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Open data
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Basic information
Entry | Database: PDB / ID: 1kfu | |||||||||
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Title | Crystal Structure of Human m-Calpain Form II | |||||||||
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![]() | HYDROLASE / REGULATION / PAPAIN-LIKE / THIOL-PROTEASE | |||||||||
Function / homology | ![]() calpain-2 / positive regulation of phosphatidylcholine biosynthetic process / calpain complex / calcium-dependent cysteine-type endopeptidase activity / perinuclear endoplasmic reticulum / Formation of the cornified envelope / myoblast fusion / regulation of interleukin-6 production / cortical actin cytoskeleton / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models ...calpain-2 / positive regulation of phosphatidylcholine biosynthetic process / calpain complex / calcium-dependent cysteine-type endopeptidase activity / perinuclear endoplasmic reticulum / Formation of the cornified envelope / myoblast fusion / regulation of interleukin-6 production / cortical actin cytoskeleton / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / positive regulation of myoblast fusion / positive regulation of cardiac muscle cell apoptotic process / behavioral response to pain / regulation of cytoskeleton organization / pseudopodium / blastocyst development / protein autoprocessing / cellular response to interferon-beta / regulation of macroautophagy / response to mechanical stimulus / cysteine-type peptidase activity / cytoskeletal protein binding / Degradation of the extracellular matrix / proteolysis involved in protein catabolic process / female pregnancy / cellular response to amino acid stimulus / response to hydrogen peroxide / cellular response to lipopolysaccharide / lysosome / response to hypoxia / membrane raft / external side of plasma membrane / focal adhesion / neuronal cell body / calcium ion binding / dendrite / positive regulation of cell population proliferation / protein-containing complex binding / chromatin / Golgi apparatus / enzyme binding / endoplasmic reticulum / proteolysis / extracellular exosome / membrane / nucleus / plasma membrane / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Strobl, S. / Fernandez-Catalan, C. / Braun, M. / Huber, R. / Masumoto, H. / Nakagawa, K. / Irie, A. / Sorimachi, H. / Bourenkow, G. / Bartunik, H. ...Strobl, S. / Fernandez-Catalan, C. / Braun, M. / Huber, R. / Masumoto, H. / Nakagawa, K. / Irie, A. / Sorimachi, H. / Bourenkow, G. / Bartunik, H. / Suzuki, K. / Bode, W. | |||||||||
![]() | ![]() Title: The crystal structure of calcium-free human m-calpain suggests an electrostatic switch mechanism for activation by calcium. Authors: Strobl, S. / Fernandez-Catalan, C. / Braun, M. / Huber, R. / Masumoto, H. / Nakagawa, K. / Irie, A. / Sorimachi, H. / Bourenkow, G. / Bartunik, H. / Suzuki, K. / Bode, W. #1: ![]() Title: Crystallization and preliminary X-ray analysis of recombinant full-length m-calpain Authors: Masumoto, H. / Nakagawa, K. / Irie, S. / Sorimachi, H. / Suzuki, K. / Bourenkow, G. / Bartunik, H. / Fernandez-Catalan, C. / Bode, W. / Strobl, S. #2: ![]() Title: Structural basis for possible calcium-induced activation mechanisms of calpains Authors: Reverter, D. / Strobl, S. / Fernandez-Catalan, C. / Sorimachi, H. / Suzuki, K. / Bode, W. #3: ![]() Title: The structure of calcium-free human m-calpain Authors: Reverter, D. / Sorimachi, H. / Bode, W. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 195.5 KB | Display | ![]() |
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PDB format | ![]() | 152.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 381.2 KB | Display | ![]() |
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Full document | ![]() | 444.4 KB | Display | |
Data in XML | ![]() | 27.2 KB | Display | |
Data in CIF | ![]() | 41.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components
#1: Protein | Mass: 79968.023 Da / Num. of mol.: 1 / Fragment: CATALYTIC SUBUNIT Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Protein | Mass: 21263.859 Da / Num. of mol.: 1 / Fragment: REGULATORY SUBUNIT Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.79 Å3/Da / Density % sol: 55.95 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: PEG 10000, isopropanol, guanidinium chloride, pH 7.5, VAPOR DIFFUSION, SITTING DROP at 293K, VAPOR DIFFUSION, SITTING DROP | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusionDetails: Masumoto, H., (2000) Acta Crystallogr., Sect.D, 56, 73. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Oct 11, 1998 |
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Highest resolution: 2.3 Å / Num. all: 47236 / Num. obs: 47236 / % possible obs: 94.8 % / Rmerge(I) obs: 0.045 |
Reflection | *PLUS Num. measured all: 400680 |
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Processing
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Refinement | Method to determine structure: ![]()
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Displacement parameters | Biso mean: 19 Å2 | ||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→30 Å
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Refine LS restraints |
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Software | *PLUS Name: CNS / Classification: refinement | ||||||||||||||||
Refinement | *PLUS Lowest resolution: 30 Å / Num. reflection obs: 38544 / σ(F): 2 / % reflection Rfree: 4 % / Rfactor obs: 0.206 / Rfactor Rfree: 0.266 | ||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||
Displacement parameters | *PLUS Biso mean: 19 Å2 | ||||||||||||||||
Refine LS restraints | *PLUS
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