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- PDB-4wq2: Human calpain PEF(S) with (Z)-3-(6-bromondol-3-yl)-2-mercaptoacry... -

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Basic information

Entry
Database: PDB / ID: 4wq2
TitleHuman calpain PEF(S) with (Z)-3-(6-bromondol-3-yl)-2-mercaptoacrylic acid bound
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 / positive regulation of cell population proliferation / calcium ion binding / 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 / positive regulation of cell population proliferation / calcium ion binding / 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
Chem-3SU / Calpain small subunit 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.64 Å
AuthorsAdams, S.E. / Rizkallah, P.J. / Miller, D.J. / Hallett, M.B. / Allemann, R.K.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)G0701192 United Kingdom
CitationJournal: Chem Sci / Year: 2015
Title: Conformationally restricted calpain inhibitors.
Authors: Adams, S.E. / Robinson, E.J. / Miller, D.J. / Rizkallah, P.J. / Hallett, M.B. / Allemann, R.K.
History
DepositionOct 21, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Sep 2, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 30, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_id_ISSN / _citation.journal_volume ..._citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 2.0Sep 13, 2017Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Derived calculations
Category: atom_site / diffrn_radiation_wavelength ...atom_site / diffrn_radiation_wavelength / pdbx_audit_support / pdbx_distant_solvent_atoms / 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_distant_solvent_atoms.auth_seq_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.ptnr2_auth_seq_id / _struct_site_gen.auth_seq_id
Revision 2.1Jan 10, 2024Group: 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_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)41,19816
Polymers40,0332
Non-polymers1,16514
Water2,828157
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6030 Å2
ΔGint-106 kcal/mol
Surface area16400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.720, 78.430, 56.300
Angle α, β, γ (deg.)90.000, 91.120, 90.000
Int Tables number4
Space group name H-MP1211
Detailsbiological unit is the same as asym.

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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: Protease domain, UNP residues 92-268
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CAPNS1, CAPN4, CAPNS / Plasmid: pET21d / Production host: Escherichia Coli BL21(DE3) (bacteria) / References: UniProt: P04632
#2: Chemical ChemComp-3SU / (2Z)-3-(6-bromo-1H-indol-3-yl)-2-sulfanylprop-2-enoic 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: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 157 / 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: 2.74 Å3/Da / Density % sol: 55.13 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 3 UL PROTEIN (10 MG/ML PEF(S), 5 MM SODIUM CACODYLATE, 2 MM EDTA, 5 MM BME, 1 MM CALCIUM CHLORIDE, PH 7.0) + 3 UL PRECIPITANT (50 MM SODIUM CACODYLATE, 12.5% PEG6000, 20 MM CALCIUM CHLORIDE, PH 7.0) + 1 UL WATER

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.976 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 16, 2013
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.64→41.99 Å / Num. all: 51550 / Num. obs: 51550 / % possible obs: 97.5 % / Redundancy: 3.7 % / CC1/2: 0.997 / Rmerge(I) obs: 0.052 / Rpim(I) all: 0.031 / Net I/σ(I): 16.1 / Num. measured all: 190491
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
1.64-1.683.60.9011.71358337490.6660.54796.5
7.33-41.993.40.03340.219345620.9890.02289.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
Aimless0.2.12data scaling
Coot0.6.2model building
REFMAC5.8.0049refinement
PDB_EXTRACT3.15data extraction
xia2data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4phj

4phj


Resolution: 1.64→41.99 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.964 / WRfactor Rfree: 0.2032 / WRfactor Rwork: 0.1735 / FOM work R set: 0.8594 / SU B: 3.918 / SU ML: 0.062 / SU R Cruickshank DPI: 0.0853 / SU Rfree: 0.0848 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.085 / ESU R Free: 0.085 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1966 2620 5.1 %RANDOM
Rwork0.1699 48906 --
obs0.1713 48906 97.33 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 93.85 Å2 / Biso mean: 34.082 Å2 / Biso min: 14.12 Å2
Baniso -1Baniso -2Baniso -3
1--0.14 Å20 Å2-0.38 Å2
2--1.07 Å20 Å2
3----0.91 Å2
Refinement stepCycle: final / Resolution: 1.64→41.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2806 0 56 157 3019
Biso mean--53.53 41.46 -
Num. residues----346
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0193113
X-RAY DIFFRACTIONr_bond_other_d0.0020.022863
X-RAY DIFFRACTIONr_angle_refined_deg1.9671.9534215
X-RAY DIFFRACTIONr_angle_other_deg1.0043.0016591
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1925390
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.42424.268157
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.97915556
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.2461522
X-RAY DIFFRACTIONr_chiral_restr0.1420.2443
X-RAY DIFFRACTIONr_gen_planes_refined0.010.023656
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02774
X-RAY DIFFRACTIONr_mcbond_it2.2032.161506
X-RAY DIFFRACTIONr_mcbond_other2.2032.161505
X-RAY DIFFRACTIONr_mcangle_it3.0583.2281914
LS refinement shellResolution: 1.64→1.683 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.295 202 -
Rwork0.27 3542 -
all-3744 -
obs--96.4 %
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)
11.10760.0346-0.21320.9144-0.56460.50610.0022-0.05120.07930.09090.07580.0477-0.0778-0.0825-0.0780.02830.0015-0.00050.06040.00020.05920.32410.089527.7861
21.1902-0.3880.3820.21820.12491.3270.14690.0598-0.0163-0.0455-0.0622-0.04910.1891-0.1138-0.08470.0759-0.0335-0.00030.09460.02580.067935.60870.007912.685
318.5742-15.58391.791217.13982.48534.0858-0.0264-0.1324-0.0715-0.3164-0.14150.2357-0.3356-0.25780.16790.1372-0.00080.00240.10490.01570.148.89876.943933.1037
429.5398-3.6482-16.47891.7328-0.573717.8330.6359-0.31180.6305-0.1295-0.0398-0.1564-0.23910.6097-0.5960.1641-0.0165-0.01950.1863-0.02430.16136.9509-11.40436.7792
51.93251.0384-1.65261.4115-0.74271.43810.0422-0.0064-0.01730.0909-0.0735-0.0272-0.0011-0.01040.03130.09-0.0157-0.03980.083-0.01250.08519.22113.882428.3406
62.32811.2654-0.0521.64930.85050.80460.06040.0467-0.01470.0988-0.14190.08240.0642-0.15730.08150.1773-0.05020.0050.13110.02010.035230.4349-3.412911.8867
70.5543-0.1841-1.74340.57210.05286.11680.08460.03030.0237-0.0184-0.0759-0.0462-0.2582-0.0581-0.00870.0213-0.0117-0.00230.03770.01680.033224.21174.684120.912
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
7X-RAY DIFFRACTION7E1 - 4

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