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- PDB-7w7o: The crystal structure of human Calpain-1 protease core in complex... -

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Basic information

Entry
Database: PDB / ID: 7w7o
TitleThe crystal structure of human Calpain-1 protease core in complex with 14a
ComponentsCalpain-1 catalytic subunit
KeywordsHYDROLASE / Human protease / Calpain-1 / Antiviral inhibitor / 14a
Function / homology
Function and homology information


calpain-1 / calpain complex / mammary gland involution / calcium-dependent cysteine-type endopeptidase activity / receptor catabolic process / Formation of the cornified envelope / self proteolysis / cornified envelope / regulation of catalytic activity / regulation of NMDA receptor activity ...calpain-1 / calpain complex / mammary gland involution / calcium-dependent cysteine-type endopeptidase activity / receptor catabolic process / Formation of the cornified envelope / self proteolysis / cornified envelope / regulation of catalytic activity / regulation of NMDA receptor activity / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / regulation of macroautophagy / Degradation of the extracellular matrix / peptidase activity / ficolin-1-rich granule lumen / lysosome / focal adhesion / calcium ion binding / Neutrophil degranulation / positive regulation of cell population proliferation / mitochondrion / proteolysis / extracellular exosome / extracellular region / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Calpain subdomain III / 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 subdomain III / 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 peptidase, cysteine active site / Eukaryotic thiol (cysteine) proteases cysteine active site. / 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
Similarity search - Domain/homology
Chem-06Q / HYDROSULFURIC ACID / Calpain-1 catalytic subunit
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.59 Å
AuthorsZhao, Y. / Zhao, J. / Shao, M. / Yang, H. / Rao, Z.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)813300237 China
CitationJournal: To Be Published
Title: The crystal structure of human Calpain-1 protease core in complex with 14a
Authors: Zhao, Y. / Zhao, J. / Shao, M. / Yang, H. / Rao, Z.
History
DepositionDec 6, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 7, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 29, 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

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Assembly

Deposited unit
A: Calpain-1 catalytic subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,4445
Polymers37,7151
Non-polymers7294
Water5,657314
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area170 Å2
ΔGint-25 kcal/mol
Surface area14890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.126, 63.980, 99.754
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Calpain-1 catalytic subunit / / Calcium-activated neutral proteinase 1 / CANP 1 / Calpain mu-type / Calpain-1 large subunit / Cell ...Calcium-activated neutral proteinase 1 / CANP 1 / Calpain mu-type / Calpain-1 large subunit / Cell proliferation-inducing gene 30 protein / Micromolar-calpain / muCANP


Mass: 37715.465 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CAPN1, CANPL1, PIG30 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P07384, calpain-1
#2: Chemical ChemComp-06Q / N-[(2S)-3-(4-fluorophenyl)-1-oxidanylidene-1-[[(2S,3S)-3-oxidanyl-4-oxidanylidene-1-[(3S)-2-oxidanylidenepiperidin-3-yl]-4-[(phenylmethyl)amino]butan-2-yl]amino]propan-2-yl]-1-benzofuran-2-carboxamide


Mass: 614.663 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H35FN4O6 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-H2S / HYDROSULFURIC ACID / HYDROGEN SULFIDE / Hydrogen sulfide


Mass: 34.081 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H2S
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 314 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 0.1M sodium acetate (pH 4.6), 8% (w/v) PEG 4000, protein concentration 13mg/ml

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 14, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 1.59→30.46 Å / Num. obs: 42389 / % possible obs: 96.8 % / Redundancy: 13.067 % / Biso Wilson estimate: 22.29 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.074 / Rrim(I) all: 0.077 / Χ2: 0.876 / Net I/σ(I): 19.25 / Num. measured all: 553890 / Scaling rejects: 197
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.59-1.6312.2771.1982.1334252320027900.7411.25187.2
1.63-1.6813.5841.0522.6440506309429820.8421.09396.4
1.68-1.7313.3940.7663.6539377305529400.9110.79696.2
1.73-1.7813.6650.6174.6638605292528250.9470.64196.6
1.78-1.8413.6940.4536.2637837285227630.9710.4796.9
1.84-1.913.1460.3587.5135125275126720.9820.37297.1
1.9-1.9713.5930.25511.0835518268626130.9880.26597.3
1.97-2.0513.2350.19213.6433101257125010.9940.19997.3
2.05-2.1513.6540.14717.6933315249624400.9960.15397.8
2.15-2.2513.3720.12620.6431062237023230.9960.13198
2.25-2.3712.830.10522.8328214226121990.9970.10997.3
2.37-2.5213.2530.08528.0127897213321050.9980.08898.7
2.52-2.6912.9530.07132.1425633201919790.9980.07498
2.69-2.9113.1110.0636.7524531189818710.9990.06398.6
2.91-3.1812.2820.05240.6621088173517170.9990.05499
3.18-3.5612.3050.04445.8119381159915750.9990.04698.5
3.56-4.1112.5450.04249.4517425140513890.9990.04498.9
4.11-5.0311.7650.0450.9414200121812070.9990.04299.1
5.03-7.1211.5360.04349.14109719609510.9980.04599.1
7.12-30.4610.6980.0548.2158525665470.9980.05296.6

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XSCALEdata scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ZCM

1zcm


Resolution: 1.59→30.46 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 20.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1954 2000 4.72 %
Rwork0.1634 40375 -
obs0.1649 42375 96.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 82.69 Å2 / Biso mean: 30.4564 Å2 / Biso min: 14.37 Å2
Refinement stepCycle: final / Resolution: 1.59→30.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2608 0 48 315 2971
Biso mean--30.61 41.38 -
Num. residues----327
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.59-1.630.29591260.26832557268387
1.63-1.680.27021400.2332832297296
1.68-1.720.22491410.20332833297496
1.72-1.780.26451400.19842824296496
1.78-1.840.22351410.18792843298497
1.84-1.920.25221410.19172858299997
1.92-20.23381440.17392899304397
2-2.110.18271420.15712869301198
2.11-2.240.21011430.15852905304898
2.24-2.420.19721450.16532917306298
2.42-2.660.20611460.1622935308198
2.66-3.040.20521470.16662964311199
3.04-3.830.17621480.14793009315799
3.83-30.460.16251560.14953130328698
Refinement TLS params.Method: refined / Origin x: -36.57 Å / Origin y: 10.0215 Å / Origin z: 34.9881 Å
111213212223313233
T0.1327 Å20.0126 Å2-0.0104 Å2-0.1571 Å2-0.0227 Å2--0.1635 Å2
L0.9198 °20.4532 °2-0.2969 °2-1.6354 °2-0.3861 °2--1.6282 °2
S-0.0856 Å °0.0085 Å °-0.0495 Å °-0.0044 Å °0.0092 Å °-0.0846 Å °0.1173 Å °-0.0048 Å °0.0696 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA33 - 501
2X-RAY DIFFRACTION1allB1 - 2
3X-RAY DIFFRACTION1allS1 - 328

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