1YAE | pdb_00001yae

Structure of the Kainate Receptor Subunit GluR6 Agonist Binding Domain Complexed with Domoic Acid

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
E	d1yaee1	Alpha and beta proteins (a/b)	Periplasmic binding protein-like II	Periplasmic binding protein-like II	Phosphate binding protein-like	Glutamate receptor ligand binding core	Norway rat (Rattus norvegicus ) [TaxId: 10116 ], Norway rat (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)
D	d1yaed1	Alpha and beta proteins (a/b)	Periplasmic binding protein-like II	Periplasmic binding protein-like II	Phosphate binding protein-like	Glutamate receptor ligand binding core	Norway rat (Rattus norvegicus ) [TaxId: 10116 ], Norway rat (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)
C	d1yaec1	Alpha and beta proteins (a/b)	Periplasmic binding protein-like II	Periplasmic binding protein-like II	Phosphate binding protein-like	Glutamate receptor ligand binding core	Norway rat (Rattus norvegicus ) [TaxId: 10116 ], Norway rat (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)
B	d1yaeb1	Alpha and beta proteins (a/b)	Periplasmic binding protein-like II	Periplasmic binding protein-like II	Phosphate binding protein-like	Glutamate receptor ligand binding core	Norway rat (Rattus norvegicus ) [TaxId: 10116 ], Norway rat (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)
A	d1yaea1	Alpha and beta proteins (a/b)	Periplasmic binding protein-like II	Periplasmic binding protein-like II	Phosphate binding protein-like	Glutamate receptor ligand binding core	Norway rat (Rattus norvegicus ) [TaxId: 10116 ], Norway rat (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
F	SCOP2B Superfamily	Type 2 solute binding protein-like	8032346	3000083	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Type 2 solute binding protein-like	8032346	3000083	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Type 2 solute binding protein-like	8032346	3000083	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Type 2 solute binding protein-like	8032346	3000083	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Type 2 solute binding protein-like	8032346	3000083	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Type 2 solute binding protein-like	8032346	3000083	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)
F	DctP	e1yaeF1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Glycosyl hydrolase domain	T: Glycosyl hydrolase domain	F: DctP	ECOD (v294.1)
F	DUF34_NIF3	e1yaeF2	A: a/b three-layered sandwiches	X: Rubredoxin-like	H: Ferritin/Heme oxygenase	T: Heme oxygenase/Ribonucleotide reductase	F: DUF34_NIF3	ECOD (v294.1)
E	DctP	e1yaeE2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Glycosyl hydrolase domain	T: Glycosyl hydrolase domain	F: DctP	ECOD (v294.1)
E	DUF34_NIF3	e1yaeE3	A: a/b three-layered sandwiches	X: Rubredoxin-like	H: Ferritin/Heme oxygenase	T: Heme oxygenase/Ribonucleotide reductase	F: DUF34_NIF3	ECOD (v294.1)
D	DctP	e1yaeD1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Glycosyl hydrolase domain	T: Glycosyl hydrolase domain	F: DctP	ECOD (v294.1)
D	DUF34_NIF3	e1yaeD2	A: a/b three-layered sandwiches	X: Rubredoxin-like	H: Ferritin/Heme oxygenase	T: Heme oxygenase/Ribonucleotide reductase	F: DUF34_NIF3	ECOD (v294.1)
C	DctP	e1yaeC2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Glycosyl hydrolase domain	T: Glycosyl hydrolase domain	F: DctP	ECOD (v294.1)
C	DUF34_NIF3	e1yaeC3	A: a/b three-layered sandwiches	X: Rubredoxin-like	H: Ferritin/Heme oxygenase	T: Heme oxygenase/Ribonucleotide reductase	F: DUF34_NIF3	ECOD (v294.1)
B	DctP	e1yaeB2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Glycosyl hydrolase domain	T: Glycosyl hydrolase domain	F: DctP	ECOD (v294.1)
B	DUF34_NIF3	e1yaeB3	A: a/b three-layered sandwiches	X: Rubredoxin-like	H: Ferritin/Heme oxygenase	T: Heme oxygenase/Ribonucleotide reductase	F: DUF34_NIF3	ECOD (v294.1)
A	DctP	e1yaeA1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Glycosyl hydrolase domain	T: Glycosyl hydrolase domain	F: DctP	ECOD (v294.1)
A	DUF34_NIF3	e1yaeA2	A: a/b three-layered sandwiches	X: Rubredoxin-like	H: Ferritin/Heme oxygenase	T: Heme oxygenase/Ribonucleotide reductase	F: DUF34_NIF3	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
F	3.40.190.10	Alpha Beta	3-Layer(aba) Sandwich	D-Maltodextrin-Binding Protein	domain 2	CATH (4.3.0)
E	3.40.190.10	Alpha Beta	3-Layer(aba) Sandwich	D-Maltodextrin-Binding Protein	domain 2	CATH (4.3.0)
D	3.40.190.10	Alpha Beta	3-Layer(aba) Sandwich	D-Maltodextrin-Binding Protein	domain 2	CATH (4.3.0)
C	3.40.190.10	Alpha Beta	3-Layer(aba) Sandwich	D-Maltodextrin-Binding Protein	domain 2	CATH (4.3.0)
B	3.40.190.10	Alpha Beta	3-Layer(aba) Sandwich	D-Maltodextrin-Binding Protein	domain 2	CATH (4.3.0)
A	3.40.190.10	Alpha Beta	3-Layer(aba) Sandwich	D-Maltodextrin-Binding Protein	domain 2	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E A, B, C, D, E, F	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
A, B, C, D, E A, B, C, D, E, F	Glutamate receptor, ionotropic kainate 2	gated channel activity monoatomic ion channel activity excitatory extracellular ligand-gated monoatomic ion channel activity ligand-gated channel activity ligand-gated monoatomic ion channel activity extracellular ligand-gated monoatomic ion channel activity passive transmembrane transporter activity extracellularly glutamate-gated ion channel activity channel activity monoatomic ion transmembrane transporter activity transporter activity transmembrane transporter activity ubiquitin protein ligase binding protein binding gated channel activity monoatomic ion channel activity excitatory extracellular ligand-gated monoatomic ion channel activity ligand-gated channel activity ligand-gated monoatomic ion channel activity extracellular ligand-gated monoatomic ion channel activity passive transmembrane transporter activity extracellularly glutamate-gated ion channel activity channel activity monoatomic ion transmembrane transporter activity transporter activity transmembrane transporter activity ubiquitin protein ligase binding protein binding binding ubiquitin-like protein ligase binding enzyme binding identical protein binding PDZ domain binding protein domain specific binding glutamate receptor activity molecular transducer activity transmembrane signaling receptor activity signaling receptor activity ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential scaffold protein binding monoatomic cation transmembrane transporter activity transmitter-gated monoatomic ion channel activity glutamate-gated receptor activity neurotransmitter receptor activity ligand-gated calcium channel activity ligand-gated monoatomic cation channel activity calcium channel activity glutamate-gated calcium ion channel activity carboxylic acid transmembrane transporter activity amino acid transmembrane transporter activity monoatomic cation channel activity calcium ion transmembrane transporter activity transmitter-gated channel activity metal ion transmembrane transporter activity ubiquitin-like protein conjugating enzyme binding ubiquitin conjugating enzyme binding SNARE binding transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential sodium 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	cellular response to stimulus multicellular organismal process regulation of postsynaptic membrane potential system process regulation of cellular process response to stimulus signaling modulation of chemical synaptic transmission regulation of system process regulation of signal transduction chemical synaptic transmission, postsynaptic cell communication synaptic signaling modulation of excitatory postsynaptic potential cellular response to stimulus multicellular organismal process regulation of postsynaptic membrane potential system process regulation of cellular process response to stimulus signaling modulation of chemical synaptic transmission regulation of system process regulation of signal transduction chemical synaptic transmission, postsynaptic cell communication synaptic signaling modulation of excitatory postsynaptic potential regulation of multicellular organismal process signal transduction regulation of biological quality 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 regulation of JNK cascade regulation of MAPK cascade intracellular signal transduction regulation of intracellular signal transduction JNK cascade intracellular signaling cassette MAPK cascade presynaptic modulation of chemical synaptic transmission detection of external stimulus thermoception detection of cold stimulus involved in thermoception response to external stimulus sensory perception of temperature stimulus detection of temperature stimulus involved in sensory perception response to temperature stimulus detection of abiotic stimulus detection of stimulus sensory perception detection of temperature stimulus involved in thermoception sensory perception of cold stimulus detection of temperature stimulus response to abiotic stimulus detection of stimulus involved in sensory perception neuron apoptotic process positive regulation of programmed cell death regulation of apoptotic process positive regulation of biological process regulation of programmed cell death cell death positive regulation of apoptotic process apoptotic process positive regulation of neuron apoptotic process programmed cell death positive regulation of cellular process regulation of neuron apoptotic process inorganic ion homeostasis intracellular calcium ion homeostasis homeostatic process calcium ion homeostasis cellular homeostasis chemical homeostasis intracellular monoatomic cation homeostasis monoatomic ion homeostasis intracellular chemical homeostasis monoatomic cation homeostasis intracellular monoatomic ion homeostasis regulation of neuronal synaptic plasticity regulation of synaptic plasticity regulation of long-term neuronal synaptic plasticity negative regulation of signaling synaptic transmission, glutamatergic negative regulation of biological process regulation of synaptic transmission, glutamatergic negative regulation of synaptic transmission negative regulation of cell communication negative regulation of cellular process negative regulation of synaptic transmission, glutamatergic inhibitory postsynaptic potential localization cellular localization receptor clustering macromolecule localization intracellular protein localization localization within membrane protein localization to membrane positive regulation of cell communication positive regulation of synaptic transmission positive regulation of signaling negative regulation of neuron apoptotic process negative regulation of programmed cell death negative regulation of apoptotic process regulation of short-term neuronal synaptic plasticity action potential transmission of nerve impulse neuronal action potential establishment of protein localization transport intracellular transport establishment of localization protein transport establishment of localization in cell intracellular protein transport behavioral defense response behavior fear response behavioral fear response defense response response to stress multicellular organismal response to stress	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 cell body perikaryon neuronal cell body protein-containing complex sodium channel complex plasma membrane protein complex membrane protein complex potassium channel complex cation channel complex transporter complex kainate selective glutamate receptor complex ionotropic glutamate receptor complex transmembrane transporter complex neurotransmitter receptor complex plasma membrane signaling receptor complex signaling receptor complex monoatomic ion channel complex presynapse presynaptic membrane cell projection dendrite dendritic tree neuron projection plasma membrane bounded cell projection glutamatergic synapse axon axon terminus distal axon terminal bouton neuron projection terminus mossy fiber rosette neuron projection cytoplasm intracellular anatomical structure dendrite cytoplasm cytoplasm hippocampal mossy fiber to CA3 synapse

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F	IPR028082	Periplasmic binding protein-like I	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR001508	Ionotropic glutamate receptor, metazoa	Family
A, B, C, D, E A, B, C, D, E, F	IPR001828	Receptor, ligand binding region	Domain
A, B, C, D, E A, B, C, D, E, F	IPR001320	Ionotropic glutamate receptor, C-terminal	Domain
A, B, C, D, E A, B, C, D, E, F	IPR019594	Ionotropic glutamate receptor, L-glutamate and glycine-binding domain	Domain
A, B, C, D, E A, B, C, D, E, F	IPR015683	Ionotropic glutamate receptor	Family

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.