9B13 | pdb_00009b13

Cryo-EM structure of phospholipase Cepsilon PH-COOH in complex with an antigen-binding fragment (composite structure)

External Resource: Annotation

Domain Annotation: ECOD Classification
SAbDab Antibody Annotation
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
B [auth H]		e9b13H01	A: a/b three-layered sandwiches	X: ATP-grasp_6	H: ATP-grasp_6	T: ATP-grasp_6	F:	ECOD (v294.1)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
C [auth L]	Light Chain	IGKV1	Kappa	1-phosphatidylinositol 4,5-bisphosphate phosphodiesteraseepsilon-1	SAbDab (2026-03-27)
B [auth H]	Heavy Chain	IGHV3	-	1-phosphatidylinositol 4,5-bisphosphate phosphodiesteraseepsilon-1	SAbDab (2026-03-27)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF00168	C2 domain (C2)	C2 domain		Domain
A	PF00388	Phosphatidylinositol-specific phospholipase C, X domain (PI-PLC-X)	Phosphatidylinositol-specific phospholipase C, X domain	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C [auth L]	Antigen-binding fragment light chain	-	-	-
B [auth H]	Antigen-binding fragment heavy chain	-	-	-
A	1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase epsilon-1	small GTPase binding protein binding binding enzyme binding GTPase binding phosphoric ester hydrolase activity phospholipase activity hydrolase activity, acting on ester bonds phosphoric diester hydrolase activity glycerophospholipase activity hydrolase activity C-type glycerophospholipase activity phosphatidylinositol-4,5-bisphosphate phospholipase C activity catalytic activity small GTPase binding protein binding binding enzyme binding GTPase binding phosphoric ester hydrolase activity phospholipase activity hydrolase activity, acting on ester bonds phosphoric diester hydrolase activity glycerophospholipase activity hydrolase activity C-type glycerophospholipase activity phosphatidylinositol-4,5-bisphosphate phospholipase C activity catalytic activity lipase activity GTPase regulator activity enzyme regulator activity guanyl-nucleotide exchange factor activity nucleoside-triphosphatase regulator activity molecular function regulator activity cation binding ion binding metal ion binding small molecule binding	cellular response to stimulus regulation of biological process small GTPase-mediated signal transduction regulation of cellular process response to stimulus signaling Ras protein signal transduction biological regulation intracellular signal transduction cell communication intracellular signaling cassette cellular process signal transduction phosphatidylinositol-mediated signaling cellular response to stimulus regulation of biological process small GTPase-mediated signal transduction regulation of cellular process response to stimulus signaling Ras protein signal transduction biological regulation intracellular signal transduction cell communication intracellular signaling cassette cellular process signal transduction phosphatidylinositol-mediated signaling lipid catabolic process catabolic process metabolic process primary metabolic process lipid metabolic process cell surface receptor signaling pathway cell surface receptor protein tyrosine kinase signaling pathway ERBB signaling pathway epidermal growth factor receptor signaling pathway enzyme-linked receptor protein signaling pathway phospholipase C-activating G protein-coupled receptor signaling pathway G protein-coupled receptor signaling pathway calcium ion transmembrane import into cytosol transport monoatomic ion transmembrane transport establishment of localization calcium ion transport metal ion transport monoatomic cation transmembrane transport transmembrane transport release of sequestered calcium ion into cytosol localization monoatomic ion transport monoatomic cation transport calcium ion transmembrane transport developmental process glomerulus development multicellular organism development multicellular organismal process anatomical structure development animal organ development nephron development kidney development renal system development system development neutral lipid metabolic process diacylglycerol biosynthetic process neutral lipid biosynthetic process lipid biosynthetic process acylglycerol biosynthetic process diacylglycerol metabolic process biosynthetic process glycerolipid biosynthetic process glycerolipid metabolic process acylglycerol metabolic process phosphatidylinositol metabolic process glycerophospholipid metabolic process phospholipid metabolic process organophosphate metabolic process phosphate-containing compound metabolic process phosphorus metabolic process regulation of cellular component organization positive regulation of cellular component organization cell projection organization positive regulation of biological process plasma membrane bounded cell projection assembly cellular component biogenesis cellular component organization cellular component assembly regulation of lamellipodium assembly regulation of lamellipodium organization positive regulation of cell projection organization cellular component organization or biogenesis positive regulation of cellular process lamellipodium assembly plasma membrane bounded cell projection organization positive regulation of cellular component biogenesis regulation of cell projection organization regulation of cell projection assembly positive regulation of lamellipodium assembly regulation of cellular component biogenesis positive regulation of lamellipodium organization regulation of plasma membrane bounded cell projection assembly lamellipodium organization cell projection assembly regulation of plasma membrane bounded cell projection organization positive regulation of plasma membrane bounded cell projection assembly	cell projection cellular anatomical structure cell leading edge plasma membrane bounded cell projection lamellipodium intracellular anatomical structure cytoplasm cytosol cell periphery plasma membrane membrane membrane-bounded organelle Golgi membrane Golgi apparatus cell projection cellular anatomical structure cell leading edge plasma membrane bounded cell projection lamellipodium intracellular anatomical structure cytoplasm cytosol cell periphery plasma membrane membrane membrane-bounded organelle Golgi membrane Golgi apparatus intracellular membrane-bounded organelle endomembrane system intracellular organelle bounding membrane of organelle organelle organelle membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR046974	1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase epsilon-1, EF-hand domain	Domain
A	IPR001711	Phospholipase C, phosphatidylinositol-specific, Y domain	Domain
A	IPR000008	C2 domain	Domain
A	IPR000909	Phosphatidylinositol-specific phospholipase C, X domain	Domain
A	IPR001895	Ras guanine-nucleotide exchange factors catalytic domain	Domain
A	IPR011992	EF-hand domain pair	Homologous Superfamily
A	IPR000159	Ras-associating domain	Domain
A	IPR001192	Phosphoinositide phospholipase C family	Family
A	IPR046973	1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase epsilon-1, catalytic domain	Domain
A	IPR017946	PLC-like phosphodiesterase, TIM beta/alpha-barrel domain superfamily	Homologous Superfamily
A	IPR028398	1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase epsilon-1, RA domain 2	Domain
A	IPR036964	Ras guanine-nucleotide exchange factor, catalytic domain superfamily	Homologous Superfamily
A	IPR035892	C2 domain superfamily	Homologous Superfamily
A	IPR023578	Ras guanine nucleotide exchange factor domain superfamily	Homologous Superfamily
A	IPR029071	Ubiquitin-like 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.