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- PDB-8gx3: The crystal structure of human Calpain-1 protease core in complex... -

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Basic information

Entry
Database: PDB / ID: 8gx3
TitleThe crystal structure of human Calpain-1 protease core in complex with 14c
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 / regulation of catalytic activity / receptor catabolic process / Formation of the cornified envelope / cornified envelope / self proteolysis / regulation of NMDA receptor activity ...calpain-1 / calpain complex / mammary gland involution / calcium-dependent cysteine-type endopeptidase activity / regulation of catalytic activity / receptor catabolic process / Formation of the cornified envelope / cornified envelope / self proteolysis / 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 / positive regulation of cell population proliferation / calcium ion binding / Neutrophil degranulation / 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 ...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-KJ0 / Calpain-1 catalytic subunit
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 Å
AuthorsZhao, Y. / Zhao, J. / Shao, M. / Yang, H. / Rao, Z.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32200131 China
CitationJournal: To Be Published
Title: The crystal structure of human Calpain-1 protease core in complex with 14c
Authors: Zhao, Y. / Zhao, J. / Shao, M. / Yang, H. / Rao, Z.
History
DepositionSep 18, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 20, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)82,6214
Polymers81,9881
Non-polymers6333
Water5,423301
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area170 Å2
ΔGint-26 kcal/mol
Surface area15320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.329, 64.140, 99.782
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 / Calpain-1 protease core / Calcium-activated neutral proteinase 1 / CANP 1 / Calpain mu-type / ...Calpain-1 protease core / Calcium-activated neutral proteinase 1 / CANP 1 / Calpain mu-type / Calpain-1 large subunit / Cell proliferation-inducing gene 30 protein / Micromolar-calpain / muCANP


Mass: 81987.891 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-KJ0 / N-[(2S)-3-cyclohexyl-1-[[(2S,3S)-4-(cyclopropylamino)-3-oxidanyl-4-oxidanylidene-1-[(3S)-2-oxidanylidenepiperidin-3-yl]butan-2-yl]amino]-1-oxidanylidene-propan-2-yl]-1-benzofuran-2-carboxamide


Mass: 552.662 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C30H40N4O6 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 301 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 0.98 Å3/Da / Density % sol: 43.52 %
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, 13mg/ml protein

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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: Mar 10, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 1.99→44.94 Å / Num. obs: 22811 / % possible obs: 100 % / Redundancy: 13.028 % / Biso Wilson estimate: 26.78 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.191 / Rrim(I) all: 0.199 / Χ2: 0.831 / Net I/σ(I): 10.68 / Num. measured all: 297187
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
1.99-2.0413.3181.5831.6121975165216500.7181.64699.9
2.04-2.113.3041.1872.321619162516250.7931.235100
2.1-2.1612.7780.8922.9419998156515650.8560.929100
2.16-2.2313.4030.7193.7320467152715270.9160.748100
2.23-2.313.2330.5984.3619691148814880.9420.622100
2.3-2.3812.8630.4945.2418535144114410.9540.514100
2.38-2.4713.4840.4266.1418796139413940.9690.443100
2.47-2.5713.3110.367.1917637132513250.9740.375100
2.57-2.6812.5830.3028.2516282129412940.9790.315100
2.68-2.8113.3840.2589.9316676124612460.9870.268100
2.81-2.9712.9370.21311.615085116611660.990.222100
2.97-3.1513.4040.16814.6515120112811280.9930.175100
3.15-3.3613.3480.13417.8714015105010500.9950.139100
3.36-3.6312.5990.1120.83123099779770.9960.114100
3.63-3.9813.1480.09623.92120839199190.9970.1100
3.98-4.4512.6690.08127.52104398248240.9970.085100
4.45-5.1412.8530.08127.4395887467460.9970.085100
5.14-6.2912.1990.08724.7378326426420.9960.091100
6.29-8.911.9560.07925.8559664994990.9980.083100
8.9-44.9410.0790.06328.2930743083050.9980.06699

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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: 1.99→44.94 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 20.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.215 2000 8.77 %
Rwork0.1732 20805 -
obs0.1769 22805 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 82.23 Å2 / Biso mean: 28.6894 Å2 / Biso min: 12.31 Å2
Refinement stepCycle: final / Resolution: 1.99→44.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2608 0 42 301 2951
Biso mean--26.93 35.09 -
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 (%)
1.99-2.040.351380.32551437157599
2.04-2.090.28641410.23614661607100
2.09-2.160.25531400.201514651605100
2.16-2.230.2461410.190714591600100
2.23-2.310.26461400.197614641604100
2.31-2.40.22661440.191114871631100
2.4-2.510.24071400.191414561596100
2.51-2.640.27171410.181914831624100
2.64-2.80.23471430.181914801623100
2.8-3.020.22861420.191614821624100
3.02-3.320.23391440.169414861630100
3.32-3.810.18051440.145815101654100
3.81-4.790.14931480.126815261674100
4.79-44.940.19411540.16781604175899
Refinement TLS params.Method: refined / Origin x: -36.6068 Å / Origin y: 9.9672 Å / Origin z: 34.7721 Å
111213212223313233
T0.1129 Å20.0057 Å2-0.0147 Å2-0.136 Å2-0.0175 Å2--0.1354 Å2
L0.6312 °20.3734 °2-0.2541 °2-1.1003 °2-0.2568 °2--1.0805 °2
S-0.0303 Å °-0.0008 Å °-0.0135 Å °0.0283 Å °-0.0175 Å °-0.0241 Å °0.0429 Å °-0.0235 Å °0.0457 Å °
Refinement TLS groupSelection details: all

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