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- PDB-1qxp: Crystal Structure of a mu-like calpain -

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Basic information

Entry
Database: PDB / ID: 1qxp
TitleCrystal Structure of a mu-like calpain
Componentsmu-like calpain
KeywordsHYDROLASE CHIMERA / m-calpain / mu-calpain / catalytic triad / Ca(2+) requirement
Function / homology
Function and homology information


calpain-2 / calpain-1 / Degradation of the extracellular matrix / positive regulation of phosphatidylcholine biosynthetic process / calpain complex / protein catabolic process at postsynapse / mammary gland involution / positive regulation of leukocyte tethering or rolling / calcium-dependent cysteine-type endopeptidase activity / perinuclear endoplasmic reticulum ...calpain-2 / calpain-1 / Degradation of the extracellular matrix / positive regulation of phosphatidylcholine biosynthetic process / calpain complex / protein catabolic process at postsynapse / mammary gland involution / positive regulation of leukocyte tethering or rolling / calcium-dependent cysteine-type endopeptidase activity / perinuclear endoplasmic reticulum / regulation of catalytic activity / negative regulation of actin filament polymerization / receptor catabolic process / cornified envelope / self proteolysis / positive regulation of vascular permeability / myoblast fusion / response to arsenic-containing substance / response to angiotensin / negative regulation of non-canonical NF-kappaB signal transduction / regulation of interleukin-6 production / Neutrophil degranulation / positive regulation of myoblast fusion / positive regulation of cardiac muscle cell apoptotic process / behavioral response to pain / pseudopodium / protein autoprocessing / blastocyst development / synaptic vesicle endocytosis / 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 / cellular response to hydrogen peroxide / presynapse / peptidase activity / cellular response to lipopolysaccharide / postsynapse / lysosome / postsynaptic density / response to hypoxia / membrane raft / external side of plasma membrane / focal adhesion / neuronal cell body / glutamatergic synapse / dendrite / calcium ion binding / protein-containing complex binding / chromatin / Golgi apparatus / enzyme binding / endoplasmic reticulum / mitochondrion / 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 ...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-1 catalytic subunit / Calpain-2 catalytic subunit
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
Bos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsPal, G.P. / Veyra, T.D. / Elce, J.S. / Jia, Z.
CitationJournal: Structure / Year: 2003
Title: Crystal Structure of a mu-like calpain reveals a partially activated conformation with low Ca(2+) requirement
Authors: Pal, G.P. / Veyra, T.D. / Elce, J.S. / Jia, Z.
History
DepositionSep 8, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 3, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2017Group: Source and taxonomy / Category: entity_src_gen
Revision 1.4Oct 27, 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 1.5Feb 14, 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: mu-like calpain
B: mu-like calpain


Theoretical massNumber of molelcules
Total (without water)207,0202
Polymers207,0202
Non-polymers00
Water5,621312
1
A: mu-like calpain


Theoretical massNumber of molelcules
Total (without water)103,5101
Polymers103,5101
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: mu-like calpain


Theoretical massNumber of molelcules
Total (without water)103,5101
Polymers103,5101
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)72.738, 184.596, 86.370
Angle α, β, γ (deg.)90.00, 100.74, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe biological assembly is a dimer in the asymmetric unit with no local symmetry

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Components

#1: Protein mu-like calpain


Mass: 103509.961 Da / Num. of mol.: 2 / Mutation: C105S
Source method: isolated from a genetically manipulated source
Details: residues 1-49 from m-calpain, residues 60-647 of mu-calpain, residues 636-700 of m-calpain and residues 83-266 of calcium-activated neutral proteinase.
Source: (gene. exp.) Rattus norvegicus (Norway rat), (gene. exp.) Bos taurus (cattle)
Plasmid: pET24 / Production host: Escherichia coli (E. coli)
References: UniProt: Q07009, UniProt: P97571, GenBank: 505658, calpain-1
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 312 / 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: 2.75 Å3/Da / Density % sol: 55.29 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.25
Details: PEG 6000,morpholino ethane sulfonic acid, sodium chloride, n-nonyl-beta-D-maltoside , pH 6.25, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal grow
*PLUS
pH: 7.6 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110-15 mg/mlprotein1drop
250 mMTris-HCl1droppH7.6
3100 mM1dropNaCl
40.2 mMEDTA1drop
510 mMdithiothreitol1drop
68 %PEG60001reservoir
7100 mMMES1reservoirpH6.25
850 mM1reservoirNaCl
96.0 mMn-nonyl-beta-D-maltoside1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.916117 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 20, 2002
RadiationMonochromator: Synchrotron source / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.916117 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. all: 50621 / Num. obs: 50621 / % possible obs: 91.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.7→2.8 Å / % possible all: 81.2
Reflection
*PLUS
Highest resolution: 2.8 Å / Num. obs: 50920 / Num. measured all: 110989 / Rmerge(I) obs: 0.057
Reflection shell
*PLUS
% possible obs: 82.3 % / Rmerge(I) obs: 0.279 / Mean I/σ(I) obs: 3.9

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→91.29 Å / Cor.coef. Fo:Fc: 0.9 / Cor.coef. Fo:Fc free: 0.827 / SU B: 16.808 / SU ML: 0.337 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.465 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.31089 2550 5.1 %RANDOM
Rwork0.22877 ---
all0.2329 47780 --
obs0.23294 47780 91.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 49.683 Å2
Baniso -1Baniso -2Baniso -3
1--0.4 Å20 Å21.47 Å2
2--1.09 Å20 Å2
3----0.14 Å2
Refinement stepCycle: LAST / Resolution: 2.8→91.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12056 0 0 312 12368
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0740.02112336
X-RAY DIFFRACTIONr_bond_other_d0.010.0210923
X-RAY DIFFRACTIONr_angle_refined_deg4.431.93416671
X-RAY DIFFRACTIONr_angle_other_deg1.871325280
X-RAY DIFFRACTIONr_dihedral_angle_1_deg10.19151532
X-RAY DIFFRACTIONr_chiral_restr0.2840.21810
X-RAY DIFFRACTIONr_gen_planes_refined0.0240.0214055
X-RAY DIFFRACTIONr_gen_planes_other0.0230.022659
X-RAY DIFFRACTIONr_nbd_refined0.340.24376
X-RAY DIFFRACTIONr_nbd_other0.320.214802
X-RAY DIFFRACTIONr_nbtor_other0.1440.27714
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2770.2546
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.4350.242
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3680.285
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.4770.29
X-RAY DIFFRACTIONr_mcbond_it3.3411.57787
X-RAY DIFFRACTIONr_mcangle_it5.565212237
X-RAY DIFFRACTIONr_scbond_it7.3834549
X-RAY DIFFRACTIONr_scangle_it10.7024.54434
LS refinement shellResolution: 2.8→2.873 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.432 174
Rwork0.327 3175
Refinement
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 50 Å / Num. reflection obs: 47246 / Rfactor Rfree: 0.31 / Rfactor Rwork: 0.228
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.009
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.4

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