9PZZ | pdb_00009pzz

Genetically encoded fluorescent nanobody H11 with 4-(7-nitro-2,1,3-benzoxadiazolyl)-alanine (NBDO) at the W37 position complexed with Arc-NL

External Resource: Annotation

Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B, D	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
B, D	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 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 animal gross anatomical part developmental process regulation of plasma membrane bounded cell projection organization import into cell endocytosis behavior system process learning or memory long-term memory nervous system process cognition memory 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 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 cytosol membrane microdomain membrane raft membrane-bounded organelle intracellular vesicle intracellular membrane-bounded organelle intracellular organelle coated vesicle membrane cytoplasmic vesicle membrane bounding membrane of organelle vesicle membrane cytoplasmic vesicle organelle clathrin-coated vesicle coated vesicle vesicle organelle membrane clathrin-coated vesicle membrane glutamatergic synapse neuron projection cytoplasm cytoplasmic ribonucleoprotein granule neuron projection intracellular membraneless organelle plasma membrane bounded cell projection ribonucleoprotein granule cell projection neuronal ribonucleoprotein granule membraneless organelle supramolecular complex cytoskeleton 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
A, C	Fluorescent nanobody H11	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

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

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
B, D	: 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

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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.