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- PDB-1df0: Crystal structure of M-Calpain -

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Basic information

Entry
Database: PDB / ID: 1df0
TitleCrystal structure of M-Calpain
Components
  • CALPAIN
  • M-CALPAINCalpain-2
KeywordsHYDROLASE / CYSTEINE PROTEASE / CALMODULIN / PAPAIN / CATALYTIC TRIAD / ZYMOGEN ACTIVATION / C2 DOMAIN / PROTEASE / ZYMOGEN / CALPAIN
Function / homology
Function and homology information


calpain-2 / Degradation of the extracellular matrix / positive regulation of phosphatidylcholine biosynthetic process / calpain complex / calcium-dependent cysteine-type endopeptidase activity / perinuclear endoplasmic reticulum / myoblast fusion / regulation of interleukin-6 production / positive regulation of myoblast fusion / behavioral response to pain ...calpain-2 / Degradation of the extracellular matrix / positive regulation of phosphatidylcholine biosynthetic process / calpain complex / calcium-dependent cysteine-type endopeptidase activity / perinuclear endoplasmic reticulum / myoblast fusion / regulation of interleukin-6 production / positive regulation of myoblast fusion / behavioral response to pain / positive regulation of cardiac muscle cell apoptotic process / pseudopodium / blastocyst development / protein autoprocessing / cellular response to interferon-beta / response to mechanical stimulus / cytoskeletal protein binding / proteolysis involved in protein catabolic process / cell projection / female pregnancy / cellular response to amino acid stimulus / protein catabolic process / response to hydrogen peroxide / peptidase activity / cellular response to lipopolysaccharide / lysosome / response to hypoxia / membrane raft / external side of plasma membrane / focal adhesion / dendrite / neuronal cell body / calcium ion binding / chromatin / protein-containing complex binding / Golgi apparatus / enzyme binding / endoplasmic reticulum / proteolysis / membrane / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
CAPN2, penta-EF hand, calcium binding motif / Calpain subdomain III / Jelly Rolls - #380 / Peptidase C2, calpain, domain III / calpain_III / 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 / Jelly Rolls - #380 / Peptidase C2, calpain, domain III / calpain_III / 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-2 catalytic subunit / Calpain small subunit 1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.6 Å
AuthorsHosfield, C.M. / Elce, J.S. / Davies, P.L. / Jia, Z.
Citation
Journal: EMBO J. / Year: 1999
Title: Crystal structure of calpain reveals the structural basis for Ca(2+)-dependent protease activity and a novel mode of enzyme activation.
Authors: Hosfield, C.M. / Elce, J.S. / Davies, P.L. / Jia, Z.
#1: Journal: Nat.Struct.Biol. / Year: 1997
Title: Structure of a Calpain Ca(2+)-Binding Domain Reveals a Novel EF-Hand and Ca(2+) -Induced Conformational Changes
Authors: Blanchard, H. / Grochulski, P. / Li, Y. / Arthur, J.S.C. / Davies, P.L. / Elce, J.S. / Cygler, M.
#2: Journal: Nat.Struct.Biol. / Year: 1997
Title: Crystal Structure of Calcium Bound Domain VI of Calpain at 1.9 A Resolution and its Role in Enzyme Assembly, Regulation, and Inhibitor Binding
Authors: Lin, G.D. / Chattopadhyay, D. / Maki, M. / Wang, K.K. / Carson, M. / Jin, L. / Hatanaka, M. / Takano, E. / Narayana, S.V.
#3: Journal: Acta Crystallogr.,Sect.D / Year: 1999
Title: Crystallization and X-Ray Crystallographic Analysis of M-Calpain: A Ca2+- Dependent Protease
Authors: Hosfield, C.M. / Ye, Q. / Arthur, J.S.C. / Hegadorn, C. / Croall, D.E. / Elce, J.S. / Jia, Z.
History
DepositionNov 16, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 21, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 9, 2012Group: Structure summary
Revision 1.4Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.5Nov 3, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.6Feb 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: M-CALPAIN
B: CALPAIN


Theoretical massNumber of molelcules
Total (without water)101,2992
Polymers101,2992
Non-polymers00
Water6,449358
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5500 Å2
ΔGint-27 kcal/mol
Surface area36280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.696, 80.181, 80.72
Angle α, β, γ (deg.)60.371, 70.848, 79.486
Int Tables number1
Space group name H-MP1
DetailsThe biological assembly is a heterodimer constructed from chain A and chain B

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Components

#1: Protein M-CALPAIN / Calpain-2 / CALCIUM-ACTIVATED NEUTRAL PROTEINASE / CALPAIN 2


Mass: 79994.039 Da / Num. of mol.: 1 / Fragment: LARGE (CATALYTIC) SUBUNIT / Mutation: C105S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Production host: Escherichia coli (E. coli) / References: UniProt: Q07009, calpain-2
#2: Protein CALPAIN / / CALCIUM-ACTIVATED NEUTRAL PROTEINASE


Mass: 21304.979 Da / Num. of mol.: 1
Fragment: DOMAIN VI (CALCIUM-BINDING DOMAIN), SMALL (REGULATORY) SUBUNIT
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Production host: Escherichia coli (E. coli) / References: UniProt: Q64537
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 358 / 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: 3.03 Å3/Da / Density % sol: 59.34 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.25
Details: PEG 6000, MES, SODIUM CHLORIDE, DITHIOTHREITOL, EDTA, pH 6.25, VAPOR DIFFUSION, HANGING DROP
Crystal grow
*PLUS
pH: 6.5
Details: Hosfield, C.M., (1999) Acta Crystallogr., Sect.D, 55, 1484.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
1100 mMMES1droppH6.5
210-12 %PEG60001drop
350 mM1dropNaCl
410 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F2 / Wavelength: 0.923
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 25, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.923 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. all: 227921 / Num. obs: 227921 / % possible obs: 97.7 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.1 % / Biso Wilson estimate: 68.052 Å2 / Rmerge(I) obs: 0.041 / Net I/σ(I): 17.1
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 2.91 % / Rmerge(I) obs: 0.11 / % possible all: 98.1
Reflection
*PLUS

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Processing

Software
NameClassification
SHARPphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 2.6→25 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.293 3454 -RANDOM
Rwork0.223 ---
all0.223 34974 --
obs0.223 34794 96.6 %-
Refinement stepCycle: LAST / Resolution: 2.6→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6391 0 0 358 6749
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.6 Å / Lowest resolution: 25 Å / σ(F): 0
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0095
X-RAY DIFFRACTIONc_angle_deg1.452

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