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- PDB-3bow: Structure of M-calpain in complex with Calpastatin -

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Basic information

Entry
Database: PDB / ID: 3bow
TitleStructure of M-calpain in complex with Calpastatin
Components
  • Calpain small subunit 1
  • Calpain-2 catalytic subunit
  • Calpastatin
Keywordshydrolase/hydrolase inhibitor / cysteine protease / inhibitor / Cell membrane / Hydrolase / Membrane / Protease / Thiol protease / Phosphoprotein / Protease inhibitor / Thiol protease inhibitor / hydrolase-hydrolase inhibitor COMPLEX
Function / homology
Function and homology information


egg activation / calcium-dependent cysteine-type endopeptidase inhibitor activity / calpain-2 / negative regulation of type B pancreatic cell apoptotic process / Degradation of the extracellular matrix / positive regulation of phosphatidylcholine biosynthetic process / calpain complex / calcium-dependent cysteine-type endopeptidase activity / perinuclear endoplasmic reticulum / myoblast fusion ...egg activation / calcium-dependent cysteine-type endopeptidase inhibitor activity / calpain-2 / negative regulation of type B pancreatic cell apoptotic process / Degradation of the extracellular matrix / positive regulation of phosphatidylcholine biosynthetic process / calpain complex / calcium-dependent cysteine-type endopeptidase activity / perinuclear endoplasmic reticulum / myoblast fusion / myoblast differentiation / regulation of interleukin-6 production / positive regulation of myoblast fusion / positive regulation of cardiac muscle cell apoptotic process / regulation of protein catabolic process / behavioral response to pain / pseudopodium / blastocyst development / protein autoprocessing / cellular response to interferon-beta / animal organ regeneration / response to mechanical stimulus / cytoskeletal protein binding / liver development / 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 / protease binding / postsynaptic density / lysosome / response to hypoxia / membrane raft / external side of plasma membrane / focal adhesion / neuronal cell body / calcium ion binding / dendrite / protein-containing complex binding / chromatin / Golgi apparatus / enzyme binding / endoplasmic reticulum / proteolysis / membrane / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Proteinase inhibitor I27, calpastatin / Calpastatin / Calpain inhibitor / 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 ...Proteinase inhibitor I27, calpastatin / Calpastatin / Calpain inhibitor / 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
Calpastatin / Calpain-2 catalytic subunit / Calpain small subunit 1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.4 Å
AuthorsHanna, R.A. / Campbell, R.L. / Davies, P.L.
CitationJournal: Nature / Year: 2008
Title: Calcium-bound structure of calpain and its mechanism of inhibition by calpastatin.
Authors: Hanna, R.A. / Campbell, R.L. / Davies, P.L.
History
DepositionDec 17, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 25, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Calpain-2 catalytic subunit
B: Calpain small subunit 1
C: Calpastatin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,04913
Polymers113,6483
Non-polymers40110
Water3,171176
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12230 Å2
ΔGint-164 kcal/mol
Surface area39320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.477, 66.985, 108.656
Angle α, β, γ (deg.)90.00, 100.76, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Calpain-2 catalytic subunit / Calpain-2 large subunit / Calcium-activated neutral proteinase 2 / CANP 2 / Calpain M-type / M- ...Calpain-2 large subunit / Calcium-activated neutral proteinase 2 / CANP 2 / Calpain M-type / M-calpain / Millimolar-calpain


Mass: 81577.836 Da / Num. of mol.: 1 / Mutation: C105S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Capn2 / Plasmid: pET24d / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q07009, calpain-2
#2: Protein Calpain small subunit 1 / CSS1 / Calcium-dependent protease small subunit 1 / Calcium-dependent protease small subunit / CDPS ...CSS1 / Calcium-dependent protease small subunit 1 / Calcium-dependent protease small subunit / CDPS / Calpain regulatory subunit / Calcium-activated neutral proteinase small subunit / CANP small subunit


Mass: 21304.979 Da / Num. of mol.: 1 / Fragment: UNP residues 88-270
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Capns1, Capn4, Css1 / Plasmid: pACYC177 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q64537, calpain-2
#3: Protein Calpastatin / Calpain inhibitor


Mass: 10765.660 Da / Num. of mol.: 1 / Fragment: UNP residues 571-664
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Cast / Plasmid: pET24a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P27321
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 176 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsCONFLICT IN UNP DB P27321 AT RESIDUE 646:LEU TO PRO

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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: 2.12 Å3/Da / Density % sol: 42.05 %
Crystal growTemperature: 298 K / pH: 6.5
Details: pH 6.5, microbatch under paraffin oil, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 1
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 24, 2007 / Details: MIRRORS
RadiationMonochromator: SI(111) CHANNEL CUT MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→66.965 Å / Num. obs: 36208 / % possible obs: 96.7 % / Redundancy: 3.6 % / Biso Wilson estimate: 34.1 Å2 / Rmerge(I) obs: 0.084 / Rsym value: 0.084 / Net I/σ(I): 7.7
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.317 / Mean I/σ(I) obs: 2.2 / Rsym value: 0.317 / % possible all: 82.5

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å33.57 Å
Translation2.5 Å33.57 Å

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.004data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1KFU PDB ENTRY 1TL9

1kfu

1tl9


Resolution: 2.4→66.23 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.888 / SU B: 16.918 / SU ML: 0.204 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.67 / ESU R Free: 0.299 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.25784 1819 5 %RANDOM
Rwork0.19756 ---
obs0.20062 34375 96.47 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 11.827 Å2
Baniso -1Baniso -2Baniso -3
1-0.48 Å20 Å2-0.33 Å2
2--0.22 Å20 Å2
3----0.83 Å2
Refinement stepCycle: LAST / Resolution: 2.4→66.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7396 0 10 176 7582
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0227612
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2371.95510200
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1385915
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.76524.513390
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.628151340
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.4451552
X-RAY DIFFRACTIONr_chiral_restr0.0860.21090
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.025788
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2030.23470
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2990.25145
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1440.2360
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.1220.225
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1870.244
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1150.213
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.511.54749
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.84127324
X-RAY DIFFRACTIONr_scbond_it1.16633270
X-RAY DIFFRACTIONr_scangle_it1.9194.52875
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.308 100 -
Rwork0.212 1972 -
obs--75.65 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.92100.29591.88590.13471.868-0.0134-0.3285-0.07260.27830.01580.00910.10490.0921-0.00250.00110.034700.09240.00770.089414.4229.4739.413
23.3101-0.9142-0.01831.1107-0.01661.1205-0.01550.15560.1427-0.04090.0260.0336-0.0787-0.0243-0.0105-0.0345-0.00430.00860.02590.01810.0923-2.36218.21119.012
32.38470.71830.3631.38120.15791.11510.01710.2665-0.0795-0.0146-0.0092-0.00140.09720.1385-0.008-0.01940.05460.01410.060.01750.115525.083.6177.208
41.8721-1.4870.56651.1841-0.43190.28430.00340.0637-0.07070.0223-0.0218-0.04310.0559-0.04520.01840.03120.00760.02050.1111-0.00350.19347.827-13.42115.452
52.03770.7564-1.17331.9767-1.71993.4570.0545-0.0997-0.0596-0.0126-0.04810.20360.225-0.1265-0.0064-0.01190.01590.01740.0482-0.04180.108638.97-12.1324.263
615.5584-0.8071-5.15286.77693.292316.29560.116-1.74631.46631.30850.5157-0.0142-0.033-0.1199-0.63170.26330.0731-0.01940.2541-0.09860.292538.94115.24945.876
74.6837-0.4678-0.17173.7779-1.35362.9998-0.2609-0.25180.02090.32250.0428-0.14810.09140.13630.21810.01850.02440.0270.0657-0.0390.075648.972.54342.079
86.73571.77930.353417.1426-0.91695.4136-0.5016-0.0127-1.01180.06060.5762-0.28320.6440.399-0.07470.16880.14220.08550.12690.12220.233553.116-14.26845.197
92.65541.64360.44781.1296-0.28312.87220.208-0.2972-0.14940.25290.0787-0.03160.0625-0.5467-0.28670.06630.02930.08460.12170.08860.233135.847-11.75838.814
1035.5799-19.792215.783331.0399-13.131815.25970.75382.68271.0812-1.2996-1.1983-0.6005-0.24881.16750.44460.1554-0.02120.16130.180.04520.196661.746-12.3576.977
1142.9703-22.9763-40.60718.434626.108441.55180.2998-0.01150.0645-0.4157-0.27430.3837-0.75450.3879-0.02550.16940.0148-0.06440.18530.15310.21828.80617.0521.669
123.9034-4.49541.48688.99283.77928.47-0.1036-0.15440.7073-0.8680.4475-0.8994-1.07020.7968-0.34390.1473-0.046-0.05570.1173-0.0850.323712.79827.15827.686
131.8357-5.62583.476928.66946.401232.0428-0.44410.23451.34810.7520.2404-0.2974-1.79361.02930.20370.23480.0216-0.03080.2612-0.07140.239111.74930.18939.286
1422.24243.537714.186934.68074.561632.2637-0.5325-1.16780.33581.78810.0135-0.0102-1.32130.32940.5190.30130.0399-0.06010.3029-0.07780.290351.56313.50148.092
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A23 - 203
2X-RAY DIFFRACTION2A204 - 343
3X-RAY DIFFRACTION3A344 - 475
4X-RAY DIFFRACTION4A476 - 620
5X-RAY DIFFRACTION5A621 - 696
6X-RAY DIFFRACTION6B97 - 117
7X-RAY DIFFRACTION7B118 - 191
8X-RAY DIFFRACTION8B192 - 228
9X-RAY DIFFRACTION9B229 - 270
10X-RAY DIFFRACTION10C571 - 588
11X-RAY DIFFRACTION11C595 - 609
12X-RAY DIFFRACTION12C610 - 619
13X-RAY DIFFRACTION13C620 - 629
14X-RAY DIFFRACTION14C650 - 661

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