927 / SU B: 11.429 / SU ML: 0.254 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.403 / ESU R Free: 0.253 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 157.96 Å2 / Biso mean: 60.172 Å2 / Biso min: 27.19 Å2
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Refinement step | Cycle: final / Resolution: 2.3→17.99 Å
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Refine LS restraints |
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Refine LS restraints NCS | Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05
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LS refinement shell | Resolution: 2.304→2.363 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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