7QN5

Cryo-EM structure of human full-length extrasynaptic alpha4beta3delta GABA(A)R in complex with nanobody Nb25

External Resource: Annotation

Domain Annotation: ECOD Classification
SAbDab Antibody Annotation
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations
Membrane Protein Annotation: OPM
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	Neur_chan_LBD	e7qn5A1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Nicotinic receptor ligand binding domain-like (From Topology)	T: Nicotinic receptor ligand binding domain-like	F: Neur_chan_LBD	ECOD (1.6)
A	Neur_chan_memb	e7qn5A2	A: alpha bundles	X: Neurotransmitter-gated ion-channel transmembrane pore (From Topology)	H: Neurotransmitter-gated ion-channel transmembrane pore (From Topology)	T: Neurotransmitter-gated ion-channel transmembrane pore	F: Neur_chan_memb	ECOD (1.6)
B	Neur_chan_LBD	e7qn5B1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Nicotinic receptor ligand binding domain-like (From Topology)	T: Nicotinic receptor ligand binding domain-like	F: Neur_chan_LBD	ECOD (1.6)
B	Neur_chan_memb	e7qn5B2	A: alpha bundles	X: Neurotransmitter-gated ion-channel transmembrane pore (From Topology)	H: Neurotransmitter-gated ion-channel transmembrane pore (From Topology)	T: Neurotransmitter-gated ion-channel transmembrane pore	F: Neur_chan_memb	ECOD (1.6)
C	Neur_chan_LBD	e7qn5C2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Nicotinic receptor ligand binding domain-like (From Topology)	T: Nicotinic receptor ligand binding domain-like	F: Neur_chan_LBD	ECOD (1.6)
C	Neur_chan_memb	e7qn5C1	A: alpha bundles	X: Neurotransmitter-gated ion-channel transmembrane pore (From Topology)	H: Neurotransmitter-gated ion-channel transmembrane pore (From Topology)	T: Neurotransmitter-gated ion-channel transmembrane pore	F: Neur_chan_memb	ECOD (1.6)
D	Neur_chan_LBD	e7qn5D1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Nicotinic receptor ligand binding domain-like (From Topology)	T: Nicotinic receptor ligand binding domain-like	F: Neur_chan_LBD	ECOD (1.6)
D	Neur_chan_memb	e7qn5D2	A: alpha bundles	X: Neurotransmitter-gated ion-channel transmembrane pore (From Topology)	H: Neurotransmitter-gated ion-channel transmembrane pore (From Topology)	T: Neurotransmitter-gated ion-channel transmembrane pore	F: Neur_chan_memb	ECOD (1.6)
E	Neur_chan_LBD	e7qn5E2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Nicotinic receptor ligand binding domain-like (From Topology)	T: Nicotinic receptor ligand binding domain-like	F: Neur_chan_LBD	ECOD (1.6)
E	Neur_chan_memb	e7qn5E1	A: alpha bundles	X: Neurotransmitter-gated ion-channel transmembrane pore (From Topology)	H: Neurotransmitter-gated ion-channel transmembrane pore (From Topology)	T: Neurotransmitter-gated ion-channel transmembrane pore	F: Neur_chan_memb	ECOD (1.6)
F	V-set_12	e7qn5F1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_12	ECOD (1.6)
G	V-set_12	e7qn5G1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_12	ECOD (1.6)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
F, G	Heavy Chain	IGHV1	-	gamma-aminobutyric acid receptor subunit beta-3	SAbDab (2024-11-15)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF02932	Neurotransmitter-gated ion-channel transmembrane region (Neur_chan_memb)	Neurotransmitter-gated ion-channel transmembrane region	-	Family
A	PF02931	Neurotransmitter-gated ion-channel ligand binding domain (Neur_chan_LBD)	Neurotransmitter-gated ion-channel ligand binding domain	-	Family
B, C, D	PF02932	Neurotransmitter-gated ion-channel transmembrane region (Neur_chan_memb)	Neurotransmitter-gated ion-channel transmembrane region	-	Family
B, C, D	PF02931	Neurotransmitter-gated ion-channel ligand binding domain (Neur_chan_LBD)	Neurotransmitter-gated ion-channel ligand binding domain	-	Family
E	PF02932	Neurotransmitter-gated ion-channel transmembrane region (Neur_chan_memb)	Neurotransmitter-gated ion-channel transmembrane region	-	Family
E	PF02931	Neurotransmitter-gated ion-channel ligand binding domain (Neur_chan_LBD)	Neurotransmitter-gated ion-channel ligand binding domain	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Gamma-aminobutyric acid receptor subunit alpha-4	transmitter-gated monoatomic ion channel activity monoatomic anion transmembrane transporter activity chloride transmembrane transporter activity molecular transducer activity monoatomic ion channel activity neurotransmitter receptor activity ligand-gated channel activity passive transmembrane transporter activity inorganic molecular entity transmembrane transporter activity transporter activity GABA-gated chloride ion channel activity gated channel activity signaling receptor activity ligand-gated monoatomic anion channel activity transmitter-gated monoatomic ion channel activity monoatomic anion transmembrane transporter activity chloride transmembrane transporter activity molecular transducer activity monoatomic ion channel activity neurotransmitter receptor activity ligand-gated channel activity passive transmembrane transporter activity inorganic molecular entity transmembrane transporter activity transporter activity GABA-gated chloride ion channel activity gated channel activity signaling receptor activity ligand-gated monoatomic anion channel activity ligand-gated monoatomic ion channel activity extracellular ligand-gated monoatomic ion channel activity channel activity transmitter-gated channel activity monoatomic ion transmembrane transporter activity monoatomic anion channel activity transmembrane transporter activity inorganic anion transmembrane transporter activity chloride channel activity benzodiazepine receptor activity GABA-A receptor activity GABA receptor activity transmembrane signaling receptor activity 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	transport monoatomic ion transmembrane transport inorganic ion transmembrane transport inorganic anion transmembrane transport establishment of localization chloride transport transmembrane transport localization chloride transmembrane transport monoatomic anion transport monoatomic anion transmembrane transport monoatomic ion transport cellular process inorganic anion transport transport monoatomic ion transmembrane transport inorganic ion transmembrane transport inorganic anion transmembrane transport establishment of localization chloride transport transmembrane transport localization chloride transmembrane transport monoatomic anion transport monoatomic anion transmembrane transport monoatomic ion transport cellular process inorganic anion transport regulation of biological process signaling biological regulation cell-cell signaling gamma-aminobutyric acid signaling pathway cell communication regulation of postsynaptic membrane potential regulation of biological quality regulation of membrane potential developmental process multicellular organismal process inhibitory synapse assembly nervous system development cellular component organization cellular component biogenesis multicellular organism development cell junction organization cellular component assembly cell junction assembly anatomical structure development synapse organization cellular component organization or biogenesis synapse assembly system development trans-synaptic signaling synaptic transmission, GABAergic chemical synaptic transmission synaptic signaling anterograde trans-synaptic signaling	protein-containing complex cellular anatomical structure transmembrane transporter complex membrane chloride channel complex membrane protein complex transporter complex monoatomic ion channel complex cell periphery plasma membrane postsynaptic specialization membrane postsynaptic specialization synapse synaptic membrane protein-containing complex cellular anatomical structure transmembrane transporter complex membrane chloride channel complex membrane protein complex transporter complex monoatomic ion channel complex cell periphery plasma membrane postsynaptic specialization membrane postsynaptic specialization synapse synaptic membrane postsynapse organelle postsynaptic membrane cell junction plasma membrane region GABA receptor complex GABA-A receptor complex receptor complex GABA-ergic synapse cell projection neuron projection plasma membrane bounded cell projection cell leading edge leading edge membrane somatodendritic compartment neuron projection membrane dendrite membrane dendrite dendritic tree cell projection membrane
B, C, D	Gamma-aminobutyric acid receptor subunit beta-3	transmitter-gated monoatomic ion channel activity monoatomic anion transmembrane transporter activity chloride transmembrane transporter activity molecular transducer activity monoatomic ion channel activity neurotransmitter receptor activity ligand-gated channel activity passive transmembrane transporter activity inorganic molecular entity transmembrane transporter activity transporter activity GABA-gated chloride ion channel activity gated channel activity signaling receptor activity ligand-gated monoatomic anion channel activity transmitter-gated monoatomic ion channel activity monoatomic anion transmembrane transporter activity chloride transmembrane transporter activity molecular transducer activity monoatomic ion channel activity neurotransmitter receptor activity ligand-gated channel activity passive transmembrane transporter activity inorganic molecular entity transmembrane transporter activity transporter activity GABA-gated chloride ion channel activity gated channel activity signaling receptor activity ligand-gated monoatomic anion channel activity ligand-gated monoatomic ion channel activity extracellular ligand-gated monoatomic ion channel activity channel activity transmitter-gated channel activity monoatomic ion transmembrane transporter activity monoatomic anion channel activity transmembrane transporter activity inorganic anion transmembrane transporter activity chloride channel activity GABA-A receptor activity GABA receptor activity transmembrane signaling receptor activity identical protein binding protein binding binding	transport monoatomic ion transmembrane transport inorganic ion transmembrane transport inorganic anion transmembrane transport establishment of localization chloride transport transmembrane transport localization chloride transmembrane transport monoatomic anion transport monoatomic anion transmembrane transport monoatomic ion transport cellular process inorganic anion transport transport monoatomic ion transmembrane transport inorganic ion transmembrane transport inorganic anion transmembrane transport establishment of localization chloride transport transmembrane transport localization chloride transmembrane transport monoatomic anion transport monoatomic anion transmembrane transport monoatomic ion transport cellular process inorganic anion transport cellular response to nitrogen compound cellular response to stimulus response to stimulus cellular response to organic cyclic compound response to nitrogen compound cellular response to chemical stimulus response to histamine response to chemical cellular response to histamine response to organic cyclic compound regulation of biological process signaling biological regulation cell-cell signaling gamma-aminobutyric acid signaling pathway cell communication regulation of cellular process signal transduction developmental process multicellular organismal process inhibitory synapse assembly nervous system development cellular component organization cellular component biogenesis multicellular organism development cell junction organization cellular component assembly cell junction assembly anatomical structure development synapse organization cellular component organization or biogenesis synapse assembly system development trans-synaptic signaling synaptic transmission, GABAergic chemical synaptic transmission synaptic signaling anterograde trans-synaptic signaling roof of mouth development	protein-containing complex cellular anatomical structure transmembrane transporter complex membrane chloride channel complex membrane protein complex transporter complex monoatomic ion channel complex cell periphery postsynapse postsynaptic membrane synapse cell junction plasma membrane protein-containing complex cellular anatomical structure transmembrane transporter complex membrane chloride channel complex membrane protein complex transporter complex monoatomic ion channel complex cell periphery postsynapse postsynaptic membrane synapse cell junction plasma membrane plasma membrane region synaptic membrane postsynaptic specialization membrane postsynaptic specialization organelle GABA receptor complex GABA-A receptor complex receptor complex cell projection neuron projection plasma membrane bounded cell projection membrane-bounded organelle intracellular anatomical structure intracellular vesicle intracellular membrane-bounded organelle intracellular organelle cytoplasmic vesicle membrane vesicle membrane cytoplasmic vesicle cytoplasm vesicle organelle membrane neuron spine dendritic spine somatodendritic compartment dendrite dendritic tree
E	Gamma-aminobutyric acid receptor subunit delta	neurotransmitter receptor activity molecular transducer activity signaling receptor activity GABA-A receptor activity GABA receptor activity transmembrane signaling receptor activity monoatomic anion transmembrane transporter activity chloride transmembrane transporter activity monoatomic ion channel activity passive transmembrane transporter activity inorganic molecular entity transmembrane transporter activity channel activity monoatomic anion channel activity monoatomic ion transmembrane transporter activity neurotransmitter receptor activity molecular transducer activity signaling receptor activity GABA-A receptor activity GABA receptor activity transmembrane signaling receptor activity monoatomic anion transmembrane transporter activity chloride transmembrane transporter activity monoatomic ion channel activity passive transmembrane transporter activity inorganic molecular entity transmembrane transporter activity channel activity monoatomic anion channel activity monoatomic ion transmembrane transporter activity transporter activity transmembrane transporter activity inorganic anion transmembrane transporter activity chloride channel activity transmitter-gated monoatomic ion channel activity gated channel activity transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential ligand-gated channel activity ligand-gated monoatomic ion channel activity extracellular ligand-gated monoatomic ion channel activity postsynaptic neurotransmitter receptor activity neurotransmitter receptor activity involved in regulation of postsynaptic membrane potential transmitter-gated channel activity	transport monoatomic ion transmembrane transport inorganic ion transmembrane transport inorganic anion transmembrane transport establishment of localization chloride transport transmembrane transport localization chloride transmembrane transport monoatomic anion transport monoatomic anion transmembrane transport monoatomic ion transport cellular process inorganic anion transport transport monoatomic ion transmembrane transport inorganic ion transmembrane transport inorganic anion transmembrane transport establishment of localization chloride transport transmembrane transport localization chloride transmembrane transport monoatomic anion transport monoatomic anion transmembrane transport monoatomic ion transport cellular process inorganic anion transport regulation of biological process signaling biological regulation cell-cell signaling gamma-aminobutyric acid signaling pathway cell communication cellular response to stimulus regulation of cellular process response to stimulus signal transduction trans-synaptic signaling synaptic transmission, GABAergic chemical synaptic transmission synaptic signaling anterograde trans-synaptic signaling	protein-containing complex cellular anatomical structure transmembrane transporter complex membrane chloride channel complex membrane protein complex transporter complex monoatomic ion channel complex cell periphery postsynapse postsynaptic membrane synapse cell junction plasma membrane protein-containing complex cellular anatomical structure transmembrane transporter complex membrane chloride channel complex membrane protein complex transporter complex monoatomic ion channel complex cell periphery postsynapse postsynaptic membrane synapse cell junction plasma membrane plasma membrane region synaptic membrane somatodendritic compartment cell projection dendrite dendritic tree neuron projection plasma membrane bounded cell projection GABA receptor complex GABA-A receptor complex receptor complex GABA-ergic synapse cell body neuronal cell body axon
F, G	Nanobody Nb25	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR001390	Gamma-aminobutyric-acid A receptor, alpha subunit	Family
A	IPR006202	Neurotransmitter-gated ion-channel ligand-binding domain	Domain
A	IPR036719	Neurotransmitter-gated ion-channel transmembrane domain superfamily	Homologous Superfamily
A	IPR006028	Gamma-aminobutyric acid A receptor/Glycine receptor alpha	Family
A	IPR006029	Neurotransmitter-gated ion-channel transmembrane domain	Domain
A	IPR036734	Neurotransmitter-gated ion-channel ligand-binding domain superfamily	Homologous Superfamily
A	IPR018000	Neurotransmitter-gated ion-channel, conserved site	Conserved Site
A	IPR038050	Neuronal acetylcholine receptor	Homologous Superfamily
A	IPR047024	Gamma-aminobutyric acid receptor subunit alpha 1-6, transmembrane domain	Domain
A	IPR005434	Gamma-aminobutyric-acid A receptor, alpha 4 subunit	Family
A	IPR006201	Neurotransmitter-gated ion-channel	Family
B, C, D	IPR006202	Neurotransmitter-gated ion-channel ligand-binding domain	Domain
B, C, D	IPR036719	Neurotransmitter-gated ion-channel transmembrane domain superfamily	Homologous Superfamily
B, C, D	IPR006028	Gamma-aminobutyric acid A receptor/Glycine receptor alpha	Family
B, C, D	IPR002289	Gamma-aminobutyric-acid A receptor, beta subunit	Family
B, C, D	IPR006029	Neurotransmitter-gated ion-channel transmembrane domain	Domain
B, C, D	IPR036734	Neurotransmitter-gated ion-channel ligand-binding domain superfamily	Homologous Superfamily
B, C, D	IPR018000	Neurotransmitter-gated ion-channel, conserved site	Conserved Site
B, C, D	IPR038050	Neuronal acetylcholine receptor	Homologous Superfamily
B, C, D	IPR006201	Neurotransmitter-gated ion-channel	Family
E	IPR006202	Neurotransmitter-gated ion-channel ligand-binding domain	Domain
E	IPR036719	Neurotransmitter-gated ion-channel transmembrane domain superfamily	Homologous Superfamily
E	IPR006028	Gamma-aminobutyric acid A receptor/Glycine receptor alpha	Family
E	IPR006029	Neurotransmitter-gated ion-channel transmembrane domain	Domain
E	IPR036734	Neurotransmitter-gated ion-channel ligand-binding domain superfamily	Homologous Superfamily
E	IPR008098	Gamma-aminobutyric-acid A receptor delta subunit	Family
E	IPR018000	Neurotransmitter-gated ion-channel, conserved site	Conserved Site
E	IPR038050	Neuronal acetylcholine receptor	Homologous Superfamily
E	IPR006201	Neurotransmitter-gated ion-channel	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	Pharos: P48169	Ataxia large cell medulloblastoma oligodendroglioma primitive neuroectodermal tumor atypical teratoid rhabdoid tumor epilepsy glioblastoma malignant ependymoma maturity-onset diabetes of the young pilocytic astrocytoma psoriasis schizophrenia type 2 diabetes mellitus autism epilepsy with generalized tonic-clonic seizures Ataxia large cell medulloblastoma oligodendroglioma primitive neuroectodermal tumor atypical teratoid rhabdoid tumor epilepsy glioblastoma malignant ependymoma maturity-onset diabetes of the young pilocytic astrocytoma psoriasis schizophrenia type 2 diabetes mellitus autism epilepsy with generalized tonic-clonic seizures insomnia malignant glioma medulloblastoma pituitary cancer schizoaffective disorder astrocytic tumor attention deficit hyperactivity disorder, inattentive type
B, C, D	Pharos: P28472	epilepsy Angelman syndrome childhood absence epilepsy Lennox-Gastaut syndrome developmental and epileptic encephalopathy, 43 epilepsy, childhood absence, susceptibility to, 5 absence epilepsy autism insomnia autism spectrum disorder intellectual disability schizophrenia depressive disorder malignant ependymoma duplication/inversion 15q11 epilepsy Angelman syndrome childhood absence epilepsy Lennox-Gastaut syndrome developmental and epileptic encephalopathy, 43 epilepsy, childhood absence, susceptibility to, 5 absence epilepsy autism insomnia autism spectrum disorder intellectual disability schizophrenia depressive disorder malignant ependymoma duplication/inversion 15q11 status epilepticus pancreatic intraductal papillary-mucinous neoplasm astrocytic tumor gastric carcinoma pilocytic astrocytoma glioblastoma primitive neuroectodermal tumor bipolar disorder interstitial cystitis brain injury juvenile absence epilepsy malignant glioma Sjogren syndrome mixed anxiety and depressive disorder epilepsy with generalized tonic-clonic seizures oligodendroglioma epilepsy, childhood absence, susceptibility to, 1 pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia peptic ulcer disease pituitary cancer psoriasis irritable bowel syndrome schizoaffective disorder large cell medulloblastoma Crohn disease lung carcinoma medulloblastoma alcohol withdrawal delirium early myoclonic encephalopathy tetanus panic disorder atypical teratoid rhabdoid tumor Pick disease generalized anxiety disorder Prader-Willi syndrome
E	Pharos: O14764	chromosome 1p36 deletion syndrome juvenile myoclonic epilepsy epilepsy, idiopathic generalized, susceptibility to, 10 epilepsy generalized epilepsy with febrile seizures plus schizophrenia large cell medulloblastoma medulloblastoma osteosarcoma primitive neuroectodermal tumor Anxiety glioblastoma insomnia malignant ependymoma Pick disease chromosome 1p36 deletion syndrome juvenile myoclonic epilepsy epilepsy, idiopathic generalized, susceptibility to, 10 epilepsy generalized epilepsy with febrile seizures plus schizophrenia large cell medulloblastoma medulloblastoma osteosarcoma primitive neuroectodermal tumor Anxiety glioblastoma insomnia malignant ependymoma Pick disease psoriasis astrocytic tumor subependymal giant cell astrocytoma EIG1 epilepsy with generalized tonic-clonic seizures generalized epilepsy with febrile seizures plus, type 1 hepatocellular carcinoma malignant glioma oligodendroglioma pilocytic astrocytoma atypical teratoid rhabdoid tumor swine influenza EJM1

Membrane Protein Annotation: OPM OPM Database Homepage

Chains	External Link	Type	Class	Superfamily	Family
A, B, C, D, E	OPM	Transmembrane	Alpha-helical polytopic	Pentameric ligand-gated ion channels	Ligand-gated ion channel of neurotransmitter receptors

Membrane Protein Annotation: PDBTM PDBTM Database Homepage

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

Membrane Protein Annotation: MemProtMD MemProtMD Database Homepage

Chains	External Link	Comment
A, B, C, D, E	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	mpstruc	TRANSMEMBRANE PROTEINS: ALPHA-HELICAL	Cys-Loop Receptor Family	GABA_A receptor (α4β3δ), apo

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.

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7QN5

Cryo-EM structure of human full-length extrasynaptic alpha4beta3delta GABA(A)R in complex with nanobody Nb25

External Resource: Annotation

Domain Annotation: ECOD Classification ECOD Database Homepage

SAbDab Antibody Annotation SAbDab Database Homepage

Protein Family Annotation Pfam Database Homepage

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

InterPro: Protein Family Classification InterPro Database Homepage

Pharos: Disease Associations Pharos Homepage Annotation

Membrane Protein Annotation: OPM OPM Database Homepage

Membrane Protein Annotation: PDBTM PDBTM Database Homepage

Membrane Protein Annotation: MemProtMD MemProtMD Database Homepage

Membrane Protein Annotation: mpstruc mpstruc Database Homepage