4Y1T | pdb_00004y1t

Structural basis for Ca2+-mediated interaction of the perforin C2 domain with lipid membranes

External Resource: Annotation

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: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	C2 domain (calcium/lipid-binding domain, calb)	8052103	3000965	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A		e4y1tA1	A: jelly-roll	X: Double-stranded beta-helix	H: Double-stranded beta-helix	T: Ribosomal_L24e	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.60.40.150	Mainly Beta	Sandwich	Immunoglobulin-like	C2 domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF00168	C2 domain (C2)	C2 domain		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Perforin-1	cation binding ion binding binding calcium ion binding metal ion binding small molecule binding wide pore channel activity passive transmembrane transporter activity channel activity transporter activity transmembrane transporter activity pore-forming activity identical protein binding protein binding	response to tumor cell response to stimulus defense response response to stress defense response to tumor cell response to biotic stimulus rhythmic process circadian rhythm ceramide metabolic process sphingolipid biosynthetic process biosynthetic process ceramide biosynthetic process lipid biosynthetic process sphingolipid metabolic process response to tumor cell response to stimulus defense response response to stress defense response to tumor cell response to biotic stimulus rhythmic process circadian rhythm ceramide metabolic process sphingolipid biosynthetic process biosynthetic process ceramide biosynthetic process lipid biosynthetic process sphingolipid metabolic process primary metabolic process metabolic process cellular process lipid metabolic process cellular response to stimulus regulation of biological process regulation of cellular process signaling biological regulation granzyme-mediated programmed cell death signaling pathway cell death cell communication signal transduction programmed cell death adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains T cell mediated cytotoxicity lymphocyte mediated immunity T cell mediated immunity immune response leukocyte mediated cytotoxicity adaptive immune response immune effector process immune system process leukocyte mediated immunity cell killing protein import localization establishment of protein localization protein transport transport macromolecule localization intracellular protein localization establishment of localization transmembrane transport protein transmembrane transport positive regulation of response to biotic stimulus regulation of response to biotic stimulus positive regulation of immune response to tumor cell immune response to tumor cell positive regulation of biological process regulation of immune response to tumor cell regulation of response to tumor cell positive regulation of response to stimulus regulation of response to stimulus positive regulation of immune response regulation of immune response regulation of immune system process positive regulation of immune system process positive regulation of response to tumor cell pyroptotic cell death pyroptotic inflammatory response inflammatory response secretion establishment of protein localization to extracellular region export from cell protein secretion protein localization to extracellular region secretion by cell biological process involved in interspecies interaction between organisms disruption of cell in another organism disruption of anatomical structure in another organism killing of cells of another organism positive regulation of programmed cell death positive regulation of killing of cells of another organism regulation of killing of cells of another organism regulation of programmed cell death regulation of cell killing positive regulation of cell killing modulation of process of another organism positive regulation of cellular process multicellular organismal process immunological synapse formation cell-cell recognition cell activation cell recognition lymphocyte activation leukocyte activation protein metabolic process macromolecule metabolic process gene expression macromolecule biosynthetic process protein maturation cellular component organization cellular component biogenesis cellular component assembly protein-containing complex organization protein complex oligomerization protein-containing complex assembly protein homooligomerization cellular component organization or biogenesis defense response to virus response to other organism response to external stimulus response to external biotic stimulus response to virus membrane organization wound healing plasma membrane repair plasma membrane organization response to wounding endomembrane system organization	cellular anatomical structure membrane membrane-bounded organelle intracellular anatomical structure lytic vacuole cytolytic granule vacuole intracellular membrane-bounded organelle intracellular organelle organelle cytoplasm lysosome cytosol cell periphery cellular anatomical structure membrane membrane-bounded organelle intracellular anatomical structure lytic vacuole cytolytic granule vacuole intracellular membrane-bounded organelle intracellular organelle organelle cytoplasm lysosome cytosol cell periphery plasma membrane cytoplasmic vesicle intracellular vesicle vesicle immunological synapse extracellular region extracellular space endosome membrane-enclosed lumen endomembrane system intracellular organelle lumen organelle lumen endosome lumen

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR000008	C2 domain	Domain
A	IPR020863	Membrane attack complex component/perforin domain, conserved site	Conserved Site
A	IPR037300	Perforin-1, C2 domain	Domain
A	IPR052784	Perforin-1 pore-forming	Family
A	IPR020864	Membrane attack complex component/perforin (MACPF) domain	Domain
A	IPR035892	C2 domain superfamily	Homologous Superfamily

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.