3GCI | pdb_00003gci

Crystal Structure of the Complex Formed Between a New Isoform of Phospholipase A2 with C-terminal Amyloid Beta Heptapeptide at 2 A Resolution

External Resource: Annotation

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

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d3gcia_	All alpha proteins	Phospholipase A2, PLA2	Phospholipase A2, PLA2	Vertebrate phospholipase A2	Snake phospholipase A2	(Naja sagittifera ) [TaxId: 195058 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Phospholipase A2, PLA2	8035017	3001690	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	Phospholip_A2_1	e3gciA1	A: few secondary structure elements	X: Phospholipase A2, PLA2 (From Topology)	H: Phospholipase A2, PLA2 (From Topology)	T: Phospholipase A2, PLA2	F: Phospholip_A2_1	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	1.20.90.10	Mainly Alpha	Up-down Bundle	Phospholipase A2	Phospholipase A2 domain	CATH (4.2.0)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B [auth P]	Heptapeptide from Amyloid beta A4 protein	DNA binding binding nucleic acid binding enzyme regulator activity enzyme activator activity peptidase regulator activity molecular function activator activity molecular function regulator activity peptidase activator activity protein binding signaling receptor binding cation binding transition metal ion binding ion binding DNA binding binding nucleic acid binding enzyme regulator activity enzyme activator activity peptidase regulator activity molecular function activator activity molecular function regulator activity peptidase activator activity protein binding signaling receptor binding cation binding transition metal ion binding ion binding metal ion binding small molecule binding growth factor receptor binding PTB domain binding protein domain specific binding identical protein binding signaling receptor regulator activity receptor ligand activity signaling receptor activator activity molecular function inhibitor activity serine-type endopeptidase inhibitor activity enzyme inhibitor activity peptidase inhibitor activity endopeptidase regulator activity endopeptidase inhibitor activity protein serine/threonine kinase binding kinase binding enzyme binding protein kinase binding heparin binding glycosaminoglycan binding carbohydrate derivative binding sulfur compound binding	negative regulation of long-term synaptic potentiation positive regulation of cell communication regulation of cellular process modulation of chemical synaptic transmission signaling positive regulation of biological process negative regulation of biological process cell communication long-term synaptic potentiation synaptic signaling regulation of biological quality positive regulation of cellular process regulation of synaptic plasticity trans-synaptic signaling negative regulation of long-term synaptic potentiation positive regulation of cell communication regulation of cellular process modulation of chemical synaptic transmission signaling positive regulation of biological process negative regulation of biological process cell communication long-term synaptic potentiation synaptic signaling regulation of biological quality positive regulation of cellular process regulation of synaptic plasticity trans-synaptic signaling regulation of biological process regulation of signaling biological regulation cell-cell signaling positive regulation of synaptic transmission chemical synaptic transmission regulation of trans-synaptic signaling anterograde trans-synaptic signaling regulation of long-term synaptic potentiation regulation of cell communication cellular process positive regulation of signaling regulation of synapse structure or activity cellular response to stimulus multicellular organismal process regulation of postsynaptic membrane potential system process response to stimulus regulation of system process regulation of signal transduction chemical synaptic transmission, postsynaptic modulation of excitatory postsynaptic potential regulation of multicellular organismal process signal transduction cell surface receptor signaling pathway nervous system process regulation of nervous system process regulation of response to stimulus excitatory postsynaptic potential regulation of membrane potential positive regulation of signal transduction intracellular signal transduction positive regulation of response to stimulus regulation of intracellular signal transduction intracellular signaling cassette regulation of calcium-mediated signaling positive regulation of calcium-mediated signaling positive regulation of intracellular signal transduction calcium-mediated signaling cellular component organization extracellular matrix organization cellular component organization or biogenesis extracellular structure organization external encapsulating structure organization apoptotic process cell death programmed cell death regulation of multicellular organism growth developmental process regulation of growth regulation of developmental growth regulation of developmental process developmental growth growth multicellular organism growth axonogenesis cellular developmental process cell projection organization plasma membrane bounded cell projection morphogenesis cell development neuron projection development cell morphogenesis neurogenesis multicellular organism development cell projection morphogenesis neuron differentiation neuron projection morphogenesis cell differentiation anatomical structure development system development plasma membrane bounded cell projection organization nervous system development axon development cell morphogenesis involved in neuron differentiation generation of neurons anatomical structure morphogenesis neuron development cell growth collateral sprouting in absence of injury collateral sprouting developmental cell growth developmental growth involved in morphogenesis positive regulation of macromolecule biosynthetic process positive regulation of metabolic process positive regulation of biosynthetic process regulation of cytokine production cytokine production positive regulation of macromolecule metabolic process regulation of biosynthetic process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of chemokine production regulation of gene expression biosynthetic process positive regulation of gene expression chemokine production positive regulation of chemokine production positive regulation of multicellular organismal process regulation of macromolecule biosynthetic process metabolic process macromolecule metabolic process positive regulation of cytokine production regulation of metabolic process astrocyte differentiation astrocyte activation glial cell development astrocyte development gliogenesis response to stress defense response cell activation central nervous system development glial cell differentiation glial cell activation inflammatory response neuroinflammatory response Notch signaling pathway myeloid leukocyte activation leukocyte activation macrophage activation immune system process leukocyte activation involved in inflammatory response microglial cell activation neuron recognition axon choice point recognition cell recognition axon midline choice point recognition axon guidance neuron projection guidance positive regulation of protein metabolic process regulation of protein metabolic process primary metabolic process regulation of primary metabolic process protein metabolic process ribonucleotide catabolic process pyridine nucleotide catabolic process aerobic respiration oxoacid metabolic process carbohydrate catabolic process carbohydrate derivative metabolic process organophosphate catabolic process regulation of generation of precursor metabolites and energy positive regulation of phosphate metabolic process nucleoside phosphate catabolic process organic acid metabolic process regulation of ATP metabolic process nucleobase-containing compound metabolic process regulation of purine nucleotide catabolic process positive regulation of nucleotide catabolic process regulation of small molecule metabolic process glycolytic process regulation of nucleotide metabolic process phosphate-containing compound metabolic process pyridine-containing compound metabolic process small molecule metabolic process regulation of nucleobase-containing compound metabolic process purine ribonucleotide catabolic process phosphorus metabolic process nucleoside phosphate metabolic process nicotinamide nucleotide metabolic process pyruvate metabolic process regulation of carbohydrate catabolic process positive regulation of phosphorus metabolic process purine nucleoside diphosphate metabolic process purine-containing compound catabolic process nucleotide metabolic process regulation of purine nucleotide metabolic process nucleobase-containing compound catabolic process positive regulation of ATP metabolic process nucleoside diphosphate metabolic process purine nucleoside diphosphate catabolic process nucleoside diphosphate catabolic process regulation of phosphorus metabolic process regulation of nucleotide catabolic process positive regulation of carbohydrate metabolic process nucleoside triphosphate metabolic process monocarboxylic acid metabolic process purine ribonucleotide metabolic process pyridine-containing compound catabolic process ribose phosphate metabolic process cellular respiration ATP metabolic process catabolic process energy derivation by oxidation of organic compounds positive regulation of nucleotide metabolic process positive regulation of purine nucleotide catabolic process purine nucleotide metabolic process ribonucleotide metabolic process nucleobase-containing small molecule metabolic process purine ribonucleoside triphosphate metabolic process ribonucleoside diphosphate metabolic process ribonucleoside diphosphate catabolic process regulation of carbohydrate metabolic process nucleotide catabolic process purine nucleoside triphosphate metabolic process carbohydrate metabolic process purine nucleotide catabolic process carbohydrate derivative catabolic process positive regulation of glycolytic process ADP catabolic process carboxylic acid metabolic process generation of precursor metabolites and energy regulation of catabolic process regulation of glycolytic process purine-containing compound metabolic process positive regulation of purine nucleotide metabolic process positive regulation of catabolic process ADP metabolic process organophosphate metabolic process purine ribonucleoside diphosphate metabolic process positive regulation of small molecule metabolic process purine ribonucleoside diphosphate catabolic process myeloid leukocyte differentiation mononuclear cell differentiation microglia differentiation hemopoiesis macrophage differentiation microglia development myeloid cell differentiation myeloid cell development leukocyte differentiation regulation of cellular component organization positive regulation of cellular component organization positive regulation of amyloid fibril formation regulation of amyloid fibril formation amyloid fibril formation positive regulation of supramolecular fiber organization regulation of supramolecular fiber organization supramolecular fiber organization positive regulation of ERK1 and ERK2 cascade positive regulation of MAPK cascade regulation of MAPK cascade MAPK cascade ERK1 and ERK2 cascade regulation of ERK1 and ERK2 cascade positive regulation of long-term synaptic potentiation cellular localization transport intracellular transport establishment of localization localization axo-dendritic transport establishment of localization in cell microtubule-based transport transport along microtubule cytoskeleton-dependent intracellular transport microtubule-based movement microtubule-based process cell junction organization synapse organization cellular response to metal ion cellular response to chemical stimulus response to metal ion response to chemical cellular response to manganese ion response to manganese ion regulation of Wnt signaling pathway Wnt signaling pathway response to lead ion ligand-gated ion channel signaling pathway ionotropic glutamate receptor signaling pathway glutamate receptor signaling pathway regulation of non-canonical NF-kappaB signal transduction non-canonical NF-kappaB signal transduction positive regulation of non-canonical NF-kappaB signal transduction cell activation involved in immune response astrocyte activation involved in immune response immune response immune effector process negative regulation of metabolic process negative regulation of gene expression negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process negative regulation of cellular process negative regulation of macromolecule metabolic process positive regulation of cell cycle mitotic cell cycle regulation of mitotic cell cycle positive regulation of mitotic cell cycle cell cycle regulation of cell cycle regulation of tumor necrosis factor production positive regulation of tumor necrosis factor superfamily cytokine production tumor necrosis factor superfamily cytokine production positive regulation of tumor necrosis factor production tumor necrosis factor production regulation of tumor necrosis factor superfamily cytokine production neuron projection maintenance neuron projection organization cellular response to nitrogen compound response to oxygen-containing compound response to nitrogen compound cellular response to amyloid-beta cellular response to oxygen-containing compound response to amyloid-beta behavior learning learning or memory cognition regulation of defense response regulation of response to external stimulus response to external stimulus regulation of inflammatory response positive regulation of response to external stimulus positive regulation of inflammatory response regulation of response to stress positive regulation of defense response inorganic ion homeostasis homeostatic process intracellular copper ion homeostasis copper ion homeostasis cellular homeostasis chemical homeostasis intracellular monoatomic cation homeostasis monoatomic ion homeostasis intracellular chemical homeostasis monoatomic cation homeostasis intracellular monoatomic ion homeostasis developmental maturation neuron remodeling anatomical structure maturation neuron maturation cell maturation reproductive process multicellular organismal reproductive process reproductive behavior mating behavior translation protein biosynthetic process post-transcriptional regulation of gene expression regulation of translation cellular response to endogenous stimulus cellular response to growth factor stimulus response to endogenous stimulus cellular response to nerve growth factor stimulus response to nerve growth factor response to growth factor interleukin-1 production regulation of interleukin-1 beta production positive regulation of interleukin-1 beta production positive regulation of interleukin-1 production regulation of interleukin-1 production interleukin-1 beta production regulation of neuronal synaptic plasticity regulation of long-term neuronal synaptic plasticity positive regulation of JNK cascade JNK cascade regulation of JNK cascade positive regulation of locomotion regulation of cell motility regulation of lymphocyte migration positive regulation of cell migration positive regulation of cell motility regulation of cell migration positive regulation of mononuclear cell migration cell migration regulation of immune system process cell motility regulation of mononuclear cell migration positive regulation of immune system process locomotion positive regulation of lymphocyte migration regulation of leukocyte migration positive regulation of T cell migration lymphocyte migration positive regulation of leukocyte migration leukocyte migration regulation of locomotion regulation of T cell migration mononuclear cell migration T cell migration cell adhesion NMDA selective glutamate receptor signaling pathway positive regulation of DNA-templated transcription RNA metabolic process RNA biosynthetic process nucleic acid biosynthetic process DNA-templated transcription regulation of RNA metabolic process transcription by RNA polymerase II regulation of RNA biosynthetic process regulation of transcription by RNA polymerase II positive regulation of transcription by RNA polymerase II nucleobase-containing compound biosynthetic process nucleic acid metabolic process positive regulation of RNA metabolic process positive regulation of RNA biosynthetic process regulation of DNA-templated transcription locomotory behavior response to norepinephrine response to monoamine cellular response to norepinephrine stimulus cellular response to monoamine stimulus response to catecholamine cellular response to catecholamine stimulus adult locomotory behavior adult behavior interleukin-6 production positive regulation of interleukin-6 production regulation of interleukin-6 production import into cell endocytosis vesicle-mediated transport regulation of presynapse assembly cellular component biogenesis cellular component assembly regulation of presynapse organization cell junction assembly regulation of synapse assembly presynapse organization regulation of cellular component biogenesis regulation of cell junction assembly regulation of synapse organization synapse assembly presynapse assembly spontaneous synaptic transmission regulation of spontaneous synaptic transmission response to peptide response to cytokine response to interleukin-1 response to organophosphorus response to purine-containing compound response to cAMP cellular response to cAMP response to light stimulus visual learning visual behavior associative learning response to radiation response to abiotic stimulus response to copper ion cellular response to copper ion dendrite development negative regulation of cell population proliferation cell population proliferation regulation of cell population proliferation	somatodendritic compartment cell body cellular anatomical structure perikaryon neuronal cell body intracellular anatomical structure cytoplasm cytosol axon cell leading edge neuron projection growth cone lamellipodium plasma membrane bounded cell projection growth cone somatodendritic compartment cell body cellular anatomical structure perikaryon neuronal cell body intracellular anatomical structure cytoplasm cytosol axon cell leading edge neuron projection growth cone lamellipodium plasma membrane bounded cell projection growth cone cell projection distal axon site of polarized growth lamellipodium protein-containing complex receptor complex membrane-bounded organelle membrane-enclosed lumen intracellular membrane-bounded organelle endomembrane system intracellular organelle lumen endoplasmic reticulum lumen intracellular organelle organelle lumen organelle endoplasmic reticulum endosome intracellular vesicle recycling endosome cytoplasmic vesicle vesicle neuron spine synapse dendritic spine postsynapse cell junction dendrite dendritic tree extracellular region extracellular space mitochondrial membrane organelle inner membrane mitochondrion membrane mitochondrial inner membrane organelle envelope mitochondrial envelope organelle membrane glial cell projection astrocyte projection cell surface cell periphery plasma membrane membrane microdomain membrane raft main axon growth cone filopodium actin-based cell projection filopodium Golgi apparatus subcompartment Golgi apparatus organelle subcompartment trans-Golgi network membrane trans-Golgi network clathrin-coated pit dense core granule secretory granule secretory vesicle neuronal dense core vesicle extracellular exosome extracellular vesicle extracellular organelle extracellular membrane-bounded organelle amyloid-beta complex nucleus organelle envelope lumen nuclear envelope lumen nuclear envelope dendritic shaft perinuclear region of cytoplasm vesicle lumen cytoplasmic vesicle lumen secretory granule lumen platelet alpha granule platelet alpha granule lumen Golgi-associated vesicle early endosome Golgi lumen endosome membrane early endosome membrane cytoplasmic vesicle membrane bounding membrane of organelle vesicle membrane endosome lumen
A	Phospholipase A2 isoform 3	cation binding ion binding binding calcium ion binding metal ion binding small molecule binding protein binding signaling receptor binding phospholipase A2 activity calcium-dependent phospholipase A2 activity hydrolase activity, acting on ester bonds carboxylic ester hydrolase activity hydrolase activity catalytic activity cation binding ion binding binding calcium ion binding metal ion binding small molecule binding protein binding signaling receptor binding phospholipase A2 activity calcium-dependent phospholipase A2 activity hydrolase activity, acting on ester bonds carboxylic ester hydrolase activity hydrolase activity catalytic activity phospholipase activity lipase activity phospholipid binding lipid binding	organic anion transport carboxylic acid transport secretion transport arachidonate transport lipid localization lipid transport establishment of localization organic acid transport localization arachidonate secretion monocarboxylic acid transport fatty acid transport icosanoid transport macromolecule localization organic anion transport carboxylic acid transport secretion transport arachidonate transport lipid localization lipid transport establishment of localization organic acid transport localization arachidonate secretion monocarboxylic acid transport fatty acid transport icosanoid transport macromolecule localization icosanoid secretion long-chain fatty acid transport lipid catabolic process catabolic process metabolic process cellular process primary metabolic process lipid metabolic process fatty acid metabolic process monocarboxylic acid biosynthetic process small molecule biosynthetic process oxoacid metabolic process carboxylic acid metabolic process lipid biosynthetic process organic acid biosynthetic process organic acid metabolic process fatty acid biosynthetic process carboxylic acid biosynthetic process biosynthetic process small molecule metabolic process monocarboxylic acid metabolic process phospholipid metabolic process organophosphate metabolic process phosphate-containing compound metabolic process phosphorus metabolic process regulation of biological process fibroblast proliferation cell population proliferation regulation of cellular process positive regulation of cell population proliferation biological regulation positive regulation of biological process regulation of fibroblast proliferation regulation of cell population proliferation positive regulation of fibroblast proliferation positive regulation of cellular process	cellular anatomical structure extracellular region

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B [auth P]	IPR013803	Amyloidogenic glycoprotein, amyloid-beta peptide	Domain
B [auth P]	IPR008154	Amyloidogenic glycoprotein, extracellular	Domain
B [auth P]	IPR036176	E2 domain superfamily	Homologous Superfamily
B [auth P]	IPR024329	Amyloidogenic glycoprotein, E2 domain	Domain
B [auth P]	IPR036669	Amyloidogenic glycoprotein, copper-binding domain superfamily	Homologous Superfamily
B [auth P]	IPR019745	Amyloidogenic glycoprotein, intracellular domain, conserved site	Conserved Site
B [auth P]	IPR011178	Amyloidogenic glycoprotein, copper-binding	Domain
B [auth P]	IPR037071	Amyloidogenic glycoprotein, amyloid-beta peptide superfamily	Homologous Superfamily
B [auth P]	IPR020901	Proteinase inhibitor I2, Kunitz, conserved site	Conserved Site
B [auth P]	IPR019744	Amyloidogenic glycoprotein, copper-binding domain conserved site	Conserved Site
B [auth P]	IPR002223	Pancreatic trypsin inhibitor Kunitz domain	Domain
B [auth P]	IPR015849	Amyloidogenic glycoprotein, heparin-binding	Domain
B [auth P]	IPR036454	Amyloidogenic glycoprotein, heparin-binding domain superfamily	Homologous Superfamily
B [auth P]	IPR011993	PH-like domain superfamily	Homologous Superfamily
B [auth P]	IPR019543	Beta-amyloid precursor protein C-terminal	Domain
B [auth P]	IPR036880	Pancreatic trypsin inhibitor Kunitz domain superfamily	Homologous Superfamily
B [auth P]	IPR008155	Amyloidogenic glycoprotein	Family
A	IPR033112	Phospholipase A2, aspartic acid active site	Active Site
A	IPR033113	Phospholipase A2, histidine active site	Active Site
A	IPR016090	Phospholipase A2-like, central domain	Domain
A	IPR001211	Phospholipase A2	Family
A	IPR036444	Phospholipase A2 domain superfamily	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
B [auth P]	Pharos: P05067	Alzheimer disease amyloidosis cerebral amyloid angiopathy dementia cerebral amyloid angiopathy, APP-related fragile X syndrome Down syndrome neurodegenerative disease Necrosis brain disease premature aging syndrome Alzheimer disease type 1 spinal cord disease dissociative amnesia amnestic disorder Alzheimer disease amyloidosis cerebral amyloid angiopathy dementia cerebral amyloid angiopathy, APP-related fragile X syndrome Down syndrome neurodegenerative disease Necrosis brain disease premature aging syndrome Alzheimer disease type 1 spinal cord disease dissociative amnesia amnestic disorder endogenous depression osteosarcoma Gerstmann-Straussler-Scheinker syndrome astrocytic tumor Huntington disease Pick disease juvenile dermatomyositis ABeta amyloidosis, Arctic type learning disability ABeta amyloidosis, Italian type prion disease cerebrovascular disorder Lewy body dementia malignant ependymoma amyotrophic lateral sclerosis ovarian cancer Parkinson disease atypical teratoid rhabdoid tumor breast cancer large cell medulloblastoma ABeta amyloidosis, dutch type ABetaL34V amyloidosis psoriasis chronic obstructive pulmonary disease ACys amyloidosis medulloblastoma depressive disorder Emery-Dreifuss muscular dystrophy oligodendroglioma anxiety disorder FRAXE intellectual disability palsy head and neck cancer periodic fever syndrome bipolar disorder polycystic ovary syndrome cardiomyopathy ABeta amyloidosis, Iowa type acquired metabolic disease rheumatoid arthritis lung carcinoma ADan amyloidosis dermatomyositis toxic encephalopathy