← Back to search
1mdw

Crystal Structure of Calcium-Bound Protease Core of Calpain II Reveals the Basis for Intrinsic Inactivation

Method: X-RAY DIFFRACTION Dmax: 92.9 Å Quality: EXCELLENT
▼

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

Calpain II, 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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 19–346 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
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain B； UniProt 19–346 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

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 1MDW 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
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 construct 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
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 6 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 1–328； UniProt 19–346 Author chain B； PDBConstruct 1–328； UniProt 19–346

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 1mdw

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1mdw
Download Download
▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id1mdw
Deposition date deposition_date2002-08-07
Structure title titleCrystal Structure of Calcium-Bound Protease Core of Calpain II Reveals the Basis for Intrinsic Inactivation
Keywords keywordsCalpain Cysteine Protease Fold, Two Cooperative Calcium Sites, Helix Instability, Tryptophan-Based Active Site Blockage, HYDROLASE; HYDROLASE
Experimental Method methodX-RAY DIFFRACTION
▼

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

Radius of gyration Rg (Guinier) rg_guinier29.07 Å
Radius of gyration Rg (electron density) rg_electron27.95 Å
Forward intensity I(0) i081856400.00
Molecular weight molecular_weight71406.0 kDa
Excluded volume excluded_volume89353 ų
Envelope volume envelope_volume110320 ų
Hydration-shell volume shell_volume33043 ų
Envelope diameter envelope_diameter93.0 Å
Shell Rg shell_rg35.00 Å
Envelope Rg envelope_rg27.69 Å
Shape Rg shape_rg27.92 Å
Total Rg total_rg28.75 Å
Total atoms total_atoms5045
Residues n_residues637
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 dmax92.9 Å
Rg (real space) rg_real29.02 Å
Rg uncertainty (real space) rg_real_error0.66 Å
I(0) (real space) i0_real8.1860e+07
I(0) uncertainty (real space) i0_real_error1.0750e+06
Rg (reciprocal space) rg_reciprocal29.04 Å
I(0) (reciprocal space) i0_reciprocal81860000.0000
Solution quality estimate total_estimate0.9002
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary32.1 Å
Skewness Skewness skewness0.234
Kurtosis Kurtosis kurtosis-0.527
Angular range angular_range— – 0.2750 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha23250000.0000
Real-space data points n_real_points56
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.931; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.988; Smooth: 0.917
▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (3)

▼

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd1mdwa_
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_idd1mdwb_
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)

CATH v4.4 (2 domains)

Domain ID domain_id1mdwA02
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology70 — Cathepsin B; Chain A
Homologous superfamily homologous superfamily10 — Cysteine proteinases
Domain ID domain_id1mdwB02
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology70 — Cathepsin B; Chain A
Homologous superfamily homologous superfamily10 — Cysteine proteinases
▶

8. Citations (3)

▶

9. Files and Curves (10)