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- PDB-1nx0: Structure of Calpain Domain 6 in Complex with Calpastatin DIC -

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Basic information

Entry
Database: PDB / ID: 1nx0
TitleStructure of Calpain Domain 6 in Complex with Calpastatin DIC
Components
  • Calcium-dependent protease, small subunit
  • Calpastatin
  • Small molecule inhibitor
KeywordsHYDROLASE/HYDROLASE INHIBITOR / CALCIUM BINDING / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


calcium-dependent cysteine-type endopeptidase inhibitor activity / Degradation of the extracellular matrix / calpain complex / calcium-dependent cysteine-type endopeptidase activity / cysteine-type endopeptidase inhibitor activity / protein catabolic process / calcium ion binding / proteolysis / plasma membrane / cytoplasm
Similarity search - Function
Proteinase inhibitor I27, calpastatin / Calpastatin / Calpain inhibitor / EF-hand / Recoverin; domain 1 / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair ...Proteinase inhibitor I27, calpastatin / Calpastatin / Calpain inhibitor / EF-hand / Recoverin; domain 1 / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Calpain small subunit 1 / Calpastatin / Calpastatin
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsTodd, B. / Moore, D. / Deivanayagam, C.C.S. / Lin, G.-D. / Chattopadhyay, D. / Maki, M. / Wang, K.K.W. / Narayana, S.V.L.
CitationJournal: J.Mol.Biol. / Year: 2003
Title: A structural model for the inhibition of calpain by calpastatin: crystal structures of the native domain VI of calpain and its complexes with calpastatin peptide and a small molecule inhibitor.
Authors: Todd, B. / Moore, D. / Deivanayagam, C.C.S. / Lin, G.-D. / Chattopadhyay, D. / Maki, M. / Wang, K.K.W. / Narayana, S.V.L.
History
DepositionFeb 7, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 19, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary / Version format compliance
Revision 1.3May 2, 2012Group: Structure summary
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Calcium-dependent protease, small subunit
B: Calcium-dependent protease, small subunit
C: Calpastatin
D: Calpastatin
E: Small molecule inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,96411
Polymers42,7235
Non-polymers2406
Water2,702150
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.780, 83.300, 92.150
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Calcium-dependent protease, small subunit / Calpain regulatory subunit / Calcium-activated neutral proteinase / CANP


Mass: 19883.477 Da / Num. of mol.: 2 / Fragment: Domain VI
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Gene: CAPNS1 OR CAPN4 / Production host: Escherichia coli (E. coli) / References: UniProt: P04574
#2: Protein/peptide Calpastatin / / calpain inhibitor


Mass: 1241.261 Da / Num. of mol.: 2 / Fragment: DIC, residues 230-241
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Production host: Escherichia coli (E. coli) / References: UniProt: P49342, UniProt: P12675*PLUS
#3: Protein/peptide Small molecule inhibitor


Mass: 473.586 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: THE Peptide WAS CHEMICALLY SYNTHESIZED.
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 150 / 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: 2.42 Å3/Da / Density % sol: 49.08 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 5.5
Details: PEG 6000, BME, EDTA, CaCl2, NaCl, pH 5.5, VAPOR DIFFUSION, HANGING DROP
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
150 mMCAC1reservoir
220 %PEG60001reservoir
35 mMbeta-mercaptoethanol1reservoir
42 mMEDTA1reservoir
52 mM1reservoirCaCl2
6200 mM1reservoirNaCl
75 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 103 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→100 Å / Num. all: 18854 / Num. obs: 18854 / % possible obs: 98.2 % / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.06 / Net I/σ(I): 17.5
Reflection
*PLUS
Highest resolution: 2.3 Å / Rmerge(I) obs: 0.06

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS0.9refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→100 Å / σ(F): 3 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.261 1885 10 %random
Rwork0.218 ---
all0.218 18854 --
obs0.218 18854 --
Refinement stepCycle: LAST / Resolution: 2.3→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2989 0 6 150 3145
Refinement
*PLUS
Highest resolution: 2.3 Å / Rfactor Rfree: 0.213 / Rfactor Rwork: 0.264
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONbond_d0.0101
X-RAY DIFFRACTIONangle_d
X-RAY DIFFRACTIONangle_deg1.327

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