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- PDB-6bjd: Crystal Structure of Human Calpain-3 Protease Core in Complex wit... -

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Basic information

Entry
Database: PDB / ID: 6bjd
TitleCrystal Structure of Human Calpain-3 Protease Core in Complex with E-64
ComponentsCalpain-3
KeywordsHYDROLASE / Calcium binding / Cysteine protease / Calpain / P94 / Complex / E-64
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 / cellular response to salt stress / regulation of myoblast differentiation / 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 / cellular response to salt stress / regulation of myoblast differentiation / 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
Chem-E64 / sorbitol / Calpain-3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 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
DepositionNov 6, 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 1.4Jul 29, 2020Group: Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_entity_nonpoly / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _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 1.6Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)179,91121
Polymers177,8254
Non-polymers2,08617
Water1,54986
1
A: Calpain-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,9325
Polymers44,4561
Non-polymers4764
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Calpain-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,1146
Polymers44,4561
Non-polymers6585
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Calpain-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,9325
Polymers44,4561
Non-polymers4764
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Calpain-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,9325
Polymers44,4561
Non-polymers4764
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.280, 105.360, 225.360
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: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLUGLULEULEUAA58 - 41613 - 371
21GLUGLULEULEUBB58 - 41613 - 371
12GLUGLULEULEUAA58 - 41613 - 371
22GLUGLULEULEUCC58 - 41613 - 371
13LYSLYSLEULEUAA59 - 41614 - 371
23LYSLYSLEULEUDD59 - 41614 - 371
14GLUGLUTHRTHRBB58 - 41713 - 372
24GLUGLUTHRTHRCC58 - 41713 - 372
15LYSLYSTHRTHRBB59 - 41714 - 372
25LYSLYSTHRTHRDD59 - 41714 - 372
16LYSLYSTHRTHRCC59 - 41714 - 372
26LYSLYSTHRTHRDD59 - 41714 - 372

NCS ensembles :
ID
1
2
3
4
5
6

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Components

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Protein / Sugars , 2 types, 5 molecules ABCD

#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: 44456.176 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: Muscle-specific calcium-activated neutral protease 3 cysteine-129 from active-site covalently connects inhibitor E-64.
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
#5: Sugar ChemComp-SOR / sorbitol / D-sorbitol / D-glucitol


Type: D-saccharide / Mass: 182.172 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H14O6

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Non-polymers , 4 types, 102 molecules

#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: Chemical
ChemComp-E64 / N-[N-[1-HYDROXYCARBOXYETHYL-CARBONYL]LEUCYLAMINO-BUTYL]-GUANIDINE


Mass: 360.429 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C15H30N5O5
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 86 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.01 Å3/Da / Density % sol: 38.87 %
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: APS / Beamline: 23-ID-B / Wavelength: 1.0332 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Nov 19, 2015
RadiationMonochromator: Double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.8→30 Å / Num. obs: 36048 / % possible obs: 99.3 % / Redundancy: 4.29 % / CC1/2: 0.99 / Rrim(I) all: 0.18 / Χ2: 0.97 / Net I/σ(I): 9.54
Reflection shellResolution: 2.8→2.815 Å / Redundancy: 4.31 % / Mean I/σ(I) obs: 3.29 / Num. unique obs: 17406 / CC1/2: 0.91 / Rrim(I) all: 0.58 / Χ2: 0.88 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6BDT

6bdt


Resolution: 2.8→17.93 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.9 / SU B: 19.525 / SU ML: 0.363 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.416
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2643 1800 5 %RANDOM
Rwork0.2055 ---
obs0.2084 34197 99.15 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 163.62 Å2 / Biso mean: 61.078 Å2 / Biso min: 27.61 Å2
Baniso -1Baniso -2Baniso -3
1-4.44 Å2-0 Å20 Å2
2---1.28 Å2-0 Å2
3----3.16 Å2
Refinement stepCycle: final / Resolution: 2.8→17.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10159 0 124 86 10369
Biso mean--83.71 44.2 -
Num. residues----1229
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01910567
X-RAY DIFFRACTIONr_bond_other_d0.0070.029412
X-RAY DIFFRACTIONr_angle_refined_deg1.3541.93714277
X-RAY DIFFRACTIONr_angle_other_deg0.938321847
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.06351220
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.29724.076552
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.506151765
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.9731556
X-RAY DIFFRACTIONr_chiral_restr0.0810.21452
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211747
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022409
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A201260.09
12B201260.09
21A199900.09
22C199900.09
31A198200.09
32D198200.09
41B203860.08
42C203860.08
51B199420.08
52D199420.08
61C199920.09
62D199920.09
LS refinement shellResolution: 2.8→2.871 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.422 127 -
Rwork0.41 2428 -
all-2555 -
obs--98.5 %

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