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- PDB-6p3q: Calpain-5 (CAPN5) Protease Core (PC) -

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Basic information

Entry
Database: PDB / ID: 6p3q
TitleCalpain-5 (CAPN5) Protease Core (PC)
ComponentsCalpain-5
KeywordsHYDROLASE / Cystein protease / peptide binding protein / Calcium binding protein / protease domain
Function / homology
Function and homology information


calcium-dependent cysteine-type endopeptidase activity / Degradation of the extracellular matrix / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / focal adhesion / synapse / cell surface / signal transduction / proteolysis / extracellular exosome / cytoplasm
Similarity search - Function
Calpain C2 domain / 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 C2 domain / 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. / C2 domain / Protein kinase C conserved region 2 (CalB) / Cysteine proteinases / Cysteine peptidase, cysteine active site / Eukaryotic thiol (cysteine) proteases cysteine active site. / C2 domain / C2 domain profile. / Cathepsin B; Chain A / C2 domain superfamily / Papain-like cysteine peptidase superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsVelez, G. / Sun, Y.J. / Khan, S. / Yang, J. / Koster, H.J. / Lokesh, G. / Mahajan, V.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Eye Institute (NIH/NEI)R01EY024665 United States
CitationJournal: Cell Rep / Year: 2020
Title: Structural Insights into the Unique Activation Mechanisms of a Non-classical Calpain and Its Disease-Causing Variants.
Authors: Velez, G. / Sun, Y.J. / Khan, S. / Yang, J. / Herrmann, J. / Chemudupati, T. / MacLaren, R.E. / Gakhar, L. / Wakatsuki, S. / Bassuk, A.G. / Mahajan, V.B.
History
DepositionMay 24, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 5, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.2Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Calpain-5
B: Calpain-5


Theoretical massNumber of molelcules
Total (without water)82,7332
Polymers82,7332
Non-polymers00
Water0
1
A: Calpain-5


Theoretical massNumber of molelcules
Total (without water)41,3671
Polymers41,3671
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Calpain-5


Theoretical massNumber of molelcules
Total (without water)41,3671
Polymers41,3671
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)84.038, 51.576, 110.635
Angle α, β, γ (deg.)90.000, 110.425, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11VALVALSERSER(chain 'A' and (resid 5 through 303 or (resid 304...AA5 - 698 - 72
12HISHISPHEPHE(chain 'A' and (resid 5 through 303 or (resid 304...AA71 - 34974 - 352
23VALVALSERSER(chain 'B' and (resid 5 through 69 or resid 71...BB5 - 698 - 72
24HISHISPHEPHE(chain 'B' and (resid 5 through 69 or resid 71...BB71 - 34974 - 352

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Components

#1: Protein Calpain-5 / / Calpain htra-3 / New calpain 3 / nCL-3


Mass: 41366.598 Da / Num. of mol.: 2 / Fragment: residues 1-343
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CAPN5, NCL3 / Production host: Escherichia coli BL21 (bacteria) / Variant (production host): BL21
References: UniProt: O15484, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases

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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: 2.71 Å3/Da / Density % sol: 54.68 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 250 mM sodium phosphate, 12 % PEG 8000, 36 mM EDTA, 10 mM Calcium chloride, 0.4 mM H-E(EDANS)-KIEIVRKKPIFKKATV-K(DASBCYL)-OH

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1 Å
DetectorType: RDI CMOS_8M / Detector: CMOS / Date: Jul 16, 2016
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→51.84 Å / Num. obs: 22239 / % possible obs: 99.44 % / Redundancy: 2 % / Biso Wilson estimate: 50.65 Å2 / CC1/2: 0.996 / Rrim(I) all: 0.087 / Net I/σ(I): 10.8
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 2 % / Mean I/σ(I) obs: 1.73 / Num. unique obs: 2233 / CC1/2: 0.804 / Rrim(I) all: 0.623 / % possible all: 99.07

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
Blu-Icedata collection
XDSdata reduction
Aimlessdata scaling
Cootmodel building
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: SAXS guided homology model

Resolution: 2.8→51.84 Å / SU ML: 0.5058 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.5476
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2851 1060 4.77 %RANDOM
Rwork0.2268 21142 --
obs0.2295 22202 99.48 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 50.18 Å2
Refinement stepCycle: LAST / Resolution: 2.8→51.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5595 0 0 0 5595
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00975746
X-RAY DIFFRACTIONf_angle_d1.11997783
X-RAY DIFFRACTIONf_chiral_restr0.0593798
X-RAY DIFFRACTIONf_plane_restr0.00681014
X-RAY DIFFRACTIONf_dihedral_angle_d11.43443376
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.930.42621400.33582593X-RAY DIFFRACTION99.24
2.93-3.080.37381180.3112652X-RAY DIFFRACTION99.71
3.08-3.270.3221500.27382575X-RAY DIFFRACTION98.95
3.27-3.530.32941420.26412616X-RAY DIFFRACTION99.57
3.53-3.880.29081230.22462632X-RAY DIFFRACTION99.64
3.88-4.440.24631250.19562671X-RAY DIFFRACTION99.71
4.44-5.60.25421330.18692655X-RAY DIFFRACTION99.64
5.6-51.840.2231290.19782748X-RAY DIFFRACTION99.34

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