[English] 日本語
Yorodumi
- PDB-6bjd: Crystal Structure of Human Calpain-3 Protease Core in Complex wit... -

+
Open data


ID or keywords:

Loading...

-
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 / 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 / sodium ion binding / self proteolysis / regulation of catalytic activity / negative regulation of protein sumoylation / protein localization to membrane / response to muscle activity / regulation of canonical NF-kappaB signal transduction / muscle organ development / structural constituent of muscle / sarcomere organization / muscle cell cellular homeostasis / myofibril / positive regulation of proteolysis / cysteine-type peptidase activity / catalytic activity / titin binding / T-tubule / cellular response to calcium ion / Degradation of the extracellular matrix / positive regulation of release of sequestered calcium ion into cytosol / protein catabolic process / protein destabilization / Z disc / response to calcium ion / positive regulation of NF-kappaB transcription factor activity / peptidase activity / protein-containing complex assembly / molecular adaptor activity / negative regulation of DNA-templated transcription / apoptotic process / calcium ion binding / nucleolus / negative regulation of 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 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-3 / Unstructured region on Calpain-3 / 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 / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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: 0 / Refine code: 0

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

-
Components

-
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 / Sorbitol


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

-
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 / Chloride


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 / Water


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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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 %

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more