← Back to search
3bow

Structure of M-calpain in complex with Calpastatin

Method: X-RAY DIFFRACTION Dmax: 107.2 Å Quality: GOOD
▼

1. Protein Identity and Related Structures Protein Identity & Related Structures

Calpain-2 catalytic subunit

Rattus norvegicus

UniProt Q07009

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count Chain A； UniProt 1–700 Mutation：C105S Calpain small subunit 1 × 1 （Q64537） Calpastatin × 1 （P27321） CA CALCIUM ION × 10 X-RAY DIFFRACTION X-ray crystallization conditions：pH 6.5；298 K；pH 6.5, microbatch under paraffin oil, temperature 298K Resolution 2.40 Å R-free 0.258

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 3BOW Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1DF0 Crystal structure of M-Calpain Deposited 1999-11-16 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–700（700 aa） Fragment：LARGE (CATALYTIC) SUBUNIT
Mutation：C105S No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.25；298 K；PEG 6000, MES, SODIUM CHLORIDE, DITHIOTHREITOL, EDTA, pH 6.25, VAPOR DIFFUSION, HANGING DROP
Resolution 2.60 Å R-free 0.293
1MDW Crystal Structure of Calcium-Bound Protease Core of Calpain II Reveals the Basis for Intrinsic Inactivation Deposited 2002-08-07 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 19–346（328 aa） Fragment：Protease Core Domains I and II (Residues 17-346)
Mutation：C105S CA CALCIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；298 K；10% PEG6000, 0.1M Sodium Acetate, 30mM calcium chloride, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 1.95 Å R-free 0.243
1MDW Crystal Structure of Calcium-Bound Protease Core of Calpain II Reveals the Basis for Intrinsic Inactivation Deposited 2002-08-07 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 19–346（328 aa） Fragment：Protease Core Domains I and II (Residues 17-346)
Mutation：C105S CA CALCIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；298 K；10% PEG6000, 0.1M Sodium Acetate, 30mM calcium chloride, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 1.95 Å R-free 0.243
1QXP Crystal Structure of a mu-like calpain Deposited 2003-09-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–49（49 aa）
Chain A 636–700（65 aa）
Mutation：C105S Mutation：C105S No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.25；295 K；PEG 6000,morpholino ethane sulfonic acid, sodium chloride, n-nonyl-beta-D-maltoside , pH 6.25, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Resolution 2.80 Å R-free 0.311
1QXP Crystal Structure of a mu-like calpain Deposited 2003-09-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–49（49 aa）
Chain B 636–700（65 aa）
Mutation：C105S Mutation：C105S No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.25；295 K；PEG 6000,morpholino ethane sulfonic acid, sodium chloride, n-nonyl-beta-D-maltoside , pH 6.25, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Resolution 2.80 Å R-free 0.311
1U5I Crystal Structure analysis of rat m-calpain mutant Lys10 Thr Deposited 2004-07-27 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–700（700 aa）
Mutation：K10T, C105S No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.6；298 K；PEG 6000, MES, sodium chloride, pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.86 Å R-free 0.283
3DF0 Calcium-dependent complex between m-calpain and calpastatin Deposited 2008-06-11 Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–700（700 aa）
Mutation：C105S CA CALCIUM ION × 10 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；298 K；4-9% PEG 3350, 5-10 mM CaCl2, 50-100 mM NaOAc (pH 5.5) , VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Resolution 2.95 Å R-free 0.299

5 other PDB entries and 7 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name CAN2_RAT
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–700； UniProt 1–700

Calpain small subunit 1

Rattus norvegicus

UniProt Q64537

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count Chain B； UniProt 88–270 Fragment：UNP residues 88-270 Calpain-2 catalytic subunit × 1 （Q07009） Calpastatin × 1 （P27321） CA CALCIUM ION × 10 X-RAY DIFFRACTION X-ray crystallization conditions：pH 6.5；298 K；pH 6.5, microbatch under paraffin oil, temperature 298K Resolution 2.40 Å R-free 0.258

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 3BOW Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1AJ5 CALPAIN DOMAIN VI APO Deposited 1997-05-15 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 12–184（173 aa） Fragment：SMALL REGULATORY SUBUNIT, DOMAIN VI, MET 87 - SER 270
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.8；38%SATURATED AMMONIUM SULFATE AND 25MM PIPES BUFFER, PH 6.8
Resolution 2.30 Å R-free 0.306
1AJ5 CALPAIN DOMAIN VI APO Deposited 1997-05-15 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain B 12–184（173 aa） Fragment：SMALL REGULATORY SUBUNIT, DOMAIN VI, MET 87 - SER 270
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.8；38%SATURATED AMMONIUM SULFATE AND 25MM PIPES BUFFER, PH 6.8
Resolution 2.30 Å R-free 0.306
1DF0 Crystal structure of M-Calpain Deposited 1999-11-16 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–184（184 aa） Fragment：DOMAIN VI (CALCIUM-BINDING DOMAIN), SMALL (REGULATORY) SUBUNIT
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.25；298 K；PEG 6000, MES, SODIUM CHLORIDE, DITHIOTHREITOL, EDTA, pH 6.25, VAPOR DIFFUSION, HANGING DROP
Resolution 2.60 Å R-free 0.293
1DVI CALPAIN DOMAIN VI WITH CALCIUM BOUND Deposited 1997-05-15 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–184（184 aa） Fragment：SMALL (REGULATORY) SUBUNIT, DOMAIN VI, RESIDUES 87 - 270
Chain B 1–184（184 aa） Fragment：SMALL (REGULATORY) SUBUNIT, DOMAIN VI, RESIDUES 87 - 270
Not recorded CA CALCIUM ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；17% PEG 8K, 50MM CACODYLATE PH. 6.5 , 10% GLYCEROL, 200MM CACL2
Resolution 2.30 Å R-free 0.294
1NP8 18-k C-terminally trunucated small subunit of calpain Deposited 2003-01-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 87–245（159 aa） Fragment：residues 87-245
Chain B 87–245（159 aa） Fragment：residues 87-245
Not recorded CD CADMIUM ION × 13 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；294 K；PEG, cadmium chloride, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Resolution 2.00 Å R-free 0.239
1U5I Crystal Structure analysis of rat m-calpain mutant Lys10 Thr Deposited 2004-07-27 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 84–266（183 aa） Fragment：residues 1-184
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.6；298 K；PEG 6000, MES, sodium chloride, pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.86 Å R-free 0.283
3DF0 Calcium-dependent complex between m-calpain and calpastatin Deposited 2008-06-11 Different construct Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 87–270（184 aa） Fragment：UNP residues 87-270
Not recorded CA CALCIUM ION × 10 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；298 K；4-9% PEG 3350, 5-10 mM CaCl2, 50-100 mM NaOAc (pH 5.5) , VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Resolution 2.95 Å R-free 0.299

6 other PDB entries and 7 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name CPNS1_RAT
Isoform —
PDB entities 2
Chains and sequence ranges Author chain B； PDBConstruct 2–184； UniProt 88–270

Calpastatin

Rattus norvegicus

UniProt P27321

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count Chain C； UniProt 571–664 Fragment：UNP residues 571-664 Calpain-2 catalytic subunit × 1 （Q07009） Calpain small subunit 1 × 1 （Q64537） CA CALCIUM ION × 10 X-RAY DIFFRACTION X-ray crystallization conditions：pH 6.5；298 K；pH 6.5, microbatch under paraffin oil, temperature 298K Resolution 2.40 Å R-free 0.258

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 3BOW Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
3DF0 Calcium-dependent complex between m-calpain and calpastatin Deposited 2008-06-11 Different construct Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 193–278（86 aa） Fragment：Inhibitory domain 1, UNP residues 193-278
Not recorded CA CALCIUM ION × 10 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；298 K；4-9% PEG 3350, 5-10 mM CaCl2, 50-100 mM NaOAc (pH 5.5) , VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Resolution 2.95 Å R-free 0.299

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name ICAL_RAT
Isoform —
PDB entities 3
Chains and sequence ranges Author chain C； PDBConstruct 2–95； UniProt 571–664

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 3bow

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3bow
Download Download
▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id3bow
Deposition date deposition_date2007-12-17
Structure title titleStructure of M-calpain in complex with Calpastatin
Keywords keywords;cysteine protease, inhibitor, Cell membrane, Hydrolase, Membrane, Protease, Thiol protease, Phosphoprotein, Protease inhibitor, Thiol protease inhibitor, hydrolase-hydrolase inhibitor COMPLEX ;; hydrolase/hydrolase inhibitor
Experimental Method methodX-RAY DIFFRACTION
▼

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier31.67 Å
Radius of gyration Rg (electron density) rg_electron30.69 Å
Forward intensity I(0) i0177508000.00
Molecular weight molecular_weight105330.0 kDa
Excluded volume excluded_volume131380 ų
Envelope volume envelope_volume162270 ų
Hydration-shell volume shell_volume43538 ų
Envelope diameter envelope_diameter112.6 Å
Shell Rg shell_rg38.10 Å
Envelope Rg envelope_rg30.70 Å
Shape Rg shape_rg30.69 Å
Total Rg total_rg31.33 Å
Total atoms total_atoms7406
Residues n_residues919
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
▼

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax107.2 Å
Rg (real space) rg_real31.64 Å
Rg uncertainty (real space) rg_real_error0.82 Å
I(0) (real space) i0_real1.7750e+08
I(0) uncertainty (real space) i0_real_error2.4950e+06
Rg (reciprocal space) rg_reciprocal31.66 Å
I(0) (reciprocal space) i0_reciprocal177500000.0000
Solution quality estimate total_estimate0.8762
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary38.6 Å
Skewness Skewness skewness0.368
Kurtosis Kurtosis kurtosis-0.189
Angular range angular_range— – 0.2500 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha51510000.0000
Real-space data points n_real_points51
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.815; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.942
▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (5)

▼

7. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd3bowb_
Class classa — All alpha proteins
Fold Fold folda.39 — EF Hand-like
Superfamily Superfamily superfamilya.39.1 — EF-hand
Family Family familya.39.1.8 — Penta-EF-hand proteins

CATH v4.4 (4 domains)

Domain ID domain_id3bowA02
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology70 — Cathepsin B; Chain A
Homologous superfamily homologous superfamily10 — Cysteine proteinases
Domain ID domain_id3bowA03
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology120 — Jelly Rolls
Homologous superfamily homologous superfamily380 —
Domain ID domain_id3bowA04
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology238 — Recoverin; domain 1
Homologous superfamily homologous superfamily10 — EF-hand
Domain ID domain_id3bowB00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology238 — Recoverin; domain 1
Homologous superfamily homologous superfamily10 — EF-hand
▶

8. Citations (1)

▶

9. Files and Curves (10)