Annotations: 4X3I

The crystal structure of Arc N-lobe complexed with CAMK2A fragment

External Resource: Annotation

Domain Annotation: ECOD Classification
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)
A	Med6	e4x3iA1	A: alpha arrays	X: HTH	H: HTH	T: Three-helical HTH	F: Med6	ECOD (v295)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF21395	Activity-regulated cytoskeleton-associated protein, N-lobe (Arc_N-lobe)	Activity-regulated cytoskeleton-associated protein, N-lobe	This domain is found in Activity-regulated cytoskeleton-associated protein from humans (Arc), a master regulator of synaptic plasticity that promotes endocytosis of AMPA receptors and a postsynaptic mediator of activity-dependent synapse elimination ...	This domain is found in Activity-regulated cytoskeleton-associated protein from humans (Arc), a master regulator of synaptic plasticity that promotes endocytosis of AMPA receptors and a postsynaptic mediator of activity-dependent synapse elimination in the developing cerebellum. This protein is associated with cognitive diseases. This protein has a bi-lobar architecture that is similar to the capsid domain of HIV gag protein consisting of a N-lobe, represented in this entry, and a C-lobe (Pfam:PF18162), which have four and five alpha-helices, connected by a short non-helical segment [1-3]. This protein was originated from the Ty3/Gypsy retrotransposon family and domesticated in higher vertebrates for synaptic functions [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Activity-regulated cytoskeleton-associated protein	RNA binding binding nucleic acid binding mRNA binding structural molecule activity	localization intercellular transport transport cellular process establishment of localization vesicle-mediated intercellular transport vesicle-mediated transport behavior multicellular organismal process system process learning learning or memory nervous system process cognition localization intercellular transport transport cellular process establishment of localization vesicle-mediated intercellular transport vesicle-mediated transport behavior multicellular organismal process system process learning learning or memory nervous system process cognition cellular response to stimulus regulation of localization regulation of cellular process response to stimulus signaling regulation of signaling receptor activity monoatomic ion transmembrane transport regulation of AMPA receptor activity positive regulation of biological process regulation of transmembrane transporter activity regulation of signal transduction regulation of monoatomic ion transmembrane transport cell communication positive regulation of molecular function positive regulation of monoatomic ion transport positive regulation of transmembrane transport monoatomic ion transport positive regulation of monoatomic ion transmembrane transport signal transduction positive regulation of cellular process regulation of biological process regulation of signaling regulation of transport regulation of monoatomic ion transport biological regulation transmembrane transport regulation of molecular function positive regulation of AMPA receptor activity regulation of transmembrane transport positive regulation of transport regulation of response to stimulus positive regulation of transporter activity regulation of neurotransmitter receptor activity positive regulation of ion transmembrane transporter activity regulation of cell communication positive regulation of cell communication modulation of chemical synaptic transmission long-term synaptic potentiation synaptic signaling regulation of biological quality regulation of synaptic plasticity trans-synaptic signaling 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 positive regulation of signaling RNA transport nitrogen compound transport nucleic acid transport mRNA transport establishment of RNA localization macromolecule localization RNA localization nucleobase-containing compound transport cell projection organization neuron projection development multicellular organism development cell projection morphogenesis neuron differentiation neuron projection morphogenesis cell differentiation anatomical structure development regulation of synapse structure or activity synapse organization dendritic spine morphogenesis system development developmental process dendritic spine development postsynapse organization dendritic spine organization regulation of cell projection organization regulation of postsynapse organization nervous system development generation of neurons regulation of neuron projection development regulation of cellular component organization cellular developmental process regulation of developmental process plasma membrane bounded cell projection morphogenesis cell development cell morphogenesis cellular component organization neurogenesis dendrite development cellular component organization or biogenesis regulation of anatomical structure morphogenesis plasma membrane bounded cell projection organization dendrite morphogenesis cell morphogenesis involved in neuron differentiation anatomical structure morphogenesis regulation of synapse organization cell junction organization neuron development regulation of dendritic spine morphogenesis neuron projection organization regulation of plasma membrane bounded cell projection organization import into cell endocytosis endoderm development tissue development response to alcohol response to chemical response to oxygen-containing compound response to ethanol long-term memory memory regulation of neuronal synaptic plasticity response to morphine response to isoquinoline alkaloid response to nitrogen compound response to alkaloid negative regulation of signaling negative regulation of biological process negative regulation of synaptic transmission negative regulation of cell communication negative regulation of cellular process long-term synaptic depression regulation of long-term synaptic depression cellular component biogenesis cellular component assembly protein-containing complex organization protein complex oligomerization protein-containing complex assembly protein homooligomerization anterior/posterior pattern specification pattern specification process regionalization response to cocaine cellular localization receptor internalization postsynaptic neurotransmitter receptor internalization regulation of receptor internalization vesicle-mediated transport in synapse establishment of localization in cell regulation of postsynaptic neurotransmitter receptor internalization regulation of endocytosis regulation of receptor-mediated endocytosis regulation of vesicle-mediated transport neurotransmitter receptor internalization regulation of postsynaptic membrane neurotransmitter receptor levels postsynaptic endocytosis receptor-mediated endocytosis	postsynaptic specialization membrane postsynaptic specialization synapse membrane plasma membrane postsynaptic density membrane synaptic membrane cell periphery postsynaptic density postsynapse cellular anatomical structure neuron to neuron synapse organelle cell junction postsynaptic specialization membrane postsynaptic specialization synapse membrane plasma membrane postsynaptic density membrane synaptic membrane cell periphery postsynaptic density postsynapse cellular anatomical structure neuron to neuron synapse organelle cell junction postsynaptic membrane asymmetric synapse plasma membrane region cell cortex intracellular anatomical structure cytoplasm virus-like capsid intracellular organelle cytoskeleton membraneless organelle intracellular membraneless organelle actin cytoskeleton cytosol membrane microdomain membrane raft somatodendritic compartment cell projection dendrite dendritic tree neuron projection plasma membrane bounded cell projection membrane-bounded organelle intracellular vesicle intracellular membrane-bounded organelle coated vesicle membrane cytoplasmic vesicle membrane bounding membrane of organelle vesicle membrane cytoplasmic vesicle clathrin-coated vesicle coated vesicle vesicle organelle membrane clathrin-coated vesicle membrane glutamatergic synapse neuron projection cytoplasm cytoplasmic ribonucleoprotein granule ribonucleoprotein granule neuronal ribonucleoprotein granule supramolecular complex endosome postsynaptic endosome endomembrane system endosome membrane early endosome early endosome membrane neuron spine dendritic spine extracellular vesicle extracellular organelle extracellular region extracellular membrane-bounded organelle acrosomal vesicle secretory granule secretory vesicle
B	CALCIUM/CALMODULIN-DEPENDENT PROTEIN KINASE TYPE II SUBUNIT ALPHA	protein serine/threonine kinase activity catalytic activity, acting on a protein kinase activity protein kinase activity calcium/calmodulin-dependent protein kinase activity transferase activity catalytic activity phosphotransferase activity, alcohol group as acceptor transferase activity, transferring phosphorus-containing groups binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding protein serine/threonine kinase activity catalytic activity, acting on a protein kinase activity protein kinase activity calcium/calmodulin-dependent protein kinase activity transferase activity catalytic activity phosphotransferase activity, alcohol group as acceptor transferase activity, transferring phosphorus-containing groups binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding protein binding calmodulin binding cation binding metal ion binding identical protein binding signaling receptor binding glutamate receptor binding GTPase activating protein binding protein serine kinase activity protein homodimerization activity protein dimerization activity	apoptotic mitochondrial changes biological regulation cell death cellular component organization organelle organization cellular process regulation of membrane permeability regulation of mitochondrial membrane permeability involved in apoptotic process apoptotic process cellular component organization or biogenesis regulation of biological quality regulation of mitochondrial membrane permeability programmed cell death mitochondrion organization apoptotic mitochondrial changes biological regulation cell death cellular component organization organelle organization cellular process regulation of membrane permeability regulation of mitochondrial membrane permeability involved in apoptotic process apoptotic process cellular component organization or biogenesis regulation of biological quality regulation of mitochondrial membrane permeability programmed cell death mitochondrion organization response to stimulus response to stress response to ischemia cellular response to stimulus cellular response to nitrogen compound response to angiotensin regulation of cellular process signaling response to peptide hormone angiotensin-activated signaling pathway cellular response to angiotensin cell communication cellular response to endogenous stimulus response to hormone signal transduction cellular response to hormone stimulus regulation of biological process response to endogenous stimulus response to oxygen-containing compound cellular response to peptide hormone stimulus response to nitrogen compound cellular response to oxygen-containing compound cellular response to chemical stimulus response to chemical G protein-coupled receptor signaling pathway cellular response to interferon-beta response to peptide response to interferon-beta response to cytokine cellular response to cytokine stimulus protein phosphorylation protein autophosphorylation phosphorylation primary metabolic process macromolecule modification phosphate-containing compound metabolic process metabolic process protein metabolic process macromolecule metabolic process protein modification process regulation of localization cellular localization transport modulation of chemical synaptic transmission localization synaptic signaling regulation of secretion by cell secretion by cell signal release establishment of localization in cell trans-synaptic signaling regulation of signaling neurotransmitter secretion regulation of transport secretion regulation of neurotransmitter transport export from cell cell-cell signaling neurotransmitter transport establishment of localization regulation of secretion chemical synaptic transmission signal release from synapse regulation of trans-synaptic signaling regulation of neurotransmitter secretion anterograde trans-synaptic signaling regulation of cell communication cell surface receptor signaling pathway via STAT cell surface receptor signaling pathway cell surface receptor signaling pathway via JAK-STAT regulation of neuronal synaptic plasticity regulation of synaptic plasticity developmental process dendritic spine development multicellular organismal process plasma membrane bounded cell projection organization cellular developmental process cell projection organization cell development neuron projection development nervous system development generation of neurons neurogenesis multicellular organism development neuron differentiation dendrite development cell differentiation neuron development anatomical structure development system development regulation of calcium ion transport positive regulation of calcium ion transport regulation of monoatomic ion transport positive regulation of biological process calcium ion transport metal ion transport positive regulation of transport positive regulation of monoatomic ion transport monoatomic ion transport monoatomic cation transport regulation of metal ion transport mitotic cell cycle process cell cycle phase transition cell cycle G1/S transition of mitotic cell cycle cell cycle G1/S phase transition mitotic cell cycle mitotic cell cycle phase transition cell cycle process peptidyl-serine modification peptidyl-serine phosphorylation peptidyl-amino acid modification protein localization to cell periphery regulation of protein localization protein localization to plasma membrane regulation of protein localization to cell periphery localization within membrane protein localization to membrane regulation of cellular localization macromolecule localization intracellular protein localization regulation of protein localization to plasma membrane regulation of protein localization to membrane plasma membrane bounded cell projection morphogenesis cell morphogenesis cell projection morphogenesis neuron projection morphogenesis dendrite morphogenesis cell morphogenesis involved in neuron differentiation anatomical structure morphogenesis establishment of protein localization neurotransmitter receptor transport establishment of protein localization to membrane vesicle-mediated transport protein-containing complex localization vesicle-mediated transport to the plasma membrane neurotransmitter receptor transport to plasma membrane protein transport regulation of cell motility neuron migration regulation of neuron migration regulation of locomotion regulation of cell migration cell migration cell motility locomotion cannabinoid signaling pathway regulation of signal transduction endocannabinoid signaling pathway regulation of response to stimulus regulation of G protein-coupled receptor signaling pathway regulation of endocannabinoid signaling pathway negative regulation of ferroptosis negative regulation of programmed cell death negative regulation of biological process regulation of programmed cell death negative regulation of cellular process regulation of ferroptosis ferroptosis 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 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 positive regulation of cellular process peptidyl-threonine autophosphorylation peptidyl-threonine modification peptidyl-threonine phosphorylation protein localization to synapse regulation of neurotransmitter receptor localization to postsynaptic specialization membrane regulation of protein localization to synapse neurotransmitter receptor localization to postsynaptic specialization membrane regulation of receptor localization to synapse protein localization to postsynaptic specialization membrane protein localization to postsynaptic membrane regulation of postsynaptic membrane neurotransmitter receptor levels protein localization to organelle protein localization to postsynapse protein localization to cell junction receptor localization to synapse biological process involved in interspecies interaction between organisms immune response response to other organism defense response response to type II interferon defense response to symbiont response to external stimulus cellular response to type II interferon response to biotic stimulus immune system process defense response to other organism innate immune response response to external biotic stimulus positive regulation of cell communication positive regulation of signal transduction positive regulation of receptor signaling pathway via STAT positive regulation of receptor signaling pathway via JAK-STAT positive regulation of response to stimulus regulation of receptor signaling pathway via JAK-STAT regulation of receptor signaling pathway via STAT positive regulation of signaling ligand-gated ion channel signaling pathway ionotropic glutamate receptor signaling pathway glutamate receptor signaling pathway	somatodendritic compartment cell projection cellular anatomical structure dendrite dendritic tree neuron projection plasma membrane bounded cell projection intracellular anatomical structure cytoplasm synapse cell junction glutamatergic synapse protein-containing complex catalytic complex somatodendritic compartment cell projection cellular anatomical structure dendrite dendritic tree neuron projection plasma membrane bounded cell projection intracellular anatomical structure cytoplasm synapse cell junction glutamatergic synapse protein-containing complex catalytic complex calcium- and calmodulin-dependent protein kinase complex intracellular protein-containing complex neuron spine dendritic spine postsynapse cell body neuronal cell body axon membrane-bounded organelle intracellular organelle mitochondrion organelle intracellular membrane-bounded organelle presynapse presynaptic cytosol cytosol neuron projection cytoplasm dendrite cytoplasm postsynaptic density neuron to neuron synapse postsynaptic specialization asymmetric synapse Schaffer collateral - CA1 synapse postsynaptic cytosol

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR040814	Activity-regulated cytoskeleton-associated protein, C-lobe	Domain
A	IPR023263	Activity-regulated cytoskeleton-associated protein	Family
A	IPR045557	Activity-regulated cytoskeleton-associated protein, N-terminal domain	Domain
A	IPR048965	Activity-regulated cytoskeleton-associated protein, N-lobe	Domain
B	IPR000719	Protein kinase domain	Domain
B	IPR032710	NTF2-like domain superfamily	Homologous Superfamily
B	IPR017441	Protein kinase, ATP binding site	Binding Site
B	IPR013543	Calcium/calmodulin-dependent protein kinase II, association-domain	Domain
B	IPR011009	Protein kinase-like domain superfamily	Homologous Superfamily
B	IPR008271	Serine/threonine-protein kinase, active site	Active Site

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

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.

4X3I | pdb_00004x3i

The crystal structure of Arc N-lobe complexed with CAMK2A fragment

External Resource: Annotation

Domain Annotation: ECOD Classification ECOD Database Homepage

Protein Family Annotation Pfam Database Homepage

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

InterPro: Protein Family Classification InterPro Database Homepage