← Back to search
1df0

Crystal structure of M-Calpain

Method: X-RAY DIFFRACTION Dmax: 105.4 Å Quality: GOOD
▼

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

M-CALPAIN

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 1–700 Fragment：LARGE (CATALYTIC) SUBUNIT Mutation：C105S CALPAIN × 1 （Q64537） 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

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 1DF0 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
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 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 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 construct Different mutation/modification 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
3BOW Structure of M-calpain in complex with Calpastatin Deposited 2007-12-17 Different construct Different oligomeric state Different ligand/ion 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 pH 6.5；298 K；pH 6.5, microbatch under paraffin oil, temperature 298K
Resolution 2.40 Å R-free 0.258
3DF0 Calcium-dependent complex between m-calpain and calpastatin Deposited 2008-06-11 Different construct Different oligomeric state Different ligand/ion 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

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain B； UniProt 1–184 Fragment：DOMAIN VI (CALCIUM-BINDING DOMAIN), SMALL (REGULATORY) SUBUNIT M-CALPAIN × 1 （Q07009） 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

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 1DF0 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 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 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
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 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
3BOW Structure of M-calpain in complex with Calpastatin Deposited 2007-12-17 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 88–270（183 aa） Fragment：UNP residues 88-270
Not recorded 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
3DF0 Calcium-dependent complex between m-calpain and calpastatin Deposited 2008-06-11 Different construct Different oligomeric state Different ligand/ion 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 CANS_RAT
Isoform —
PDB entities 2
Chains and sequence ranges Author chain B； PDBConstruct 1–184； UniProt 1–184

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 1df0

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1df0
Download Download
▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id1df0
Deposition date deposition_date1999-11-16
Structure title titleCrystal structure of M-Calpain
Keywords keywordsCYSTEINE PROTEASE, CALMODULIN, PAPAIN, CATALYTIC TRIAD, ZYMOGEN ACTIVATION, C2 DOMAIN, PROTEASE, ZYMOGEN, CALPAIN, HYDROLASE; HYDROLASE
Experimental Method methodX-RAY DIFFRACTION
▼

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

Radius of gyration Rg (Guinier) rg_guinier31.46 Å
Radius of gyration Rg (electron density) rg_electron30.78 Å
Forward intensity I(0) i0130394000.00
Molecular weight molecular_weight90684.0 kDa
Excluded volume excluded_volume113370 ų
Envelope volume envelope_volume144060 ų
Hydration-shell volume shell_volume39120 ų
Envelope diameter envelope_diameter110.6 Å
Shell Rg shell_rg37.68 Å
Envelope Rg envelope_rg30.75 Å
Shape Rg shape_rg30.80 Å
Total Rg total_rg31.34 Å
Total atoms total_atoms6391
Residues n_residues800
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 dmax105.4 Å
Rg (real space) rg_real31.50 Å
Rg uncertainty (real space) rg_real_error0.63 Å
I(0) (real space) i0_real1.3040e+08
I(0) uncertainty (real space) i0_real_error1.7610e+06
Rg (reciprocal space) rg_reciprocal31.49 Å
I(0) (reciprocal space) i0_reciprocal130400000.0000
Solution quality estimate total_estimate0.8810
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary33.7 Å
Skewness Skewness skewness0.409
Kurtosis Kurtosis kurtosis-0.271
Angular range angular_range— – 0.2500 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha33420000.0000
Real-space data points n_real_points51
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.841; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.995; Smooth: 0.930
▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (3)

▼

7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_idd1df0a1
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
Domain ID domain_idd1df0a2
Class classb — All beta proteins
Fold Fold foldb.14 — Calpain large subunit, middle domain (domain III)
Superfamily Superfamily superfamilyb.14.1 — Calpain large subunit, middle domain (domain III)
Family Family familyb.14.1.1 — Calpain large subunit, middle domain (domain III)
Domain ID domain_idd1df0a3
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.3 — Cysteine proteinases
Superfamily Superfamily superfamilyd.3.1 — Cysteine proteinases
Family Family familyd.3.1.3 — Calpain large subunit, catalytic domain (domain II)
Domain ID domain_idd1df0b_
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_id1df0A02
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology70 — Cathepsin B; Chain A
Homologous superfamily homologous superfamily10 — Cysteine proteinases
Domain ID domain_id1df0A03
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology120 — Jelly Rolls
Homologous superfamily homologous superfamily380 —
Domain ID domain_id1df0A04
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology238 — Recoverin; domain 1
Homologous superfamily homologous superfamily10 — EF-hand
Domain ID domain_id1df0B00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology238 — Recoverin; domain 1
Homologous superfamily homologous superfamily10 — EF-hand
▶

8. Citations (4)

▶

9. Files and Curves (10)