7R23 | pdb_00007r23

Crystal structure of human Arc CTD in complex with two anti-Arc nanobodies

External Resource: Annotation

Domain Annotation: ECOD Classification
Domain Annotation: CATH
SAbDab Antibody Annotation
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
C	V-set_8	e7r23C1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_8	ECOD (1.6)
B	V-set_12	e7r23B1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_12	ECOD (1.6)
A	EUF08046	e7r23A1	A: alpha bundles	X: Retrovirus capsid protein	H: Retrovirus capsid protein-C (From Topology)	T: Retrovirus capsid protein-C	F: EUF08046	ECOD (1.6)
A	Retrotrans_gag_like	e7r23A2	A: alpha bundles	X: Retrovirus capsid protein	H: Retrovirus capsid protein N-terminal domain (From Topology)	T: Retrovirus capsid protein N-terminal domain	F: Retrotrans_gag_like	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
C	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (utative)
B	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (utative)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
C	Heavy Chain	IGHV1	-	arc	SAbDab (2025-12-19)
B	Heavy Chain	IGHV1	-	arc	SAbDab (2025-12-19)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF18162	Arc C-lobe (Arc_C)	Arc C-lobe	This is the C-terminal domain of Arc protein present in found in Rattus norvegicus. 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 d ...	This is the C-terminal domain of Arc protein present in found in Rattus norvegicus. 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].	Domain
A	PF21395	Activity-regulated cytoskeleton-associated protein, capsid domain (Arc_capsid_dom)	Activity-regulated cytoskeleton-associated protein, capsid domain	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 Gag-like protein has the topology of a retroviral Gag protein, with a central capsid domain (this entry) with two globular subdomains, the N-lobe and the C-lobe, consisting of four and five alpha-helices, connected by a short non-helical segment [1-3].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C	Chains: C	-	-	-
B	Chains: B	-	-	-
A	ARC	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 positive regulation of cell communication regulation of cellular process modulation of chemical synaptic transmission signaling positive regulation of biological process cell communication long-term synaptic potentiation localization intercellular transport transport cellular process establishment of localization vesicle-mediated intercellular transport vesicle-mediated transport positive regulation of cell communication regulation of cellular process modulation of chemical synaptic transmission signaling positive 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 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 multicellular organismal process 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 regulation of cell morphogenesis endoderm development tissue development cell migration cell motility behavior system process learning or memory long-term memory nervous system process cognition memory organelle organization cytoskeleton organization regulation of neuronal synaptic plasticity 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 regulation of localization 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 transport 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	cell periphery postsynapse cellular anatomical structure postsynaptic membrane synapse cell junction membrane plasma membrane plasma membrane region synaptic membrane cell cortex intracellular anatomical structure cytoplasm virus-like capsid cell periphery postsynapse cellular anatomical structure postsynaptic membrane synapse cell junction membrane plasma membrane plasma membrane region synaptic membrane cell cortex intracellular anatomical structure cytoplasm virus-like capsid intracellular organelle cytoskeleton organelle membraneless organelle intracellular membraneless organelle actin cytoskeleton cytosol membrane microdomain membrane raft 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 neuron projection cytoplasmic region plasma membrane bounded cell projection cytoplasm plasma membrane bounded cell projection ribonucleoprotein granule cell projection neuronal ribonucleoprotein granule supramolecular complex endosome membrane early endosome endosome early endosome membrane endomembrane system neuron spine dendritic spine somatodendritic compartment dendrite dendritic tree extracellular vesicle extracellular organelle extracellular region extracellular membrane-bounded organelle postsynaptic density neuron to neuron synapse postsynaptic specialization asymmetric synapse cell body neuronal cell body acrosomal vesicle secretory granule secretory vesicle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR023263	Activity-regulated cytoskeleton-associated protein	Family
A	IPR048965	Activity-regulated cytoskeleton-associated protein, capsid domain	Domain
A	IPR045557	Activity-regulated cytoskeleton-associated protein, N-terminal domain	Domain
A	IPR040814	Activity-regulated cytoskeleton-associated protein, C-terminal domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	Pharos: Q7LC44	Alzheimer disease cocaine abuse cocaine dependence medulloblastoma non-small cell lung carcinoma Presenile dementia atypical teratoid rhabdoid tumor Down syndrome lung adenocarcinoma movement disorder osteosarcoma schizophrenia breast cancer duodenal ulcer gastric carcinoma Alzheimer disease cocaine abuse cocaine dependence medulloblastoma non-small cell lung carcinoma Presenile dementia atypical teratoid rhabdoid tumor Down syndrome lung adenocarcinoma movement disorder osteosarcoma schizophrenia breast cancer duodenal ulcer gastric carcinoma malignant ependymoma pituitary cancer chronic atrophic gastritis invasive ductal breast carcinoma

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.