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- PDB-6bdt: Crystal Structure of Human Calpain-3 Protease Core Mutant-C129S -

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Basic information

Entry
Database: PDB / ID: 6bdt
TitleCrystal Structure of Human Calpain-3 Protease Core Mutant-C129S
ComponentsCalpain-3
KeywordsHYDROLASE / Calcium binding / Cysteine protease / Calpain / P94
Function / homology
Function and homology information


calpain-3 / positive regulation of satellite cell activation involved in skeletal muscle regeneration / ligase regulator activity / calcium-dependent self proteolysis / G1 to G0 transition involved in cell differentiation / regulation of myoblast differentiation / cellular response to salt stress / muscle structure development / myofibril assembly / calcium-dependent cysteine-type endopeptidase activity ...calpain-3 / positive regulation of satellite cell activation involved in skeletal muscle regeneration / ligase regulator activity / calcium-dependent self proteolysis / G1 to G0 transition involved in cell differentiation / regulation of myoblast differentiation / cellular response to salt stress / muscle structure development / myofibril assembly / calcium-dependent cysteine-type endopeptidase activity / sodium ion binding / self proteolysis / negative regulation of protein sumoylation / protein localization to membrane / regulation of canonical NF-kappaB signal transduction / structural constituent of muscle / sarcomere organization / muscle organ development / muscle cell cellular homeostasis / response to muscle activity / myofibril / positive regulation of proteolysis / catalytic activity / titin binding / Degradation of the extracellular matrix / T-tubule / cysteine-type peptidase activity / cellular response to calcium ion / positive regulation of release of sequestered calcium ion into cytosol / protein catabolic process / response to calcium ion / protein destabilization / Z disc / peptidase activity / protein-containing complex assembly / molecular adaptor activity / negative regulation of DNA-templated transcription / apoptotic process / calcium ion binding / negative regulation of apoptotic process / positive regulation of DNA-templated transcription / nucleolus / protein-containing complex / proteolysis / identical protein binding / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Calpain-3 / Unstructured region on Calpain-3 / : / Calpain-13-like, C-terminal EF-hand / 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-3 / Unstructured region on Calpain-3 / : / Calpain-13-like, C-terminal EF-hand / 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 proteinases / Cysteine peptidase, cysteine active site / Eukaryotic thiol (cysteine) proteases cysteine active site. / Cathepsin B; Chain A / Papain-like cysteine peptidase superfamily / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsYe, Q. / Campbell, R.L. / Davies, P.L.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)MOP 74681 Canada
CitationJournal: J. Biol. Chem. / Year: 2018
Title: Structures of human calpain-3 protease core with and without bound inhibitor reveal mechanisms of calpain activation.
Authors: Ye, Q. / Campbell, R.L. / Davies, P.L.
History
DepositionOct 24, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 7, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 14, 2018Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2May 2, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 2023Group: 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 / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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 / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Calpain-3
B: Calpain-3
C: Calpain-3
D: Calpain-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)178,22316
Polymers177,7604
Non-polymers46212
Water2,036113
1
A: Calpain-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,5564
Polymers44,4401
Non-polymers1163
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Calpain-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,5564
Polymers44,4401
Non-polymers1163
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Calpain-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,5564
Polymers44,4401
Non-polymers1163
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Calpain-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,5564
Polymers44,4401
Non-polymers1163
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.810, 105.490, 225.260
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: GLU / Beg label comp-ID: GLU / Refine code: _

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASPASPAA58 - 41913 - 374
21ASPASPBB58 - 41913 - 374
12ALAALAAA58 - 41813 - 373
22ALAALACC58 - 41813 - 373
13ASPASPAA58 - 41913 - 374
23ASPASPDD58 - 41913 - 374
14THRTHRBB58 - 41713 - 372
24THRTHRCC58 - 41713 - 372
15ASPASPBB58 - 41913 - 374
25ASPASPDD58 - 41913 - 374
16THRTHRCC58 - 41713 - 372
26THRTHRDD58 - 41713 - 372

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
Calpain-3 / Calcium-activated neutral proteinase 3 / CANP 3 / Calpain L3 / Calpain p94 / Muscle-specific ...Calcium-activated neutral proteinase 3 / CANP 3 / Calpain L3 / Calpain p94 / Muscle-specific calcium-activated neutral protease 3 / New calpain 1 / nCL-1


Mass: 44440.109 Da / Num. of mol.: 4 / Mutation: C129S
Source method: isolated from a genetically manipulated source
Details: Muscle-specific calcium-activated neutral protease 3
Source: (gene. exp.) Homo sapiens (human) / Gene: CAPN3, CANP3, CANPL3, NCL1 / Plasmid: pET24a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P20807, calpain-3
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 113 / 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 Å3/Da / Density % sol: 38.37 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: PEG 8000, MES, calcium chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 1.0781 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 3, 2014 / Details: Oxford Danfysik toroidal focusing mirror
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0781 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 62975 / % possible obs: 97.9 % / Redundancy: 14.2 % / CC1/2: 0.997 / Rrim(I) all: 0.21 / Χ2: 1.09 / Net I/σ(I): 11.22
Reflection shellResolution: 2.3→2.32 Å / Redundancy: 13.89 % / Mean I/σ(I) obs: 2.16 / Num. unique obs: 33695 / CC1/2: 0.8 / Rrim(I) all: 1.3 / Χ2: 0.98 / % possible all: 96.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1MDW

1mdw


Resolution: 2.3→17.99 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.927 / SU B: 11.429 / SU ML: 0.254 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.403 / ESU R Free: 0.253
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.256 3139 5 %RANDOM
Rwork0.2219 ---
obs0.2236 59691 98.17 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 157.96 Å2 / Biso mean: 60.172 Å2 / Biso min: 27.19 Å2
Baniso -1Baniso -2Baniso -3
1-3.13 Å20 Å20 Å2
2---1.3 Å2-0 Å2
3----1.83 Å2
Refinement stepCycle: final / Resolution: 2.3→17.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10374 0 12 113 10499
Biso mean--45.12 45.56 -
Num. residues----1258
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01910674
X-RAY DIFFRACTIONr_bond_other_d0.0060.029708
X-RAY DIFFRACTIONr_angle_refined_deg1.351.92614441
X-RAY DIFFRACTIONr_angle_other_deg1.218322368
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.96351249
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.37324.159565
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.999151794
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.2351556
X-RAY DIFFRACTIONr_chiral_restr0.0840.21468
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212100
X-RAY DIFFRACTIONr_gen_planes_other0.0050.022668
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A174610.14
12B174610.14
21A175270.12
22C175270.12
31A177240.13
32D177240.13
41B181580.13
42C181580.13
51B182260.12
52D182260.12
61C182940.12
62D182940.12
LS refinement shellResolution: 2.304→2.363 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.457 184 -
Rwork0.462 3546 -
all-3730 -
obs--81.67 %

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