Annotations: 9ZKM

The LBD-TMD structure of native mouse AMPAR with 4 TARPs

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)
G	ClpB_D2-small	e9zkmG1	A: alpha arrays	X: Hypothetical protein YqbG-like	H: Hypothetical protein YqbG-like	T: alpha/beta-Hydrolases	F: ClpB_D2-small	ECOD (v295.2)
F	ClpB_D2-small	e9zkmF1	A: alpha arrays	X: Hypothetical protein YqbG-like	H: Hypothetical protein YqbG-like	T: alpha/beta-Hydrolases	F: ClpB_D2-small	ECOD (v295.2)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
E, F	PF00822	PMP-22/EMP/MP20/Claudin family (PMP22_Claudin)	PMP-22/EMP/MP20/Claudin family	-	Family
A, C	PF00060	Ligand-gated ion channel (Lig_chan)	Ligand-gated ion channel	-	Family
A, C	PF10613	Ligated ion channel L-glutamate- and glycine-binding site (Lig_chan-Glu_bd)	Ligated ion channel L-glutamate- and glycine-binding site	This region, sometimes called the S1 domain, is the luminal domain just upstream of the first, M1, transmembrane region of transmembrane ion-channel proteins, and it binds L-glutamate and glycine [2]. It is found in association with Lig_chan, Pfam:PF ...	This region, sometimes called the S1 domain, is the luminal domain just upstream of the first, M1, transmembrane region of transmembrane ion-channel proteins, and it binds L-glutamate and glycine [2]. It is found in association with Lig_chan, Pfam:PF00060.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
G, H	Voltage-dependent calcium channel gamma-8 subunit	protein phosphatase binding phosphatase binding protein binding binding protein phosphatase 2B binding enzyme binding calcium channel activity monoatomic cation transmembrane transporter activity voltage-gated calcium channel activity gated channel activity monoatomic ion channel activity voltage-gated channel activity voltage-gated monoatomic ion channel activity voltage-gated monoatomic cation channel activity protein phosphatase binding phosphatase binding protein binding binding protein phosphatase 2B binding enzyme binding calcium channel activity monoatomic cation transmembrane transporter activity voltage-gated calcium channel activity gated channel activity monoatomic ion channel activity voltage-gated channel activity voltage-gated monoatomic ion channel activity voltage-gated monoatomic cation channel activity monoatomic cation channel activity passive transmembrane transporter activity calcium ion transmembrane transporter activity channel activity monoatomic ion transmembrane transporter activity transporter activity metal ion transmembrane transporter activity transmembrane transporter activity channel regulator activity molecular function regulator activity transporter regulator activity ionotropic glutamate receptor binding signaling receptor binding glutamate receptor binding ion channel regulator activity calcium channel regulator activity	regulation of postsynaptic membrane neurotransmitter receptor levels biological regulation regulation of biological quality cellular response to stimulus regulation of localization regulation of cellular process response to stimulus signaling transport 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 postsynaptic membrane neurotransmitter receptor levels biological regulation regulation of biological quality cellular response to stimulus regulation of localization regulation of cellular process response to stimulus signaling transport 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 localization 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 establishment of localization 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 cellular process multicellular organismal process system process nervous system process transmission of nerve impulse cellular localization localization within membrane neurotransmitter receptor diffusion trapping receptor diffusion trapping receptor localization to synapse postsynaptic neurotransmitter receptor diffusion trapping positive regulation of cell communication modulation of chemical synaptic transmission synaptic transmission, glutamatergic regulation of synaptic transmission, glutamatergic synaptic signaling trans-synaptic signaling positive regulation of synaptic transmission cell-cell signaling positive regulation of synaptic transmission, glutamatergic chemical synaptic transmission regulation of trans-synaptic signaling anterograde trans-synaptic signaling positive regulation of signaling	protein-containing complex plasma membrane protein complex sarcolemma voltage-gated calcium channel complex plasma membrane membrane membrane protein complex cation channel complex transporter complex cell periphery cellular anatomical structure transmembrane transporter complex T-tubule L-type voltage-gated calcium channel complex protein-containing complex plasma membrane protein complex sarcolemma voltage-gated calcium channel complex plasma membrane membrane membrane protein complex cation channel complex transporter complex cell periphery cellular anatomical structure transmembrane transporter complex T-tubule L-type voltage-gated calcium channel complex calcium channel complex monoatomic ion channel complex postsynaptic specialization membrane postsynaptic specialization synapse postsynaptic density membrane synaptic membrane postsynaptic density postsynapse neuron to neuron synapse organelle cell junction postsynaptic membrane asymmetric synapse plasma membrane region AMPA glutamate receptor complex ionotropic glutamate receptor complex neurotransmitter receptor complex plasma membrane signaling receptor complex signaling receptor complex cell leading edge neuron projection leading edge membrane plasma membrane bounded cell projection somatodendritic compartment neuron projection membrane cell projection dendrite membrane dendrite dendritic tree cell projection membrane Schaffer collateral - CA1 synapse glutamatergic synapse
E, F	Voltage-dependent calcium channel gamma-2 subunit	calcium channel activity monoatomic cation transmembrane transporter activity voltage-gated calcium channel activity gated channel activity monoatomic ion channel activity voltage-gated channel activity voltage-gated monoatomic ion channel activity voltage-gated monoatomic cation channel activity monoatomic cation channel activity passive transmembrane transporter activity calcium ion transmembrane transporter activity channel activity monoatomic ion transmembrane transporter activity transporter activity metal ion transmembrane transporter activity calcium channel activity monoatomic cation transmembrane transporter activity voltage-gated calcium channel activity gated channel activity monoatomic ion channel activity voltage-gated channel activity voltage-gated monoatomic ion channel activity voltage-gated monoatomic cation channel activity monoatomic cation channel activity passive transmembrane transporter activity calcium ion transmembrane transporter activity channel activity monoatomic ion transmembrane transporter activity transporter activity metal ion transmembrane transporter activity transmembrane transporter activity ionotropic glutamate receptor binding protein binding binding signaling receptor binding glutamate receptor binding channel regulator activity molecular function regulator activity transporter regulator activity	protein localization to postsynaptic specialization membrane protein localization to postsynaptic membrane protein localization to cell periphery cellular localization protein localization to synapse biological regulation localization within membrane protein localization to membrane protein-containing complex localization neurotransmitter receptor localization to postsynaptic specialization membrane localization regulation of postsynaptic membrane neurotransmitter receptor levels macromolecule localization protein localization to organelle protein localization to postsynaptic specialization membrane protein localization to postsynaptic membrane protein localization to cell periphery cellular localization protein localization to synapse biological regulation localization within membrane protein localization to membrane protein-containing complex localization neurotransmitter receptor localization to postsynaptic specialization membrane localization regulation of postsynaptic membrane neurotransmitter receptor levels macromolecule localization protein localization to organelle cellular process protein localization to postsynapse intracellular protein localization regulation of biological quality protein localization to cell junction receptor localization to synapse reflex response to stimulus response to external stimulus eye blink reflex cellular response to stimulus regulation of localization regulation of cellular process signaling transport 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 establishment of localization 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 neurotransmitter receptor diffusion trapping receptor diffusion trapping postsynaptic neurotransmitter receptor diffusion trapping response to metal ion response to chemical response to calcium ion positive regulation of cell communication modulation of chemical synaptic transmission synaptic transmission, glutamatergic regulation of synaptic transmission, glutamatergic synaptic signaling trans-synaptic signaling positive regulation of synaptic transmission cell-cell signaling positive regulation of synaptic transmission, glutamatergic chemical synaptic transmission regulation of trans-synaptic signaling anterograde trans-synaptic signaling positive regulation of signaling cellular component organization cell junction organization neuromuscular junction development synapse organization cellular component organization or biogenesis establishment of protein localization establishment of protein localization to membrane protein targeting protein targeting to membrane multicellular organismal process system process nervous system process positive regulation of protein localization to basolateral plasma membrane regulation of protein localization protein localization to basolateral plasma membrane regulation of protein localization to membrane positive regulation of protein localization to cell periphery regulation of protein localization to basolateral plasma membrane positive regulation of protein localization to membrane regulation of protein localization to cell periphery regulation of cellular localization positive regulation of protein localization transmission of nerve impulse regulation of membrane potential membrane hyperpolarization membrane depolarization	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 somatodendritic compartment protein-containing complex plasma membrane protein complex membrane protein complex transporter complex AMPA glutamate receptor complex ionotropic glutamate receptor complex neurotransmitter receptor complex transmembrane transporter complex plasma membrane signaling receptor complex signaling receptor complex monoatomic ion channel complex cell surface glutamatergic synapse hippocampal mossy fiber to CA3 synapse Schaffer collateral - CA1 synapse voltage-gated calcium channel complex cation channel complex calcium channel complex axon cell projection neuron projection cerebellar mossy fiber plasma membrane bounded cell projection
B, D	Glutamate receptor 2	transmitter-gated monoatomic ion channel activity molecular transducer activity gated channel activity monoatomic ion channel activity transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential signaling receptor activity neurotransmitter receptor activity ligand-gated channel activity ligand-gated monoatomic ion channel activity extracellular ligand-gated monoatomic ion channel activity passive transmembrane transporter activity channel activity transmitter-gated channel activity monoatomic ion transmembrane transporter activity transporter activity transmitter-gated monoatomic ion channel activity molecular transducer activity gated channel activity monoatomic ion channel activity transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential signaling receptor activity neurotransmitter receptor activity ligand-gated channel activity ligand-gated monoatomic ion channel activity extracellular ligand-gated monoatomic ion channel activity passive transmembrane transporter activity channel activity transmitter-gated channel activity monoatomic ion transmembrane transporter activity transporter activity transmembrane transporter activity	-	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 protein-containing complex plasma membrane protein complex membrane protein complex transporter complex AMPA glutamate receptor complex ionotropic glutamate receptor complex neurotransmitter receptor complex transmembrane transporter complex plasma membrane signaling receptor complex signaling receptor complex monoatomic ion channel complex
A, C	Glutamate receptor 1	transmitter-gated monoatomic ion channel activity glutamate receptor activity molecular transducer activity gated channel activity monoatomic ion channel activity signaling receptor activity carboxylic acid transmembrane transporter activity glutamate-gated receptor activity neurotransmitter receptor activity ligand-gated channel activity AMPA glutamate receptor activity ligand-gated monoatomic ion channel activity extracellular ligand-gated monoatomic ion channel activity amino acid transmembrane transporter activity dicarboxylic acid transmembrane transporter activity transmitter-gated monoatomic ion channel activity glutamate receptor activity molecular transducer activity gated channel activity monoatomic ion channel activity signaling receptor activity carboxylic acid transmembrane transporter activity glutamate-gated receptor activity neurotransmitter receptor activity ligand-gated channel activity AMPA glutamate receptor activity ligand-gated monoatomic ion channel activity extracellular ligand-gated monoatomic ion channel activity amino acid transmembrane transporter activity dicarboxylic acid transmembrane transporter activity passive transmembrane transporter activity channel activity transmembrane signaling receptor activity transmitter-gated channel activity monoatomic ion transmembrane transporter activity transporter activity transmembrane transporter activity amyloid-beta binding binding peptide binding protein binding G-protein alpha-subunit binding protein domain specific binding PDZ domain binding scaffold protein binding kinase binding enzyme binding protein kinase binding cytoskeletal protein binding myosin V binding myosin binding small GTPase binding GTPase binding adenylate cyclase binding calcium channel activity monoatomic cation transmembrane transporter activity monoatomic cation channel activity calcium ion transmembrane transporter activity ligand-gated calcium channel activity metal ion transmembrane transporter activity ligand-gated monoatomic cation channel activity beta-2 adrenergic receptor binding adrenergic receptor binding signaling receptor binding G protein-coupled receptor binding peptide hormone receptor binding hormone receptor binding protein-containing complex binding immunoglobulin binding protein kinase A binding identical protein binding glutamate receptor binding ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential glutamate-gated calcium ion channel activity ionotropic glutamate receptor binding G-protein beta-subunit binding transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential	response to stimulus response to chemical response to xenobiotic stimulus cellular response to stimulus positive regulation of cell communication multicellular organismal process regulation of postsynaptic membrane potential system process regulation of cellular process positive regulation of signal transduction signaling modulation of chemical synaptic transmission regulation of system process positive regulation of excitatory postsynaptic potential response to stimulus response to chemical response to xenobiotic stimulus cellular response to stimulus positive regulation of cell communication multicellular organismal process regulation of postsynaptic membrane potential system process regulation of cellular process positive regulation of signal transduction signaling modulation of chemical synaptic transmission regulation of system process positive regulation of excitatory postsynaptic potential positive regulation of biological process regulation of signal transduction chemical synaptic transmission, postsynaptic cell communication positive regulation of response to stimulus synaptic signaling modulation of excitatory postsynaptic potential regulation of multicellular organismal process signal transduction regulation of biological quality positive regulation of cellular process trans-synaptic signaling regulation of biological process regulation of signaling cell surface receptor signaling pathway nervous system process biological regulation cell-cell signaling chemical synaptic transmission regulation of nervous system process regulation of trans-synaptic signaling regulation of response to stimulus anterograde trans-synaptic signaling regulation of cell communication cellular process excitatory postsynaptic potential regulation of membrane potential positive regulation of signaling cellular response to endogenous stimulus cellular response to growth factor stimulus response to endogenous stimulus cellular response to nerve growth factor stimulus cellular response to brain-derived neurotrophic factor stimulus response to nerve growth factor response to growth factor cellular response to nitrogen compound response to peptide hormone cellular response to peptide hormone stimulus response to oxygen-containing compound response to nitrogen compound cellular response to oxygen-containing compound cellular response to chemical stimulus response to hormone cellular response to hormone stimulus response to toxic substance behavior response to stress multicellular organismal response to stress response to pain behavioral response to pain response to morphine response to isoquinoline alkaloid response to alkaloid learning learning or memory cognition conditioned place preference associative learning response to arsenic-containing substance positive regulation of synaptic transmission developmental process multicellular organism development spinal cord development central nervous system development anatomical structure development nervous system development animal gross anatomical part developmental process system development cellular response to ammonium ion response to ammonium ion response to psychosocial stress response to antibiotic response to fungicide response to lipid response to estradiol cellular response to dsRNA response to dsRNA localization import into cell receptor internalization transport receptor-mediated endocytosis endocytosis establishment of localization vesicle-mediated transport regulation of biosynthetic process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process positive regulation of macromolecule biosynthetic process regulation of gene expression positive regulation of metabolic process biosynthetic process positive regulation of gene expression positive regulation of biosynthetic process regulation of macromolecule biosynthetic process metabolic process positive regulation of macromolecule metabolic process macromolecule metabolic process regulation of metabolic process response to electrical stimulus response to abiotic stimulus response to lithium ion response to metal ion head development forebrain development animal organ development brain development pallium development cerebral cortex development telencephalon development cellular response to acid chemical cellular response to amino acid stimulus cellular response to L-glutamate response to amino acid response to acid chemical response to L-glutamate positive regulation of membrane potential regulation of localization regulation of transport monoatomic ion transmembrane transport regulation of monoatomic ion transport regulation of monoatomic ion transmembrane transport transmembrane transport regulation of transmembrane transport monoatomic ion transport response to nutrient levels positive regulation of locomotion locomotion involved in locomotory behavior regulation of behavior positive regulation of locomotion involved in locomotory behavior locomotory behavior positive regulation of behavior regulation of locomotion regulation of locomotion involved in locomotory behavior positive regulation of multicellular organismal process locomotion cellular component organization cellular component biogenesis cell junction organization cellular component assembly cell junction assembly synapse organization cellular component organization or biogenesis synapse assembly regulation of receptor recycling receptor recycling receptor metabolic process cellular response to amine stimulus response to amine response to carbohydrate response to sucrose response to disaccharide response to alcohol response to ethanol long-term memory memory action potential transmission of nerve impulse neuronal action potential response to glycine cellular response to glycine regulation of 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 long-term synaptic potentiation synaptic transmission, glutamatergic response to cocaine	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-cell junction anchoring junction intracellular anatomical structure cytoplasm cytosol axon cell projection axonal spine neuron spine neuron projection plasma membrane bounded cell projection neuromuscular junction extracellular region perisynaptic space membrane-bounded organelle endosome intracellular vesicle intracellular membrane-bounded organelle recycling endosome endomembrane system intracellular organelle cytoplasmic vesicle vesicle dendritic spine somatodendritic compartment dendrite dendritic tree neuron projection membrane dendrite membrane cell leading edge leading edge membrane dendritic spine membrane cell projection membrane cell body transport vesicle presynapse synaptic vesicle secretory vesicle exocytic vesicle cell surface protein-containing complex organelle subcompartment endoplasmic reticulum subcompartment nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum organelle membrane endoplasmic reticulum membrane presynaptic active zone membrane presynaptic membrane presynaptic active zone excitatory synapse external side of plasma membrane side of membrane plasma membrane protein complex membrane protein complex transporter complex AMPA glutamate receptor complex ionotropic glutamate receptor complex neurotransmitter receptor complex transmembrane transporter complex plasma membrane signaling receptor complex signaling receptor complex monoatomic ion channel complex proximal dendrite glutamatergic synapse dendritic shaft neuronal cell body neuronal cell body membrane cell body membrane postsynaptic density, intracellular component intracellular membraneless organelle postsynaptic specialization, intracellular component membraneless organelle transport vesicle membrane bounding membrane of organelle vesicle membrane synaptic vesicle membrane exocytic vesicle membrane cytoplasmic vesicle membrane early endosome endosome membrane recycling endosome membrane early endosome membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
G, H	IPR008372	Voltage-dependent calcium channel, gamma-8 subunit	Family
G, H	IPR051072	Voltage-dependent calcium channel gamma subunit	Family
G, H	IPR004031	PMP-22/EMP/MP20/Claudin	Family
G, H	IPR008368	Voltage-dependent calcium channel, gamma subunit	Family
E, F	IPR051072	Voltage-dependent calcium channel gamma subunit	Family
E, F	IPR004031	PMP-22/EMP/MP20/Claudin	Family
E, F	IPR005422	Voltage-dependent calcium channel, gamma-2 subunit	Family
E, F	IPR008368	Voltage-dependent calcium channel, gamma subunit	Family
B, D	IPR015683	Ionotropic glutamate receptor	Family
B, D	IPR001508	Ionotropic glutamate receptor, metazoa	Family
B, D	IPR028082	Periplasmic binding protein-like I	Homologous Superfamily
B, D	IPR001320	Ionotropic glutamate receptor, C-terminal	Domain
B, D	IPR001828	Receptor, ligand binding region	Domain
B, D	IPR019594	Ionotropic glutamate receptor, L-glutamate and glycine-binding domain	Domain
A, C	IPR028082	Periplasmic binding protein-like I	Homologous Superfamily
A, C	IPR001828	Receptor, ligand binding region	Domain
A, C	IPR001320	Ionotropic glutamate receptor, C-terminal	Domain
A, C	IPR019594	Ionotropic glutamate receptor, L-glutamate and glycine-binding domain	Domain
A, C	IPR001508	Ionotropic glutamate receptor, metazoa	Family
A, C	IPR015683	Ionotropic glutamate receptor	Family

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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.

9ZKM | pdb_00009zkm

The LBD-TMD structure of native mouse AMPAR with 4 TARPs

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