SAXSdb — 3df0

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

Calpain-2 catalytic subunit

Rattus norvegicus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	Calpain small subunit 1 × 1 （Q64537） Calpastatin × 1 （P27321） CALCIUM ION × 10	Consistent with protein count

Other States of the Same Protein in the Database

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	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	Calpain-2 catalytic subunit × 1 （Q07009） Calpastatin × 1 （P27321） CALCIUM ION × 10	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CPNS1_RAT
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–184； UniProt 87–270

Calpastatin

Rattus norvegicus

UniProt P27321

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	Calpain-2 catalytic subunit × 1 （Q07009） Calpain small subunit 1 × 1 （Q64537） CALCIUM ION × 10	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ICAL_RAT
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–86； UniProt 193–278

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	3df0
Deposition date deposition_date	2008-06-11
Structure title title	Calcium-dependent complex between m-calpain and calpastatin
Keywords keywords	;protease core domain, penta EF-hand domains, C2-like domain, inhibitor loop-out, Hydrolase, Membrane, Protease, Thiol protease, Phosphoprotein, Protease inhibitor, Thiol protease inhibitor ;; HYDROLASE
Experimental Method method	X-RAY DIFFRACTION

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

3df0__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

3df0__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3df0__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	32.32 Å
Rg (electron density)	31.39 Å
Total Rg	32.03 Å
Atom count	7300
Residues	906
Excluded volume	129740 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3df0__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Calpain-2 catalytic subunit
Molecular weight formula_weight	81577.8 kDa
EC 编号 ec_number	3.4.22.53
Mutation mutation	C105S
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	7300

MAGIAMKLAKDREAAEGLGSHERAIKYLNQDYETLRNECLEAGALFQDPSFPALPSSLGFKELGPYSSKTRGIEWKRPTEICADPQFIIGGATRTDICQGALGDSWLLAAIASLTLNEEILARVVPLDQSFQENYAGIFHFQFWQYGEWVEVVVDDRLPTKDGELLFVHSAEGSEFWSALLEKAYAKINGCYEALSGGATTEGFEDFTGGIAEWYELRKPPPNLFKIIQKALEKGSLLGCSIDITSAADSEAVTYQKLVKGHAYSVTGAEEVESSGSLQKLIRIRNPWGQVEWTGKWNDNCPSWNTVDPEVRANLTERQEDGEFWMSFSDFLRHYSRLEICNLTPDTLTCDSYKKWKLTKMDGNWRRGSTAGGCRNYPNTFWMNPQYLIKLEEEDEDDEDGERGCTFLVGLIQKHRRRQRKMGEDMHTIGFGIYEVPEELTGQTNIHLSKNFFLTTRARERSDTFINLREVLNRFKLPPGEYVLVPSTFEPHKNGDFCIRVFSEKKADYQTVDDEIEANIEEIEANEEDIGDGFRRLFAQLAGEDAEISAFELQTILRRVLAKREDIKSDGFSIETCKIMVDMLDEDGSGKLGLKEFYILWTKIQKYQKIYREIDVDRSGTMNSYEMRKALEEAGFKLPCQLHQVIVARFADDELIIDFDNFVRCLVRLEILFKIFKQLDPENTGTIQLDLISWLSFSVLGKLAAALEHHHHHH

Source Source

Source organism organism	Rattus norvegicus
Common name common_name	Rat
NCBI taxonomy ID ncbi_taxonomy_id	10116
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Calpain small subunit 1
Molecular weight formula_weight	21305.0 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MHYSNIEANESEEERQFRKLFVQLAGDDMEVSATELMNILNKVVTRHPDLKTDGFGIDTCRSMVAVMDSDTTGKLGFEEFKYLWNNIKKWQGIYKRFDTDRSGTIGSNELPGAFEAAGFHLNQHIYSMIIRRYSDETGNMDFDNFISCLVRLDAMFRAFRSLDKNGTGQIQVNIQEWLQLTMYS

Source Source

Source organism organism	Rattus norvegicus
Common name common_name	Rat
NCBI taxonomy ID ncbi_taxonomy_id	10116
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	Calpastatin
Molecular weight formula_weight	9279.3 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

AALDDLIDTLGECEDTNKDDPPYTGPVVLDPMDSTYLEALGIKEGTIPPEYRKLLEKNEAITGPLPDSPKPMGIDHAIDALSSDFT

Source Source

Source organism organism	Rattus norvegicus
Common name common_name	Rat
NCBI taxonomy ID ncbi_taxonomy_id	10116
Host organism host_organism	Escherichia coli

Entity 4 Entity 4 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	10

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6. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d3df0b_
Class class	a — All alpha proteins
Fold Fold fold	a.39 — EF Hand-like
Superfamily Superfamily superfamily	a.39.1 — EF-hand
Family Family family	a.39.1.8 — Penta-EF-hand proteins

CATH v4.4 (4 domains)

Domain ID domain_id	3df0A02
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	70 — Cathepsin B; Chain A
Homologous superfamily homologous superfamily	10 — Cysteine proteinases

Domain ID domain_id	3df0A03
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	380 —

Domain ID domain_id	3df0A04
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	238 — Recoverin; domain 1
Homologous superfamily homologous superfamily	10 — EF-hand

Domain ID domain_id	3df0B00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	238 — Recoverin; domain 1
Homologous superfamily homologous superfamily	10 — EF-hand

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7. Citations (7)

Concerted multi-pronged attack by calpastatin to occlude the catalytic cleft of heterodimeric calpains.

Nature (2008)

PMID: 19020622 · DOI: 10.1038/nature07353 PRIMARY

Crystal structures of calpain-E64 and -leupeptin inhibitor complexes reveal mobile loops gating the active site

J.Mol.Biol. (2004)

PMID: 15491615 · DOI: 10.1016/j.jmb.2004.09.016

Calpain silencing by a reversible intrinsic mechanism

Nat.Struct.Mol.Biol. (2003)

PMID: 12665854 · DOI: 10.1038/nsb917

;A structural model for the inhibition of calpain by calpastatin: crystal structures of the native domain VI of calpain and its complexes with calpastatin peptide and a small molecule inhibitor ;

J.Mol.Biol. (2003)

PMID: 12684003 · DOI: 10.1016/S0022-2836(03)00274-2

A Ca(2+) switch aligns the active site of calpain

Cell(Cambridge,Mass.) (2002)

PMID: 11893336 · DOI: 10.1016/S0092-8674(02)00659-1

The crystal structure of calcium-free human m-calpain suggests an electrostatic switch mechanism for activation by calcium

Proc.Natl.Acad.Sci.USA (2000)

PMID: 10639123 · DOI: 10.1073/pnas.97.2.588

;Crystal structure of calpain reveals the structural basis for Ca(2+)-dependent protease activity and a novel mode of enzyme activation ;

Embo J. (1999)

PMID: 10601010 · DOI: 10.1093/emboj/18.24.6880

Unit-cell length a length_a	147.390 Å
Unit-cell length b length_b	147.390 Å
Unit-cell length c length_c	47.222 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 42
Space-group number int_tables_number	77
Crystal system crystal_system	—

Resolution resolution	2.950 Å
Low-resolution limit resolution_low	49.150 Å
R factor r_factor	0.2320
R_work r_work	0.2290
R_free r_free	0.2990

Calcium-dependent complex between m-calpain and calpastatin

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

Calpain-2 catalytic subunit

State in the Current Structure

Other States of the Same Protein in the Database

Calpain small subunit 1

State in the Current Structure

Other States of the Same Protein in the Database

Calpastatin

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

3df0__assembly_1__model_1

3df0__assembly_1__model_1 | I(q)

3df0__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 non-polymer

6. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (1 domains)

CATH v4.4 (4 domains)

7. Citations (7)

Calcium-dependent complex between m-calpain and calpastatin

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

Calpain-2 catalytic subunit

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Calpain small subunit 1

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Calpastatin

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

3df0__assembly_1__model_1

3df0__assembly_1__model_1 | I(q)

3df0__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 non-polymer

6. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (1 domains)

CATH v4.4 (4 domains)

7. Citations (7)