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- PDB-1kfu: Crystal Structure of Human m-Calpain Form II -

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Basic information

Entry
Database: PDB / ID: 1kfu
TitleCrystal Structure of Human m-Calpain Form II
Components
  • M-CALPAIN LARGE SUBUNIT
  • M-CALPAIN SMALL SUBUNIT
KeywordsHYDROLASE / REGULATION / PAPAIN-LIKE / THIOL-PROTEASE
Function / homology
Function and homology information


calpain-2 / positive regulation of phosphatidylcholine biosynthetic process / calpain complex / protein catabolic process at postsynapse / calcium-dependent cysteine-type endopeptidase activity / perinuclear endoplasmic reticulum / Formation of the cornified envelope / myoblast fusion / regulation of interleukin-6 production / positive regulation of myoblast fusion ...calpain-2 / positive regulation of phosphatidylcholine biosynthetic process / calpain complex / protein catabolic process at postsynapse / calcium-dependent cysteine-type endopeptidase activity / perinuclear endoplasmic reticulum / Formation of the cornified envelope / myoblast fusion / regulation of interleukin-6 production / positive regulation of myoblast fusion / cortical actin cytoskeleton / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / regulation of cytoskeleton organization / pseudopodium / vascular endothelial cell response to oscillatory fluid shear stress / behavioral response to pain / protein autoprocessing / blastocyst development / synaptic vesicle endocytosis / regulation of macroautophagy / response to mechanical stimulus / vascular endothelial cell response to laminar fluid shear stress / positive regulation of cardiac muscle cell apoptotic process / cellular response to interferon-beta / cytoskeletal protein binding / Degradation of the extracellular matrix / cysteine-type peptidase activity / proteolysis involved in protein catabolic process / Turbulent (oscillatory, disturbed) flow shear stress activates signaling by PIEZO1 and integrins in endothelial cells / cellular response to amino acid stimulus / response to hydrogen peroxide / female pregnancy / presynapse / cellular response to lipopolysaccharide / High laminar flow shear stress activates signaling by PIEZO1 and PECAM1:CDH5:KDR in endothelial cells / response to hypoxia / lysosome / postsynapse / membrane raft / external side of plasma membrane / focal adhesion / neuronal cell body / positive regulation of cell population proliferation / dendrite / calcium ion binding / chromatin / protein-containing complex binding / enzyme binding / endoplasmic reticulum / Golgi apparatus / proteolysis / extracellular exosome / nucleus / membrane / plasma membrane / cytoplasm / cytosol
Similarity search - Function
CAPN2, penta-EF hand, calcium binding motif / Calpain subdomain III / Peptidase C2, calpain, domain III / calpain_III / Jelly Rolls - #380 / Peptidase C2, calpain, large subunit, domain III / Peptidase C2, calpain family / Calpain large subunit, domain III superfamily / Calpain large subunit, domain III / Peptidase C2, calpain, catalytic domain ...CAPN2, penta-EF hand, calcium binding motif / Calpain subdomain III / Peptidase C2, calpain, domain III / calpain_III / Jelly Rolls - #380 / Peptidase C2, calpain, large subunit, domain III / Peptidase C2, calpain family / Calpain large subunit, domain III superfamily / Calpain large subunit, domain III / Peptidase C2, calpain, catalytic domain / Calpain family cysteine protease / Cysteine proteinase, calpain-type, catalytic domain profile. / Calpain-like thiol protease family. / EF-hand domain pair / Cysteine proteinases / Cysteine peptidase, cysteine active site / Eukaryotic thiol (cysteine) proteases cysteine active site. / Cathepsin B; Chain A / EF-hand / Recoverin; domain 1 / Papain-like cysteine peptidase superfamily / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / Jelly Rolls / Alpha-Beta Complex / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Calpain small subunit 1 / Calpain-2 catalytic subunit
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.5 Å
AuthorsStrobl, 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.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 2000
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: Journal: Acta Crystallogr.,Sect.D / Year: 2000
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: Journal: Biol.Chem. / Year: 2001
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: Journal: Trends Cardiovasc.Med. / Year: 2001
Title: The structure of calcium-free human m-calpain
Authors: Reverter, D. / Sorimachi, H. / Bode, W.
History
DepositionNov 23, 2001Deposition site: RCSB / Processing site: RCSB
SupersessionDec 7, 2001ID: 1DKV
Revision 1.0Dec 7, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 2, 2012Group: Structure summary
Revision 1.4Feb 7, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
L: M-CALPAIN LARGE SUBUNIT
S: M-CALPAIN SMALL SUBUNIT


Theoretical massNumber of molelcules
Total (without water)101,2322
Polymers101,2322
Non-polymers00
Water7,404411
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6000 Å2
ΔGint-27 kcal/mol
Surface area39170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.88, 169.84, 64.44
Angle α, β, γ (deg.)90.0, 95.12, 90.0
Int Tables number4
Cell settingmonoclinic
Space group name H-MP1211

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Components

#1: Protein M-CALPAIN LARGE SUBUNIT / E.C.3.4.22.53 / CALPAIN 2 / LARGE [CATALYTIC] SUBUNIT / CALCIUM-ACTIVATED NEUTRAL PROTEINASE / CANP


Mass: 79968.023 Da / Num. of mol.: 1 / Fragment: CATALYTIC SUBUNIT
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P17655, calpain-2
#2: Protein M-CALPAIN SMALL SUBUNIT / CALCIUM-DEPENDENT PROTEASE / SMALL SUBUNIT / CALPAIN REGULATORY SUBUNIT / CALCIUM-ACTIVATED NEUTRAL ...CALCIUM-DEPENDENT PROTEASE / SMALL SUBUNIT / CALPAIN REGULATORY SUBUNIT / CALCIUM-ACTIVATED NEUTRAL PROTEINASE / CANP


Mass: 21263.859 Da / Num. of mol.: 1 / Fragment: REGULATORY SUBUNIT
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P04632
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 411 / Source method: isolated from a natural source / Formula: H2O

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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: 2.79 Å3/Da / Density % sol: 55.95 %
Crystal growTemperature: 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 diffusion
Details: Masumoto, H., (2000) Acta Crystallogr., Sect.D, 56, 73.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
114 mg/mlprotein1drop
210 mMTris-HCl1droppH7.5
350 mM1dropNaCl
41 mMEDTA1drop
51 mMDTE1drop
61 Mguanidium chloride1drop
715 %PEG100001reservoir
82.2 %2-propanol1reservoir
9100 mMHEPES-NaOH1reservoirpH7.7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 11, 1998
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionHighest 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

Software
NameVersionClassification
CNSrefinement
DENZOdata reduction
CCP4(SCALA)data scaling
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 2.5→30 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflection
Rfree0.276 1520 4 %
Rwork0.221 --
obs-37830 -
Displacement parametersBiso mean: 19 Å2
Refinement stepCycle: LAST / Resolution: 2.5→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7119 0 0 411 7530
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0108
X-RAY DIFFRACTIONc_angle_d1.6
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
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_deg1.179

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