1MDW | pdb_00001mdw

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

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
B	d1mdwb_	Alpha and beta proteins (a+b)	Cysteine proteinases	Cysteine proteinases	Calpain large subunit, catalytic domain (domain II)	Calpain large subunit, catalytic domain (domain II)	Norway rat (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)
A	d1mdwa_	Alpha and beta proteins (a+b)	Cysteine proteinases	Cysteine proteinases	Calpain large subunit, catalytic domain (domain II)	Calpain large subunit, catalytic domain (domain II)	Norway rat (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	Cysteine proteinases	8032820	3001808	SCOP2B (2022-06-29)
A	SCOP2 Family	Calpain large subunit, catalytic domain (domain II)	8020440	4000875	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Cysteine proteinases	8032820	3001808	SCOP2 (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
B		e1mdwB1	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: Peptidase_C2	F:	ECOD (20:10:01)
A		e1mdwA1	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: Peptidase_C2	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	3.90.70.10	Alpha Beta	Alpha-Beta Complex	Cathepsin B	Chain A	CATH (4.3.0)
A	3.90.70.10	Alpha Beta	Alpha-Beta Complex	Cathepsin B	Chain A	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF00648	Calpain family cysteine protease (Peptidase_C2)	Calpain family cysteine protease	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Calpain II, catalytic subunit	cysteine-type peptidase activity peptidase activity calcium-dependent cysteine-type endopeptidase activity catalytic activity, acting on a protein cysteine-type endopeptidase activity hydrolase activity catalytic activity endopeptidase activity cytoskeletal protein binding protein binding binding protein-containing complex binding cation binding ion binding cysteine-type peptidase activity peptidase activity calcium-dependent cysteine-type endopeptidase activity catalytic activity, acting on a protein cysteine-type endopeptidase activity hydrolase activity catalytic activity endopeptidase activity cytoskeletal protein binding protein binding binding protein-containing complex binding cation binding ion binding calcium ion binding metal ion binding small molecule binding enzyme binding	primary metabolic process gene expression macromolecule biosynthetic process protein maturation protein autoprocessing biosynthetic process proteolysis protein processing metabolic process cellular process protein metabolic process macromolecule metabolic process catabolic process protein catabolic process primary metabolic process gene expression macromolecule biosynthetic process protein maturation protein autoprocessing biosynthetic process proteolysis protein processing metabolic process cellular process protein metabolic process macromolecule metabolic process catabolic process protein catabolic process macromolecule catabolic process cellular response to interferon-beta response to peptide response to interferon-beta response to stimulus response to chemical response to cytokine cellular response to cytokine stimulus behavior multicellular organismal process response to stress multicellular organismal response to stress response to pain behavioral response to pain cellular response to acid chemical cellular response to stimulus cellular response to amino acid stimulus response to acid chemical cellular response to chemical stimulus response to amino acid developmental process cellular developmental process myoblast fusion cell-cell fusion muscle cell differentiation myotube differentiation muscle structure development syncytium formation by plasma membrane fusion anatomical structure morphogenesis cell differentiation anatomical structure formation involved in morphogenesis anatomical structure development syncytium formation striated muscle cell differentiation response to decreased oxygen levels response to hypoxia response to oxygen levels response to abiotic stimulus positive regulation of cellular component organization regulation of cellular process regulation of cellular component organization regulation of syncytium formation by plasma membrane fusion regulation of developmental process positive regulation of biological process cellular component organization positive regulation of developmental process cellular component organization or biogenesis positive regulation of myoblast fusion positive regulation of cellular process regulation of biological process biological regulation regulation of myoblast fusion positive regulation of syncytium formation by plasma membrane fusion regulation of biosynthetic process interleukin-6 production regulation of macromolecule metabolic process regulation of interleukin-6 production regulation of gene expression regulation of cytokine production cytokine production regulation of macromolecule biosynthetic process regulation of multicellular organismal process regulation of metabolic process protein catabolic process at postsynapse protein catabolic process at synapse response to hydrogen peroxide response to oxidative stress response to oxygen-containing compound response to reactive oxygen species synaptic vesicle endocytosis import into cell cellular localization transport synaptic vesicle cycle establishment of localization vesicle-mediated transport presynaptic endocytosis vesicle-mediated transport in synapse synaptic vesicle recycling localization establishment of localization in cell endocytosis multi-multicellular organism process reproductive process female pregnancy multi-organism reproductive process biological process involved in interspecies interaction between organisms response to lipid response to other organism cellular response to lipopolysaccharide response to external stimulus cellular response to molecule of bacterial origin response to lipopolysaccharide cellular response to oxygen-containing compound response to biotic stimulus cellular response to biotic stimulus response to bacterium cellular response to lipid response to external biotic stimulus response to molecule of bacterial origin positive regulation of cardiac muscle cell apoptotic process positive regulation of programmed cell death muscle cell apoptotic process positive regulation of striated muscle cell apoptotic process regulation of apoptotic process regulation of cardiac muscle cell apoptotic process regulation of muscle cell apoptotic process regulation of programmed cell death cell death positive regulation of apoptotic process cardiac muscle cell apoptotic process positive regulation of muscle cell apoptotic process regulation of striated muscle cell apoptotic process striated muscle cell apoptotic process apoptotic process programmed cell death regulation of lipid metabolic process glycerophospholipid metabolic process lipid biosynthetic process positive regulation of phosphate metabolic process regulation of primary metabolic process phospholipid metabolic process positive regulation of metabolic process positive regulation of biosynthetic process positive regulation of phosphatidylcholine biosynthetic process phosphate-containing compound metabolic process positive regulation of lipid metabolic process phosphatidylcholine metabolic process phosphorus metabolic process positive regulation of phosphorus metabolic process glycerophospholipid biosynthetic process regulation of phosphatidylcholine metabolic process positive regulation of phospholipid biosynthetic process regulation of phospholipid metabolic process phospholipid biosynthetic process regulation of phospholipid biosynthetic process positive regulation of phospholipid metabolic process positive regulation of lipid biosynthetic process glycerolipid biosynthetic process organophosphate metabolic process organophosphate biosynthetic process regulation of phosphorus metabolic process glycerolipid metabolic process regulation of lipid biosynthetic process phosphatidylcholine biosynthetic process regulation of phosphatidylcholine biosynthetic process lipid metabolic process response to mechanical stimulus multicellular organism development embryo development ending in birth or egg hatching chordate embryonic development embryo development in utero embryonic development blastocyst development	cell projection cellular anatomical structure pseudopodium plasma membrane bounded cell projection cell periphery cell surface membrane plasma membrane external side of plasma membrane side of membrane intracellular anatomical structure cytoplasm cytosol somatodendritic compartment cell projection cellular anatomical structure pseudopodium plasma membrane bounded cell projection cell periphery cell surface membrane plasma membrane external side of plasma membrane side of membrane intracellular anatomical structure cytoplasm cytosol somatodendritic compartment dendrite dendritic tree neuron projection intracellular organelle organelle membraneless organelle intracellular membraneless organelle chromatin chromosome membrane-bounded organelle intracellular membrane-bounded organelle endomembrane system perinuclear endoplasmic reticulum perinuclear region of cytoplasm endoplasmic reticulum Golgi apparatus protein-containing complex catalytic complex caspase complex peptidase complex calpain complex endopeptidase complex cell body neuronal cell body postsynapse synapse cell junction anchoring junction focal adhesion cell-substrate junction membrane microdomain membrane raft presynapse lytic vacuole vacuole lysosome nucleus

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR022684	Peptidase C2, calpain family	Family
A, B	IPR038765	Papain-like cysteine peptidase superfamily	Homologous Superfamily
A, B	IPR002048	EF-hand domain	Domain
A, B	IPR042736	CAPN2, penta-EF hand, calcium binding motif	Domain
A, B	IPR018247	EF-Hand 1, calcium-binding site	Binding Site
A, B	IPR033883	Calpain subdomain III	Domain
A, B	IPR036213	Calpain large subunit, domain III superfamily	Homologous Superfamily
A, B	IPR022682	Peptidase C2, calpain, large subunit, domain III	Domain
A, B	IPR000169	Cysteine peptidase, cysteine active site	Active Site
A, B	IPR011992	EF-hand domain pair	Homologous Superfamily
A, B	IPR001300	Peptidase C2, calpain, catalytic domain	Domain
A, B	IPR022683	Peptidase C2, calpain, domain III	Domain

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.