5KK2

Architecture of fully occupied GluA2 AMPA receptor - TARP complex elucidated by single particle cryo-electron microscopy

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Membrane Protein Annotation: OPM
Membrane Protein Annotation: PDBTM
Membrane Protein Annotation: MemProtMD
Membrane Protein Annotation: mpstruc

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 (2022-06-29)
B	SCOP2B Superfamily	Type 2 solute binding protein-like	8036483	3000083	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Type 2 solute binding protein-like	8036483	3000083	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Type 2 solute binding protein-like	8036483	3000083	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Claudin-like	8092551	3002606	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Claudin-like	8092551	3002606	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	Claudin-like	8092551	3002606	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
B	PF00060	e5kk2B1	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	e5kk2B2	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	PF00060	e5kk2C1	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	e5kk2C2	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	e5kk2D2	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	e5kk2D1	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)
E	PF00822	e5kk2E1	A: alpha bundles	X: Bromodomain-like	H: Claudin (From Topology)	T: Claudin	F: PF00822	ECOD (1.6)
F	PF00822	e5kk2F1	A: alpha bundles	X: Bromodomain-like	H: Claudin (From Topology)	T: Claudin	F: PF00822	ECOD (1.6)
G	PF00822	e5kk2G1	A: alpha bundles	X: Bromodomain-like	H: Claudin (From Topology)	T: Claudin	F: PF00822	ECOD (1.6)
H	PF00822	e5kk2H1	A: alpha bundles	X: Bromodomain-like	H: Claudin (From Topology)	T: Claudin	F: PF00822	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	PF00497	Bacterial extracellular solute-binding proteins, family 3 (SBP_bac_3)	Bacterial extracellular solute-binding proteins, family 3	This is a sensor domain found in solute-binding protein family 3 members from Gram-positive bacteria, Gram-negative bacteria and archaea. It can also be found in the N-terminal of the membrane-bound lytic murein transglycosylase F (MltF) protein. Th ...	This is a sensor domain found in solute-binding protein family 3 members from Gram-positive bacteria, Gram-negative bacteria and archaea. It can also be found in the N-terminal of the membrane-bound lytic murein transglycosylase F (MltF) protein. This domain recognises Nicotinate, quidalnate, pyridine-2,5-dicarboxylate and salicylate [1].	Domain
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, G, H	PF00822	PMP-22/EMP/MP20/Claudin family (PMP22_Claudin)	PMP-22/EMP/MP20/Claudin family	-	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	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	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 response to inorganic substance 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 organic substance metabolic process 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 organic substance 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 cellular response to organic substance 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	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, G, H	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 inorganic molecular entity transmembrane transporter activity channel activity inorganic cation transmembrane transporter activity monoatomic 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 inorganic molecular entity transmembrane transporter activity channel activity inorganic cation transmembrane transporter 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 ion channel regulator activity calcium channel regulator activity molecular function regulator activity transporter regulator activity	protein localization protein localization to postsynaptic specialization membrane cellular localization protein localization to postsynaptic membrane protein localization to cell periphery 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 protein localization to organelle cellular macromolecule localization protein localization protein localization to postsynaptic specialization membrane cellular localization protein localization to postsynaptic membrane protein localization to cell periphery 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 protein localization to organelle cellular macromolecule localization macromolecule localization cellular process protein localization to postsynapse regulation of biological quality protein localization to cell junction receptor localization to synapse reflex response to stimulus response to external stimulus eye blink reflex neurotransmitter receptor diffusion trapping receptor diffusion trapping postsynaptic neurotransmitter receptor diffusion trapping response to metal ion response to chemical response to calcium ion response to inorganic substance positive regulation of cell communication regulation of cellular process signaling modulation of chemical synaptic transmission synaptic transmission, glutamatergic positive regulation of biological process regulation of synaptic transmission, glutamatergic cell communication synaptic signaling positive regulation of cellular process trans-synaptic signaling regulation of signaling regulation of biological process 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 regulation of cell communication positive regulation of signaling cellular response to stimulus regulation of localization transport regulation of signaling receptor activity regulation of AMPA receptor activity regulation of transmembrane transporter activity regulation of signal transduction regulation of transporter activity signal transduction regulation of monoatomic ion transmembrane transporter activity regulation of transport establishment of localization transmembrane transport regulation of molecular function regulation of transmembrane transport regulation of response to stimulus regulation of neurotransmitter receptor activity 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 nitrogen compound transport endosome to lysosome transport establishment of protein localization to vacuole neurotransmitter receptor transport, postsynaptic endosome to lysosome lysosomal transport vesicle-mediated transport establishment of localization in cell neurotransmitter receptor transport organic substance transport protein localization to vacuole intracellular transport protein localization to lysosome establishment of protein localization to organelle protein transport vacuolar transport intracellular protein transport membrane depolarization import into cell receptor internalization neurotransmitter receptor internalization receptor-mediated endocytosis endocytosis	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 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 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

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
E, F, G, H	IPR004031	PMP-22/EMP/MP20/Claudin	Family
E, F, G, H	IPR005422	Voltage-dependent calcium channel, gamma-2 subunit	Family
E, F, G, H	IPR008368	Voltage-dependent calcium channel, gamma subunit	Family

Membrane Protein Annotation: OPM OPM Database Homepage

Chains	External Link	Type	Class	Superfamily	Family
A, B, C, D, E A, B, C, D, E, F, G, H	OPM	Transmembrane	Alpha-helical polytopic	Ion channel (VIC) superfamily	Glutamate-gated Ion Channel (GIC) family

Membrane Protein Annotation: PDBTM PDBTM Database Homepage

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

Membrane Protein Annotation: mpstruc mpstruc Database Homepage

Chains	Resource Link	Group	Subgroup	Protein
A, B, C, D, E A, B, C, D, E, F, G, H	mpstruc	TRANSMEMBRANE PROTEINS: ALPHA-HELICAL	Channels: Other Ion Channels	GluA2 Glutamate receptor (AMPA-subtype) saturated with TARPγ2 subunits

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.