Annotations: 6GSE

Solution structure of the capsid domain from the activity-regulated cytoskeleton-associated protein, Arc

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	RRM_1	e6gseA1	A: beta barrels	X: HUP domain-like	H: HUP domains	T: HUP domains	F: RRM_1	ECOD (v294.2)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF18162	Arc C-lobe (Arc_C-lobe)	Arc C-lobe	This is the C-lobe domain of Arc protein present in animals. The Arc protein modulates the trafficking of AMPA-type glutamate receptors. This domain's tertiary structure is similar to the capsid domain of HIV gag protein. The domain is thought to hav ...	This is the C-lobe domain of Arc protein present in animals. The Arc protein modulates the trafficking of AMPA-type glutamate receptors. This domain's tertiary structure is similar to the capsid domain of HIV gag protein. The domain is thought to have evolved from the capsid domain of Ty3/Gypsy retrotransposon [1-4].	Domain
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

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

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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.

6GSE | pdb_00006gse

Solution structure of the capsid domain from the activity-regulated cytoskeleton-associated protein, Arc

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