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

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Basic information

Entry
Database: PDB / ID: 6bkj
TitleCrystal Structure of Human Calpain-3 Protease Core in Complex with Leupeptin
Components
  • Calpain-3
  • Leupeptin
KeywordsHydrolase/Hydrolase Inhibitor / Calcium binding / Cysteine protease / Calpain / P94 / Inhibitor / Complex / Hydrolase-Hydrolase Inhibitor complex
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 / regulation of myoblast differentiation / G1 to G0 transition involved in cell 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 / regulation of myoblast differentiation / G1 to G0 transition involved in cell differentiation / cellular response to salt stress / muscle structure development / myofibril assembly / calcium-dependent cysteine-type endopeptidase activity / regulation of catalytic activity / sodium ion binding / self proteolysis / negative regulation of protein sumoylation / protein localization to membrane / regulation of canonical NF-kappaB signal transduction / response to muscle activity / structural constituent of muscle / sarcomere organization / muscle organ development / muscle cell cellular homeostasis / myofibril / positive regulation of proteolysis / catalytic activity / titin binding / cysteine-type peptidase activity / T-tubule / Degradation of the extracellular matrix / cellular response to calcium ion / positive regulation of release of sequestered calcium ion into cytosol / protein destabilization / protein catabolic process / Z disc / response to calcium ion / peptidase activity / positive regulation of NF-kappaB transcription factor activity / protein-containing complex assembly / molecular adaptor activity / negative regulation of DNA-templated transcription / calcium ion binding / negative regulation of apoptotic process / nucleolus / apoptotic process / positive regulation of DNA-templated transcription / protein-containing complex / proteolysis / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm
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-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
LEUPEPTIN / Calpain-3
Similarity search - Component
Biological speciesHomo sapiens (human)
Streptomyces roseus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 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 8, 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_conn_type / 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.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.ptnr2_label_seq_id / _struct_conn_type.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
Revision 1.5Oct 9, 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
F: Leupeptin
G: Leupeptin
H: Leupeptin
I: Leupeptin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)179,86416
Polymers179,5438
Non-polymers3218
Water84747
1
A: Calpain-3
F: Leupeptin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,9664
Polymers44,8862
Non-polymers802
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Calpain-3
G: Leupeptin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,9664
Polymers44,8862
Non-polymers802
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Calpain-3
H: Leupeptin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,9664
Polymers44,8862
Non-polymers802
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Calpain-3
I: Leupeptin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,9664
Polymers44,8862
Non-polymers802
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.930, 106.690, 234.630
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
12LYSLYSLEULEUAA59 - 41614 - 371
22LYSLYSLEULEUCC59 - 41614 - 371
13LYSLYSLEULEUAA57 - 41612 - 371
23LYSLYSLEULEUDD57 - 41612 - 371
14LYSLYSALAALABB59 - 41814 - 373
24LYSLYSALAALACC59 - 41814 - 373
15GLUGLUASNASNBB58 - 41513 - 370
25GLUGLUASNASNDD58 - 41513 - 370
16LYSLYSASNASNCC59 - 41514 - 370
26LYSLYSASNASNDD59 - 41514 - 370

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: 44456.176 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
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: Protein/peptide
Leupeptin


Type: Oligopeptide / Class: Enzyme inhibitor / Mass: 429.578 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Streptomyces roseus (bacteria) / References: LEUPEPTIN
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 47 / Source method: isolated from a natural source / Formula: H2O
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: 1.91 Å3/Da / Density % sol: 35.76 %
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: 1.03323 Å
DetectorType: RAYONIX MX300HE / 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: 1.03323 Å / Relative weight: 1
ReflectionResolution: 3.2→20 Å / Num. obs: 23107 / % possible obs: 98.8 % / Redundancy: 9.55 % / CC1/2: 0.98 / Rrim(I) all: 0.65 / Χ2: 0.83 / Net I/σ(I): 4.48
Reflection shellResolution: 3.205→3.222 Å / Redundancy: 9.56 % / Mean I/σ(I) obs: 1.91 / Num. unique obs: 16879 / CC1/2: 0.84 / Rrim(I) all: 1.75 / % possible all: 99.1

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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: 3.2→17.99 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.856 / SU B: 72.785 / SU ML: 1.053 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.803
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.3532 1139 5 %RANDOM
Rwork0.2773 ---
obs0.281 21642 96.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 243.05 Å2 / Biso mean: 129.525 Å2 / Biso min: 24.66 Å2
Baniso -1Baniso -2Baniso -3
1-2.22 Å20 Å20 Å2
2--1.46 Å2-0 Å2
3----3.68 Å2
Refinement stepCycle: final / Resolution: 3.2→17.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10238 0 128 47 10413
Biso mean--139.32 54.59 -
Num. residues----1225
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.01910535
X-RAY DIFFRACTIONr_bond_other_d0.0070.029406
X-RAY DIFFRACTIONr_angle_refined_deg1.481.93614248
X-RAY DIFFRACTIONr_angle_other_deg1.393321836
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.01851221
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.45724.08549
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.574151775
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6511556
X-RAY DIFFRACTIONr_chiral_restr0.1050.21449
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0211703
X-RAY DIFFRACTIONr_gen_planes_other0.010.022377
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A190700.16
12B190700.16
21A184540.17
22C184540.17
31A188760.17
32D188760.17
41B184980.18
42C184980.18
51B191060.16
52D191060.16
61C183660.18
62D183660.18
LS refinement shellResolution: 3.2→3.28 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.413 78 -
Rwork0.419 1501 -
all-1579 -
obs--94.66 %

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