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- PDB-7x79: The crystal structure of human Calpain-1 protease core in complex... -

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Basic information

Entry
Database: PDB / ID: 7x79
TitleThe crystal structure of human Calpain-1 protease core in complex with 14b
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-89K / HYDROSULFURIC ACID / Calpain-1 catalytic subunit
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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
DepositionMar 9, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 14, 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)82,7055
Polymers81,9881
Non-polymers7174
Water5,603311
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area90 Å2
ΔGint-13 kcal/mol
Surface area14840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.203, 64.070, 99.576
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-89K / N-[(2S)-3-cyclohexyl-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: 602.720 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H42N4O6 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-H2S / HYDROSULFURIC ACID / 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: isolated from a natural source / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 311 / 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: 0.98 Å3/Da / Density % sol: 25.94 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop
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: 0.9793 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 16, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.8→49.79 Å / Num. obs: 30492 / % possible obs: 99.5 % / Redundancy: 12.988 % / Biso Wilson estimate: 23.12 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.117 / Rrim(I) all: 0.122 / Χ2: 0.841 / Net I/σ(I): 16.21 / Num. measured all: 396042 / Scaling rejects: 34
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.8-1.8412.3381.3172.1621860.751.37498.1
1.84-1.8913.5341.0782.8521650.8441.11999.1
1.89-1.9513.5050.833.6421030.9110.86199.3
1.95-2.0113.3230.6514.5720480.9360.67699.4
2.01-2.0813.1130.4935.8719930.9640.51399.7
2.08-2.1512.6320.46.9919220.9660.41799.5
2.15-2.2312.4650.3198.5818090.9780.33298.4
2.23-2.3213.5830.27810.1218120.9880.28999.8
2.32-2.4213.5250.22512.2617330.9910.23399.8
2.42-2.5413.3760.18614.4216630.9930.19399.9
2.54-2.6813.0920.15117.1515720.9950.158100
2.68-2.8412.0410.12519.3414880.9960.13199.7
2.84-3.0413.5430.09925.1614240.9970.103100
3.04-3.2813.4530.07531.6713250.9990.078100
3.28-3.5913.1360.06336.7412250.9990.06699.9
3.59-4.0212.1110.05340.9711120.9990.055100
4.02-4.6412.4680.04747.799830.9990.04999.6
4.64-5.6812.9770.04748.288570.9990.049100
5.68-8.0411.5630.04443.936790.9990.04699.9
8.04-49.7911.2720.03750.173930.9990.03998.2

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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: 1.8→49.79 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 19.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2015 1999 6.56 %
Rwork0.1659 28488 -
obs0.1682 30487 99.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 88.22 Å2 / Biso mean: 30.2757 Å2 / Biso min: 13.03 Å2
Refinement stepCycle: final / Resolution: 1.8→49.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2571 0 47 311 2929
Biso mean--34.53 39.01 -
Num. residues----322
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 (%)
1.8-1.840.2851380.2511970210898
1.84-1.890.28411410.23012006214799
1.89-1.950.26251400.2041992213299
1.95-2.010.24681410.19782008214999
2.01-2.080.22621410.172420082149100
2.08-2.170.20431400.16262002214299
2.17-2.260.20461410.16492005214699
2.26-2.380.20571420.161120342176100
2.38-2.530.20771430.168820262169100
2.53-2.730.23231420.170220342176100
2.73-30.19281440.173320532197100
3-3.440.19381440.161620602204100
3.44-4.330.15771480.137520982246100
4.33-49.790.19321540.16072192234699
Refinement TLS params.Method: refined / Origin x: -36.5906 Å / Origin y: 9.9597 Å / Origin z: 35.1548 Å
111213212223313233
T0.1319 Å20.0109 Å2-0.0102 Å2-0.153 Å2-0.0205 Å2--0.1616 Å2
L0.7855 °20.4159 °2-0.2108 °2-1.5939 °2-0.3287 °2--1.4875 °2
S-0.0694 Å °-0.0111 Å °-0.0413 Å °0.0269 Å °0.0018 Å °-0.0691 Å °0.0934 Å °-0.0089 Å °0.0676 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA33 - 501
2X-RAY DIFFRACTION1allB1 - 2
3X-RAY DIFFRACTION1allS1 - 327

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