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- PDB-1mdw: Crystal Structure of Calcium-Bound Protease Core of Calpain II Re... -

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Basic information

Entry
Database: PDB / ID: 1mdw
TitleCrystal Structure of Calcium-Bound Protease Core of Calpain II Reveals the Basis for Intrinsic Inactivation
ComponentsCalpain II, catalytic subunit
KeywordsHYDROLASE / Calpain Cysteine Protease Fold / Two Cooperative Calcium Sites / Helix Instability / Tryptophan-Based Active Site Blockage
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 / positive regulation of cardiac muscle cell apoptotic process ...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 / positive regulation of cardiac muscle cell apoptotic process / behavioral response to pain / 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 / neuronal cell body / dendrite / calcium ion binding / chromatin / protein-containing complex binding / Golgi apparatus / enzyme binding / endoplasmic reticulum / proteolysis / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
CAPN2, penta-EF hand, calcium binding motif / Calpain subdomain III / 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 ...CAPN2, penta-EF hand, calcium binding motif / Calpain subdomain III / 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 / 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 / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Calpain-2 catalytic subunit
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsMoldoveanu, T. / Hosfield, C.M. / Lim, D. / Jia, Z. / Davies, P.L.
Citation
Journal: Nat.Struct.Biol. / Year: 2003
Title: Calpain silencing by a reversible intrinsic mechanism.
Authors: Moldoveanu, T. / Hosfield, C.M. / Lim, D. / Jia, Z. / Davies, P.L.
#1: Journal: Cell(Cambridge,Mass.) / Year: 2002
Title: A Ca(2+) Switch Aligns the Active Site of Calpain
Authors: Moldoveanu, T. / Hosfield, C.M. / Lim, D. / Elce, J.S. / Jia, Z. / Davies, P.L.
#2: 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.
History
DepositionAug 7, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 29, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Calpain II, catalytic subunit
B: Calpain II, catalytic subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,7766
Polymers73,6162
Non-polymers1604
Water6,575365
1
A: Calpain II, catalytic subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,8883
Polymers36,8081
Non-polymers802
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Calpain II, catalytic subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,8883
Polymers36,8081
Non-polymers802
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.6, 80.6, 75.3
Angle α, β, γ (deg.)90, 103.9, 90
Int Tables number4
Space group name H-MP1211
DetailsThe biological assembly is the monomer of the dimer in the assymetric unit

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Components

#1: Protein Calpain II, catalytic subunit / / Calcium-activated neutral proteinase / CANP / M-type / M-calpain / Millimolar-calpain


Mass: 36807.980 Da / Num. of mol.: 2 / Fragment: Protease Core Domains I and II (Residues 17-346) / Mutation: C105S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: CALPAIN II / Plasmid: pET24d / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q07009, EC: 3.4.22.17
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 365 / 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: 2.5 Å3/Da / Density % sol: 50.88 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 10% PEG6000, 0.1M Sodium Acetate, 30mM calcium chloride, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110 %(w/v)PEG60001reservoir
20.1 Msodium acetate1reservoirpH5.5
330 mM1reservoirCaCl2
415 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 7, 2001 / Details: Mirrors
RadiationMonochromator: Yale Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.95→20 Å / Num. obs: 48591 / % possible obs: 93.9 % / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.049 / Rsym value: 0.035 / Net I/σ(I): 21.1
Reflection shellResolution: 1.95→2.05 Å / Rmerge(I) obs: 0.356 / Mean I/σ(I) obs: 3.3 / Num. unique all: 4424 / Rsym value: 0.326 / % possible all: 89.9
Reflection
*PLUS
Lowest resolution: 50 Å / Num. measured all: 496583
Reflection shell
*PLUS
% possible obs: 89.9 % / Num. unique obs: 4424 / Num. measured obs: 14861

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→20 Å / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.243 2437 Random
Rwork0.207 --
all-53015 -
obs-48591 -
Refinement stepCycle: LAST / Resolution: 1.95→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5041 0 4 365 5410
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_d1.191
X-RAY DIFFRACTIONc_bond_d0.005
Refinement
*PLUS
Lowest resolution: 50 Å / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS

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