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- PDB-1nx1: Calpain Domain VI Complexed with Calpastatin Inhibitory Domain C (DIC) -

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Basic information

Entry
Database: PDB / ID: 1nx1
TitleCalpain Domain VI Complexed with Calpastatin Inhibitory Domain C (DIC)
Components
  • Calcium-dependent protease, small subunit
  • Calpastatin
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 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_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_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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)42,39612
Polymers42,0754
Non-polymers3218
Water1,874104
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7510 Å2
ΔGint-147 kcal/mol
Surface area16720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.746, 61.055, 143.704
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: 1154.183 Da / Num. of mol.: 2 / Fragment: DIC, RESIDUES 230-240
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: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 104 / 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: 3.18 Å3/Da / Density % sol: 56.1 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 6.2
Details: PEG 6000, BME, EDTA, CaCl2, NaCl, pH 6.2, 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: 1.54 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2→100 Å / Num. all: 30252 / Num. obs: 30252 / % possible obs: 92.2 % / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.041 / Net I/σ(I): 18.5
Reflection
*PLUS
Highest resolution: 2 Å

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→100 Å / σ(F): 3 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.253 3025 10 %random
Rwork0.208 ---
obs0.208 30252 --
all-30252 --
Refinement stepCycle: LAST / Resolution: 2→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2952 0 8 104 3064
Refinement
*PLUS
Highest resolution: 2 Å / Rfactor Rfree: 0.208 / Rfactor Rwork: 0.253
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONbond_d0.0097
X-RAY DIFFRACTIONangle_d
X-RAY DIFFRACTIONangle_deg1.315

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