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- PDB-1tlo: High resolution crystal structure of calpain I protease core in c... -

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Basic information

Entry
Database: PDB / ID: 1tlo
TitleHigh resolution crystal structure of calpain I protease core in complex with E64
ComponentsCalpain 1, large [catalytic] subunit
KeywordsHYDROLASE / covalently-linked inhibitor at the active site (cysteine 115) forms a thioester
Function / homology
Function and homology information


calpain-1 / Degradation of the extracellular matrix / protein catabolic process at postsynapse / mammary gland involution / calcium-dependent cysteine-type endopeptidase activity / positive regulation of leukocyte tethering or rolling / regulation of catalytic activity / negative regulation of actin filament polymerization / self proteolysis / cornified envelope ...calpain-1 / Degradation of the extracellular matrix / protein catabolic process at postsynapse / mammary gland involution / calcium-dependent cysteine-type endopeptidase activity / positive regulation of leukocyte tethering or rolling / regulation of catalytic activity / negative regulation of actin filament polymerization / self proteolysis / cornified envelope / receptor catabolic process / response to arsenic-containing substance / positive regulation of vascular permeability / response to angiotensin / negative regulation of non-canonical NF-kappaB signal transduction / Neutrophil degranulation / protein autoprocessing / positive regulation of cardiac muscle cell apoptotic process / cytoskeletal protein binding / protein catabolic process / cellular response to hydrogen peroxide / peptidase activity / presynapse / lysosome / postsynapse / postsynaptic density / calcium ion binding / glutamatergic synapse / enzyme binding / mitochondrion / proteolysis / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
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 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 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 / Calpain-1 catalytic subunit
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsMoldoveanu, T. / Campbell, R.L. / Cuerrier, D. / Davies, P.L.
Citation
Journal: J.Mol.Biol. / Year: 2004
Title: Crystal Structures of Calpain-E64 and -Leupeptin Inhibitor Complexes Reveal Mobile Loops Gating the Active Site
Authors: Moldoveanu, T. / Campbell, R.L. / Cuerrier, D. / Davies, P.L.
#1: Journal: Cell(Cambridge,Mass.) / Year: 2002
Title: A calcium switch aligns the active site of calpain
Authors: Moldoveanu, T. / Hosfield, C.M. / Lim, D. / Elce, J.S. / Jia, Z. / Davies, P.L.
#2: Journal: Nat.Struct.Mol.Biol. / Year: 2003
Title: Calpain silencing by a reversible intrinsic mechanism
Authors: Moldoveanu, T. / Hosfield, C.M. / Lim, D. / Jia, Z. / Davies, P.L.
History
DepositionJun 9, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 2, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Data collection / Category: reflns_shell
Item: _reflns_shell.number_unique_all / _reflns_shell.percent_possible_all
Revision 1.4Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.5Aug 23, 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 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Calpain 1, large [catalytic] subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,2454
Polymers38,8051
Non-polymers4413
Water95553
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.52, 69.76, 108.96
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Calpain 1, large [catalytic] subunit / Calcium-activated neutral proteinase / CANP / Mu-type / muCANP / Micromolar-calpain


Mass: 38804.551 Da / Num. of mol.: 1 / Fragment: residues 27-356
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: CAPN1, CLS1 / Plasmid: pET24d / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 DE3 / References: UniProt: P97571, calpain-1
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-E64 / N-[N-[1-HYDROXYCARBOXYETHYL-CARBONYL]LEUCYLAMINO-BUTYL]-GUANIDINE


Mass: 360.429 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H30N5O5
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 53 / 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: 1.98 Å3/Da / Density % sol: 38.01 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 6
Details: sodium chloride, calcium chloride, MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 100K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.937 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 11, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.937 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 24647 / % possible obs: 98 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.077 / Rsym value: 0.067 / Net I/σ(I): 27.8
Reflection shellResolution: 1.9→1.97 Å / Rmerge(I) obs: 0.349 / Mean I/σ(I) obs: 6 / Num. unique all: 2417 / Rsym value: 0.292

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1.1 & XFITrefinement
XFITdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1KXR

1kxr


Resolution: 1.9→50 Å / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.272 1193 random
Rwork0.238 --
obs0.272 24593 -
all-24953 -
Refinement stepCycle: LAST / Resolution: 1.9→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2594 0 27 53 2674
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.192
X-RAY DIFFRACTIONc_bond_d0.006

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