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- PDB-4phm: The Structural Basis of Differential Inhibition of Human Calpain ... -

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Basic information

Entry
Database: PDB / ID: 4phm
TitleThe Structural Basis of Differential Inhibition of Human Calpain by Indole and Phenyl alpha-Mercaptoacrylic Acids
ComponentsCalpain small subunit 1
KeywordsHYDROLASE / Calpain / Domain VI / PEF(S) / Human / Calcium Binding / Protease / EF-Hand
Function / homology
Function and homology information


calpain complex / calcium-dependent cysteine-type endopeptidase activity / Formation of the cornified envelope / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / regulation of macroautophagy / Degradation of the extracellular matrix / calcium ion binding / positive regulation of cell population proliferation / proteolysis / extracellular exosome ...calpain complex / calcium-dependent cysteine-type endopeptidase activity / Formation of the cornified envelope / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / regulation of macroautophagy / Degradation of the extracellular matrix / calcium ion binding / positive regulation of cell population proliferation / proteolysis / extracellular exosome / membrane / plasma membrane / cytosol
Similarity search - Function
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
3-(5-bromo-1H-indol-3-yl)-2-thioxopropanoic acid / Calpain small subunit 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.03 Å
AuthorsRizkallah, P.J. / Allemann, R.K. / Adams, S.E. / Miller, D.J. / Hallett, M.B.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)G0701192 United Kingdom
CitationJournal: J.Struct.Biol. / Year: 2014
Title: The structural basis of differential inhibition of human calpain by indole and phenyl alpha-mercaptoacrylic acids.
Authors: Adams, S.E. / Rizkallah, P.J. / Miller, D.J. / Robinson, E.J. / Hallett, M.B. / Allemann, R.K.
History
DepositionMay 6, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Aug 13, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 10, 2014Group: Database references
Revision 1.2Feb 4, 2015Group: Other
Revision 2.0Sep 13, 2017Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Derived calculations
Category: atom_site / pdbx_audit_support ...atom_site / pdbx_audit_support / pdbx_struct_conn_angle / pdbx_validate_close_contact / struct_conn / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _pdbx_audit_support.funding_organization / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.ptnr2_auth_seq_id / _struct_site_gen.auth_seq_id
Revision 2.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
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_asym_id / _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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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_asym_id / _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_asym_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Calpain small subunit 1
B: Calpain small subunit 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,95012
Polymers40,0332
Non-polymers91710
Water2,702150
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4930 Å2
ΔGint-108 kcal/mol
Surface area16510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.410, 79.340, 57.260
Angle α, β, γ (deg.)90.00, 91.23, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Calpain small subunit 1 / CSS1 / Calcium-activated neutral proteinase small subunit / CANP small subunit / Calcium-dependent ...CSS1 / Calcium-activated neutral proteinase small subunit / CANP small subunit / Calcium-dependent protease small subunit / CDPS / Calcium-dependent protease small subunit 1 / Calpain regulatory subunit


Mass: 20016.607 Da / Num. of mol.: 2 / Fragment: residues 96-268
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CAPNS1, CAPN4, CAPNS / Production host: Escherichia coli (E. coli) / References: UniProt: P04632
#2: Chemical ChemComp-2UD / 3-(5-bromo-1H-indol-3-yl)-2-thioxopropanoic acid


Mass: 298.156 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H8BrNO2S
#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.: 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

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Sample preparation

CrystalDensity Matthews: 2.8 Å3/Da / Density % sol: 56.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 50 mM sodium cacodylate, 12.5% PEG6000, 20 mM calcium chloride and 10 mM DTT at pH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9673 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Mar 23, 2013
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9673 Å / Relative weight: 1
ReflectionResolution: 2.03→41.93 Å / Num. all: 27196 / Num. obs: 27196 / % possible obs: 95 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.038 / Net I/σ(I): 17.9
Reflection shellResolution: 2.03→2.08 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.655 / Mean I/σ(I) obs: 2.4 / % possible all: 78.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4PHJ

4phj


Resolution: 2.03→41.93 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.927 / SU B: 11.497 / SU ML: 0.145 / Cross valid method: THROUGHOUT / ESU R: 0.194 / ESU R Free: 0.18 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25094 1360 5 %RANDOM
Rwork0.19716 ---
obs0.19987 25811 94.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 44.789 Å2
Baniso -1Baniso -2Baniso -3
1--0.61 Å2-0 Å2-0.76 Å2
2---0.19 Å20 Å2
3---0.83 Å2
Refinement stepCycle: 1 / Resolution: 2.03→41.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2806 0 40 150 2996
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.022911
X-RAY DIFFRACTIONr_bond_other_d0.0020.022672
X-RAY DIFFRACTIONr_angle_refined_deg2.0071.9543922
X-RAY DIFFRACTIONr_angle_other_deg0.9813.0016120
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5675344
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.44724.156154
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.14315512
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.271522
X-RAY DIFFRACTIONr_chiral_restr0.1250.2410
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023340
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02734
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.272.6681382
X-RAY DIFFRACTIONr_mcbond_other2.2682.6681381
X-RAY DIFFRACTIONr_mcangle_it3.2393.981724
X-RAY DIFFRACTIONr_mcangle_other3.2383.9811725
X-RAY DIFFRACTIONr_scbond_it3.4883.1951529
X-RAY DIFFRACTIONr_scbond_other3.4863.1971530
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.1774.632199
X-RAY DIFFRACTIONr_long_range_B_refined7.53223.7743742
X-RAY DIFFRACTIONr_long_range_B_other7.46823.6413707
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.03→2.083 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.52 77 -
Rwork0.499 1561 -
obs--78.07 %
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)
11.79950.45230.41471.7355-0.44771.20830.1265-0.2235-0.17840.3122-0.07630.15650.2763-0.0835-0.05020.1899-0.01730.03320.1654-0.01940.068313.5457-0.627215.3879
22.9861-0.5143-0.11992.60630.79140.70770.02980.05290.092-0.19810.0333-0.0484-0.12380.0696-0.06310.0269-0.01950.00230.03330.01630.027128.36049.51880.1232
320.9654-16.47440.617712.9546-0.49180.0231-0.1203-0.03690.39360.08420.0792-0.341-0.0054-0.02820.04120.4421-0.2048-0.00440.3856-0.06150.258812.0765-12.074722.6148
40.9674-3.64621.338615.2872-5.51691.9978-0.07740.0399-0.0236-0.2580.24390.51590.0714-0.0453-0.16650.3497-0.05-0.06990.38870.01880.24540.06257.0014-6.7583
51.2066-0.4211-0.25531.3444-0.75280.646-0.0836-0.0083-0.07290.10850.027-0.0317-0.0366-0.01310.05670.12230.00020.01160.1574-0.00710.075318.812-4.062316.318
61.129-0.4108-0.81063.2516-0.35770.71930.27480.0311-0.1492-0.0866-0.37230.0994-0.1990.05270.09740.1125-0.0215-0.05110.1138-0.03050.095429.54883.2185-0.5125
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A96 - 268
2X-RAY DIFFRACTION2B96 - 268
3X-RAY DIFFRACTION3A270
4X-RAY DIFFRACTION4B270
5X-RAY DIFFRACTION5A301 - 304
6X-RAY DIFFRACTION6B301 - 304

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