5IOU

Cryo-EM structure of GluN1/GluN2B NMDA receptor in the glutamate/glycine-bound conformation

External Resource: Annotation

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

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	PF00060	e5iouA2	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	PF01094	e5iouA1	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: Periplasmic binding protein-like I	F: PF01094	ECOD (1.6)
A	F_UNCLASSIFIED	e5iouA4	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: F_UNCLASSIFIED	ECOD (1.6)
A	PF10613	e5iouA5	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 [auth C]	PF00060	e5iouC1	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 [auth C]	PF01094	e5iouC5	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: Periplasmic binding protein-like I	F: PF01094	ECOD (1.6)
B [auth C]	F_UNCLASSIFIED	e5iouC2	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: F_UNCLASSIFIED	ECOD (1.6)
B [auth C]	PF10613	e5iouC4	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 [auth B]	PF00060	e5iouB1	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 [auth B]	F_UNCLASSIFIED	e5iouB3	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: Periplasmic binding protein-like I	F: F_UNCLASSIFIED	ECOD (1.6)
C [auth B]	PF01094	e5iouB2	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: Periplasmic binding protein-like I	F: PF01094	ECOD (1.6)
C [auth B]	F_UNCLASSIFIED	e5iouB5	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: F_UNCLASSIFIED	ECOD (1.6)
C [auth B]	PF10613	e5iouB4	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	e5iouD5	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	F_UNCLASSIFIED	e5iouD2	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: Periplasmic binding protein-like I	F: F_UNCLASSIFIED	ECOD (1.6)
D	PF01094	e5iouD1	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: Periplasmic binding protein-like I	F: PF01094	ECOD (1.6)
D	F_UNCLASSIFIED	e5iouD4	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: F_UNCLASSIFIED	ECOD (1.6)
D	PF10613	e5iouD3	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 [auth C]	PF00060	Ligand-gated ion channel (Lig_chan)	Ligand-gated ion channel	-	Family
A, B [auth C]	PF01094	Receptor family ligand binding region (ANF_receptor)	Receptor family ligand binding region	-	Family
A, B [auth C]	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 [auth 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
C [auth B], D	PF10565	N-methyl D-aspartate receptor 2B3 C-terminus (NMDAR2_C)	N-methyl D-aspartate receptor 2B3 C-terminus	-	Family
C [auth B], D	PF00060	Ligand-gated ion channel (Lig_chan)	Ligand-gated ion channel	-	Family
C [auth B], D	PF01094	Receptor family ligand binding region (ANF_receptor)	Receptor family ligand binding region	-	Family
C [auth B], 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
C [auth B], 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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B [auth C]	N-methyl-D-aspartate receptor subunit NR1-8a	transmitter-gated monoatomic ion channel activity molecular transducer activity monoatomic ion channel activity voltage-gated channel activity voltage-gated monoatomic ion channel activity glutamate-gated receptor activity neurotransmitter receptor activity ligand-gated channel activity passive transmembrane transporter activity inorganic molecular entity transmembrane transporter activity inorganic cation transmembrane transporter activity transmembrane signaling receptor activity transporter activity NMDA glutamate receptor activity transmitter-gated monoatomic ion channel activity molecular transducer activity monoatomic ion channel activity voltage-gated channel activity voltage-gated monoatomic ion channel activity glutamate-gated receptor activity neurotransmitter receptor activity ligand-gated channel activity passive transmembrane transporter activity inorganic molecular entity transmembrane transporter activity inorganic cation transmembrane transporter activity transmembrane signaling receptor activity transporter activity NMDA glutamate receptor 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 monoatomic ion transmembrane transporter activity transmitter-gated channel activity organic acid transmembrane transporter activity transmembrane transporter activity organic anion transmembrane transporter activity cation binding ion binding binding metal ion binding small molecule binding	response to stimulus response to metal ion response to chemical response to zinc ion response to inorganic substance	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 NMDA selective glutamate receptor complex receptor complex ionotropic glutamate receptor complex neurotransmitter receptor complex transmembrane transporter complex plasma membrane signaling receptor complex monoatomic ion channel complex
C [auth B], D	Ionotropic glutamate receptor subunit NR2B	transmitter-gated monoatomic ion channel activity molecular transducer activity monoatomic ion channel activity voltage-gated channel activity voltage-gated monoatomic ion channel activity glutamate-gated receptor activity neurotransmitter receptor activity ligand-gated channel activity passive transmembrane transporter activity inorganic molecular entity transmembrane transporter activity inorganic cation transmembrane transporter activity transmembrane signaling receptor activity transporter activity NMDA glutamate receptor activity transmitter-gated monoatomic ion channel activity molecular transducer activity monoatomic ion channel activity voltage-gated channel activity voltage-gated monoatomic ion channel activity glutamate-gated receptor activity neurotransmitter receptor activity ligand-gated channel activity passive transmembrane transporter activity inorganic molecular entity transmembrane transporter activity inorganic cation transmembrane transporter activity transmembrane signaling receptor activity transporter activity NMDA glutamate receptor 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 monoatomic ion transmembrane transporter activity transmitter-gated channel activity organic acid transmembrane transporter activity transmembrane transporter activity organic anion transmembrane transporter activity cation binding ion binding binding metal ion binding small molecule binding	response to stimulus response to metal ion response to chemical response to zinc ion response to inorganic substance response to magnesium ion	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 NMDA selective glutamate receptor complex receptor complex ionotropic glutamate receptor complex neurotransmitter receptor complex transmembrane transporter complex plasma membrane signaling receptor complex monoatomic ion channel complex membrane-bounded organelle intracellular anatomical structure endosome intracellular vesicle intracellular membrane-bounded organelle endomembrane system intracellular organelle cytoplasmic vesicle organelle late endosome cytoplasm vesicle lytic vacuole vacuole lysosome

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B [auth C]	IPR028082	Periplasmic binding protein-like I	Homologous Superfamily
A, B [auth C]	IPR001638	Solute-binding protein family 3/N-terminal domain of MltF	Domain
A, B [auth C]	IPR019594	Ionotropic glutamate receptor, L-glutamate and glycine-binding domain	Domain
A, B [auth C]	IPR015683	Ionotropic glutamate receptor	Family
A, B [auth C]	IPR001508	Ionotropic glutamate receptor, metazoa	Family
A, B [auth C]	IPR001320	Ionotropic glutamate receptor, C-terminal	Domain
A, B [auth C]	IPR001828	Receptor, ligand binding region	Domain
C [auth B], D	IPR028082	Periplasmic binding protein-like I	Homologous Superfamily
C [auth B], D	IPR018884	Glutamate [NMDA] receptor, epsilon subunit, C-terminal	Domain
C [auth B], D	IPR001638	Solute-binding protein family 3/N-terminal domain of MltF	Domain
C [auth B], D	IPR019594	Ionotropic glutamate receptor, L-glutamate and glycine-binding domain	Domain
C [auth B], D	IPR015683	Ionotropic glutamate receptor	Family
C [auth B], D	IPR001508	Ionotropic glutamate receptor, metazoa	Family
C [auth B], D	IPR001320	Ionotropic glutamate receptor, C-terminal	Domain
C [auth B], D	IPR001828	Receptor, ligand binding region	Domain

Membrane Protein Annotation: PDBTM PDBTM Database Homepage

Chains	External Link	Comment
A, B [auth C], C [auth B], D	PDBTM	Annotated as membrane protein by PDBTM

Membrane Protein Annotation: MemProtMD MemProtMD Database Homepage

Chains	External Link	Comment
A, B [auth C], C [auth B], D	MemProtMD	Annotated as membrane protein by MemProtMD

Membrane Protein Annotation: mpstruc mpstruc Database Homepage

Chains	Resource Link	Group	Subgroup	Protein
A, B [auth C], C [auth B], D	mpstruc	TRANSMEMBRANE PROTEINS: ALPHA-HELICAL	Channels: Other Ion Channels	GluN1a/GluN2B NMDA receptor

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.