8SS3

Structure of LBD-TMD of AMPA receptor GluA2 in complex with auxiliary subunits TARP gamma-5 and cornichon-2 bound to competitive antagonist ZK and channel blocker spermidine (closed state)

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations
Membrane Protein Annotation: PDBTM
Membrane Protein Annotation: MemProtMD

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Type 2 solute binding protein-like	8036483	3000083	SCOP2B (2021-05-27)
B	SCOP2B Superfamily	Type 2 solute binding protein-like	8036483	3000083	SCOP2B (2021-05-27)
C	SCOP2B Superfamily	Type 2 solute binding protein-like	8036483	3000083	SCOP2B (2021-05-27)
D	SCOP2B Superfamily	Type 2 solute binding protein-like	8036483	3000083	SCOP2B (2021-05-27)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	PF13903	e8ss3A2	A: alpha bundles	X: Bromodomain-like	H: Claudin (From Topology)	T: Claudin	F: PF13903	ECOD (1.6)
A	PF00060	e8ss3A1	A: alpha complex topology	X: Voltage-gated ion channels (From Topology)	H: Voltage-gated ion channels (From Topology)	T: Voltage-gated ion channels	F: PF00060	ECOD (1.6)
A	PF10613	e8ss3A3	A: a/b three-layered sandwiches	X: Periplasmic binding protein-like II (From Topology)	H: Periplasmic binding protein-like II (From Topology)	T: Periplasmic binding protein-like II	F: PF10613	ECOD (1.6)
B	PF00060	e8ss3B1	A: alpha complex topology	X: Voltage-gated ion channels (From Topology)	H: Voltage-gated ion channels (From Topology)	T: Voltage-gated ion channels	F: PF00060	ECOD (1.6)
B	PF10613	e8ss3B2	A: a/b three-layered sandwiches	X: Periplasmic binding protein-like II (From Topology)	H: Periplasmic binding protein-like II (From Topology)	T: Periplasmic binding protein-like II	F: PF10613	ECOD (1.6)
C	PF13903	e8ss3C2	A: alpha bundles	X: Bromodomain-like	H: Claudin (From Topology)	T: Claudin	F: PF13903	ECOD (1.6)
C	PF00060	e8ss3C1	A: alpha complex topology	X: Voltage-gated ion channels (From Topology)	H: Voltage-gated ion channels (From Topology)	T: Voltage-gated ion channels	F: PF00060	ECOD (1.6)
C	PF10613	e8ss3C3	A: a/b three-layered sandwiches	X: Periplasmic binding protein-like II (From Topology)	H: Periplasmic binding protein-like II (From Topology)	T: Periplasmic binding protein-like II	F: PF10613	ECOD (1.6)
D	PF00060	e8ss3D2	A: alpha complex topology	X: Voltage-gated ion channels (From Topology)	H: Voltage-gated ion channels (From Topology)	T: Voltage-gated ion channels	F: PF00060	ECOD (1.6)
D	PF10613	e8ss3D1	A: a/b three-layered sandwiches	X: Periplasmic binding protein-like II (From Topology)	H: Periplasmic binding protein-like II (From Topology)	T: Periplasmic binding protein-like II	F: PF10613	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF00060	Ligand-gated ion channel (Lig_chan)	Ligand-gated ion channel	-	Family
A, B, C, D	PF13903	PMP-22/EMP/MP20/Claudin tight junction (Claudin_2)	PMP-22/EMP/MP20/Claudin tight junction	-	Family
A, B, C, D	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
E, F	PF03311	Cornichon protein (Cornichon)	Cornichon protein	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	Glutamate receptor 2, Voltage-dependent calcium channel gamma-5 subunit chimera	transmitter-gated monoatomic ion channel activity molecular transducer activity monoatomic ion channel activity glutamate-gated receptor activity neurotransmitter receptor activity ligand-gated channel activity AMPA glutamate receptor activity passive transmembrane transporter activity inorganic molecular entity transmembrane transporter activity inorganic cation transmembrane transporter activity transmembrane signaling receptor activity transporter activity glutamate receptor activity gated channel activity transmitter-gated monoatomic ion channel activity molecular transducer activity monoatomic ion channel activity glutamate-gated receptor activity neurotransmitter receptor activity ligand-gated channel activity AMPA glutamate receptor activity passive transmembrane transporter activity inorganic molecular entity transmembrane transporter activity inorganic cation transmembrane transporter activity transmembrane signaling receptor activity transporter activity glutamate receptor activity gated channel activity signaling receptor activity carboxylic acid transmembrane transporter activity ligand-gated monoatomic ion channel activity extracellular ligand-gated monoatomic ion channel activity amino acid transmembrane transporter activity channel activity transmitter-gated channel activity monoatomic ion transmembrane transporter activity organic acid transmembrane transporter activity transmembrane transporter activity organic anion transmembrane transporter activity amide binding amyloid-beta binding binding peptide binding cytoskeletal protein binding protein binding excitatory extracellular ligand-gated monoatomic ion channel activity extracellularly glutamate-gated ion channel activity protein-containing complex binding immunoglobulin binding identical protein binding PDZ domain binding protein domain specific binding signaling receptor binding glutamate receptor binding ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential scaffold protein binding ionotropic glutamate receptor binding SNARE binding kinase binding enzyme binding protein kinase binding transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential postsynaptic neurotransmitter receptor activity neurotransmitter receptor activity involved in regulation of postsynaptic membrane potential monoatomic cation transmembrane transporter activity sodium channel activity ligand-gated monoatomic cation channel activity kainate selective glutamate receptor activity potassium ion transmembrane transporter activity ligand-gated sodium channel activity sodium ion transmembrane transporter activity potassium channel activity monoatomic cation channel activity metal ion transmembrane transporter activity calcium channel activity voltage-gated calcium channel activity voltage-gated channel activity voltage-gated monoatomic ion channel activity voltage-gated monoatomic cation channel activity calcium ion transmembrane transporter activity channel regulator activity molecular function regulator activity transporter regulator activity	localization import into cell receptor internalization transport cellular process receptor-mediated endocytosis endocytosis establishment of localization vesicle-mediated transport cellular component organization cellular component biogenesis cellular component assembly protein-containing complex organization protein complex oligomerization localization import into cell receptor internalization transport cellular process receptor-mediated endocytosis endocytosis establishment of localization vesicle-mediated transport cellular component organization cellular component biogenesis cellular component assembly protein-containing complex organization protein complex oligomerization protein tetramerization protein-containing complex assembly cellular component organization or biogenesis cellular response to endogenous stimulus cellular response to growth factor stimulus response to 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 trans-synaptic signaling regulation of biological process regulation of signaling regulation of cellular process modulation of chemical synaptic transmission signaling biological regulation cell-cell signaling chemical synaptic transmission cell communication synaptic signaling regulation of trans-synaptic signaling anterograde trans-synaptic signaling regulation of cell communication response to lithium ion response to metal ion response to chemical developmental process multicellular organismal process head development forebrain development animal organ development brain development nervous system development pallium development cerebral cortex development multicellular organism development central nervous system development anatomical structure development telencephalon development system development regulation of receptor recycling regulation of macromolecule metabolic process receptor recycling receptor metabolic process metabolic process macromolecule metabolic process regulation of metabolic process positive regulation of cell communication positive regulation of biological process positive regulation of synaptic transmission positive regulation of cellular process positive regulation of signaling protein localization establishment of protein localization cellular localization cellular macromolecule localization macromolecule localization response to antibiotic response to fungicide response to toxic substance cellular response to acid chemical cellular response to stimulus cellular response to nitrogen compound cellular response to amino acid stimulus response to glycine response to organonitrogen compound response to oxygen-containing compound response to nitrogen compound response to amino acid cellular response to glycine cellular response to oxygen-containing compound response to acid chemical cellular response to chemical stimulus cellular response to organonitrogen compound ligand-gated ion channel signaling pathway cell surface receptor signaling pathway ionotropic glutamate receptor signaling pathway glutamate receptor signaling pathway signal transduction synaptic transmission, glutamatergic regulation of synaptic transmission, glutamatergic system process nervous system process transmission of nerve impulse localization within membrane protein-containing complex localization neurotransmitter receptor diffusion trapping regulation of postsynaptic membrane neurotransmitter receptor levels receptor diffusion trapping regulation of biological quality receptor localization to synapse postsynaptic neurotransmitter receptor diffusion trapping positive regulation of synaptic transmission, glutamatergic nitrogen compound transport endosome to lysosome transport establishment of protein localization to vacuole neurotransmitter receptor transport, postsynaptic endosome to lysosome lysosomal transport establishment of localization in cell neurotransmitter receptor transport protein localization to vacuole intracellular transport protein localization to lysosome establishment of protein localization to organelle protein transport protein localization to organelle vacuolar transport intracellular protein transport regulation of localization regulation of signaling receptor activity regulation of AMPA receptor activity regulation of transmembrane transporter activity regulation of signal transduction regulation of transporter activity regulation of monoatomic ion transmembrane transporter activity regulation of transport transmembrane transport regulation of molecular function regulation of transmembrane transport regulation of response to stimulus regulation of neurotransmitter receptor activity neurotransmitter receptor internalization	postsynaptic specialization membrane postsynaptic specialization synapse membrane plasma membrane cellular anatomical entity postsynaptic density membrane synaptic membrane cell periphery postsynaptic density postsynapse neuron to neuron synapse organelle cell junction postsynaptic specialization membrane postsynaptic specialization synapse membrane plasma membrane cellular anatomical entity postsynaptic density membrane synaptic membrane cell periphery postsynaptic density postsynapse neuron to neuron synapse organelle cell junction postsynaptic membrane asymmetric synapse plasma membrane region somatodendritic compartment cell body perikaryon neuronal cell body protein-containing complex plasma membrane protein complex membrane protein complex transporter complex receptor complex AMPA glutamate receptor complex ionotropic glutamate receptor complex neurotransmitter receptor complex transmembrane transporter complex plasma membrane signaling receptor complex monoatomic ion channel complex presynapse presynaptic membrane cell projection dendrite dendritic tree neuron projection plasma membrane bounded cell projection glutamatergic synapse extracellular region perisynaptic space spine synapse dendritic shaft neuron spine dendritic spine membrane-bounded organelle intracellular anatomical structure intracellular vesicle transport vesicle membrane endomembrane system intracellular organelle bounding membrane of organelle cytoplasmic vesicle vesicle membrane synaptic vesicle synaptic vesicle membrane vesicle transport vesicle exocytic vesicle membrane intracellular membrane-bounded organelle cytoplasmic vesicle membrane secretory vesicle cytoplasm organelle membrane exocytic vesicle axon dendritic spine neck axon terminus distal axon terminal bouton neuron projection terminus cell surface dendritic spine head growth cone site of polarized growth neuron projection cytoplasm cytoplasmic region plasma membrane bounded cell projection cytoplasm dendrite cytoplasm organelle subcompartment endoplasmic reticulum subcompartment nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum endoplasmic reticulum membrane presynaptic active zone membrane presynaptic active zone cell leading edge leading edge membrane neuron projection membrane dendrite membrane cell projection membrane Schaffer collateral - CA1 synapse
E, F	Protein cornichon homolog 2	-	cellular response to stimulus regulation of localization regulation of cellular process response to stimulus signaling transport regulation of signaling receptor activity regulation of AMPA receptor activity regulation of transmembrane transporter activity regulation of signal transduction cell communication regulation of transporter activity localization signal transduction cellular response to stimulus regulation of localization regulation of cellular process response to stimulus signaling transport regulation of signaling receptor activity regulation of AMPA receptor activity regulation of transmembrane transporter activity regulation of signal transduction cell communication regulation of transporter activity localization signal transduction regulation of monoatomic ion transmembrane transporter activity regulation of biological process regulation of signaling regulation of transport biological regulation establishment of localization transmembrane transport regulation of molecular function regulation of transmembrane transport regulation of response to stimulus regulation of neurotransmitter receptor activity regulation of cell communication cellular process cellular localization establishment of localization in cell intracellular transport endoplasmic reticulum to Golgi vesicle-mediated transport Golgi vesicle transport vesicle-mediated transport	cell periphery postsynapse postsynaptic membrane synapse cell junction membrane plasma membrane plasma membrane region cellular anatomical entity synaptic membrane protein-containing complex plasma membrane protein complex membrane protein complex transporter complex cell periphery postsynapse postsynaptic membrane synapse cell junction membrane plasma membrane plasma membrane region cellular anatomical entity synaptic membrane protein-containing complex plasma membrane protein complex membrane protein complex transporter complex receptor complex AMPA glutamate receptor complex ionotropic glutamate receptor complex neurotransmitter receptor complex transmembrane transporter complex plasma membrane signaling receptor complex monoatomic ion channel complex somatodendritic compartment cell projection dendrite dendritic tree neuron projection dendritic shaft plasma membrane bounded cell projection membrane-bounded organelle intracellular anatomical structure intracellular membrane-bounded organelle intracellular organelle bounding membrane of organelle organelle endoplasmic reticulum-Golgi intermediate compartment membrane endoplasmic reticulum-Golgi intermediate compartment cytoplasm organelle membrane neuron spine dendritic spine postsynaptic density neuron to neuron synapse postsynaptic specialization asymmetric synapse transport vesicle intracellular vesicle transport vesicle membrane endomembrane system cytoplasmic vesicle membrane coated vesicle membrane COPII-coated ER to Golgi transport vesicle vesicle membrane cytoplasmic vesicle ER to Golgi transport vesicle membrane coated vesicle vesicle organelle subcompartment endoplasmic reticulum subcompartment nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum endoplasmic reticulum membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR001638	Solute-binding protein family 3/N-terminal domain of MltF	Domain
A, B, C, D	IPR028082	Periplasmic binding protein-like I	Homologous Superfamily
A, B, C, D	IPR001508	Ionotropic glutamate receptor, metazoa	Family
A, B, C, D	IPR001828	Receptor, ligand binding region	Domain
A, B, C, D	IPR001320	Ionotropic glutamate receptor, C-terminal	Domain
A, B, C, D	IPR019594	Ionotropic glutamate receptor, L-glutamate and glycine-binding domain	Domain
A, B, C, D	IPR015683	Ionotropic glutamate receptor	Family
A, B, C, D	IPR008369	Voltage-dependent calcium channel, gamma-5 subunit	Family
A, B, C, D	IPR004031	PMP-22/EMP/MP20/Claudin	Family
A, B, C, D	IPR008368	Voltage-dependent calcium channel, gamma subunit	Family
E, F	IPR033466	Cornichon, conserved site	Conserved Site
E, F	IPR003377	Cornichon	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
E, F	Pharos: Q6PI25	breast carcinoma osteosarcoma gout ovarian carcinoma lung carcinoma prostate carcinoma

Membrane Protein Annotation: PDBTM PDBTM Database Homepage

Chains	External Link	Comment
A, B, C, D, E A, B, C, D, E, F	PDBTM	Annotated as membrane protein by PDBTM

Membrane Protein Annotation: MemProtMD MemProtMD Database Homepage

Chains	External Link	Comment
A, B, C, D, E A, B, C, D, E, F	MemProtMD	Annotated as membrane protein by MemProtMD

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 R01GM133198.