6QFA | pdb_00006qfa

CryoEM structure of a beta3K279T GABA(A)R homomer in complex with histamine and megabody Mb25

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)
F [auth L]	V-set_12	e6qfaL1	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)
E [auth M]	V-set_12	e6qfaM1	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)
D [auth N]	V-set_12	e6qfaN1	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)
C [auth O]	V-set_12	e6qfaO1	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)
B [auth K]	V-set_12	e6qfaK1	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 [auth C]	Neur_chan_LBD	e6qfaC1	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)
G [auth C]	Neur_chan_memb	e6qfaC2	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)
H [auth D]	Neur_chan_LBD	e6qfaD1	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)
H [auth D]	Neur_chan_memb	e6qfaD2	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)
I [auth E]	Neur_chan_LBD	e6qfaE1	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)
I [auth E]	Neur_chan_memb	e6qfaE2	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)
J [auth A]	Neur_chan_LBD	e6qfaA1	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)
J [auth A]	Neur_chan_memb	e6qfaA2	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)
A [auth B]	Neur_chan_LBD	e6qfaB1	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 [auth B]	Neur_chan_memb	e6qfaB2	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)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
B [auth K], C [auth O], D [auth N], E [auth M], F [auth L]	Heavy Chain	IGHV1	-	gamma-aminobutyric acid receptor subunit beta-3,gamma-aminobutyric acid receptor subunit beta-3	SAbDab (2025-11-28)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B [auth K], C [auth O], D [auth N], E [auth M], F [auth L]	PF18304	SabA N-terminal extracellular adhesion domain (SabA_adhesion)	SabA N-terminal extracellular adhesion domain	This is the N-terminal extracellular adhesion domain of Sialic acid binding adhesin (SabA) present in Helicobacter pylori. The N-terminal domain of SabA functions as a sugar-binding adhesion domain with conserved disulfide bonds. Notably, these amino ...	This is the N-terminal extracellular adhesion domain of Sialic acid binding adhesin (SabA) present in Helicobacter pylori. The N-terminal domain of SabA functions as a sugar-binding adhesion domain with conserved disulfide bonds. Notably, these amino acid residues are not only conserved among SabA orthologs but also between SabA and BabA [1].	Domain
A [auth B], G [auth C], H [auth D], I [auth E], J [auth A]	PF02932	Neurotransmitter-gated ion-channel transmembrane region (Neur_chan_memb)	Neurotransmitter-gated ion-channel transmembrane region	-	Family
A [auth B], G [auth C], H [auth D], I [auth E], J [auth A]	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
B [auth K], C [auth O], D [auth N], E [auth M], F [auth L]	Outer membrane protein,Outer membrane protein,Outer membrane protein,Outer membrane protein,Uncharacterized protein,Uncharacterized protein,Mb-c7HopQ-Nb25	-	-	-
A [auth B], G [auth C], H [auth D], I [auth E], J [auth A]	Gamma-aminobutyric acid receptor subunit beta-3,Gamma-aminobutyric acid receptor subunit beta-3	transmitter-gated monoatomic ion channel activity monoatomic anion transmembrane transporter activity chloride transmembrane transporter activity GABA-gated chloride ion channel activity molecular transducer activity gated channel activity monoatomic ion channel activity signaling receptor activity ligand-gated monoatomic anion channel activity neurotransmitter receptor activity ligand-gated channel activity ligand-gated monoatomic ion channel activity extracellular ligand-gated monoatomic ion channel activity passive transmembrane transporter activity channel activity transmitter-gated monoatomic ion channel activity monoatomic anion transmembrane transporter activity chloride transmembrane transporter activity GABA-gated chloride ion channel activity molecular transducer activity gated channel activity monoatomic ion channel activity signaling receptor activity ligand-gated monoatomic anion channel activity neurotransmitter receptor activity ligand-gated channel activity ligand-gated monoatomic ion channel activity extracellular ligand-gated monoatomic ion channel activity passive transmembrane transporter activity channel activity transmitter-gated channel activity monoatomic ion transmembrane transporter activity monoatomic anion channel activity transporter activity transmembrane transporter activity chloride channel 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 identical protein binding protein binding binding	developmental process ear development sensory organ development inner ear development cochlea development animal organ development anatomical structure development response to stimulus response to chemical response to xenobiotic stimulus behavior multicellular organismal process system process learning developmental process ear development sensory organ development inner ear development cochlea development animal organ development anatomical structure development response to stimulus response to chemical response to xenobiotic stimulus behavior multicellular organismal process system process learning learning or memory nervous system process cognition exploration behavior transport monoatomic ion 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 cellular response to chemical stimulus response to histamine cellular response to histamine response to nitrogen compound circadian sleep/wake cycle, sleep rhythmic process circadian sleep/wake cycle rhythmic behavior circadian rhythm circadian behavior circadian sleep/wake cycle, REM sleep sleep circadian sleep/wake cycle process hard palate development secondary palate development roof of mouth development mechanoreceptor differentiation inner ear receptor cell development cellular developmental process cell development nervous system development inner ear receptor cell differentiation generation of neurons neurogenesis multicellular organism development neuron differentiation cell differentiation neuron development system development regulation of biological process signaling biological regulation cell-cell signaling gamma-aminobutyric acid signaling pathway cell communication memory head development brain development cerebellum development central nervous system development metencephalon development hindbrain development response to anesthetic regulation of cellular process signal transduction reproductive process multicellular organismal reproductive process reproductive behavior inhibitory synapse assembly cellular component organization cellular component biogenesis cell junction organization cellular component assembly cell junction assembly synapse organization cellular component organization or biogenesis synapse assembly cellular response to metal ion response to metal ion response to zinc ion cellular response to zinc ion regulation of postsynaptic membrane potential chemical synaptic transmission, postsynaptic synaptic signaling regulation of biological quality trans-synaptic signaling cell surface receptor signaling pathway chemical synaptic transmission anterograde trans-synaptic signaling inhibitory postsynaptic potential regulation of membrane potential biological process involved in intraspecies interaction between organisms social behavior motor behavior synaptic transmission, GABAergic nerve development innervation	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 cell surface postsynaptic specialization membrane postsynaptic specialization organelle GABA receptor complex GABA-A receptor complex receptor complex GABA-ergic synapse 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 neuron projection dendritic spine plasma membrane bounded cell projection somatodendritic compartment cell projection dendrite dendritic tree

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B [auth K], C [auth O], D [auth N], E [auth M], F [auth L]	IPR040838	SabA, N-terminal extracellular adhesion domain	Domain
B [auth K], C [auth O], D [auth N], E [auth M], F [auth L]	IPR002718	Outer membrane protein, Helicobacter	Family
A [auth B], G [auth C], H [auth D], I [auth E], J [auth A]	IPR006202	Neurotransmitter-gated ion-channel ligand-binding domain	Domain
A [auth B], G [auth C], H [auth D], I [auth E], J [auth A]	IPR036719	Neurotransmitter-gated ion-channel transmembrane domain superfamily	Homologous Superfamily
A [auth B], G [auth C], H [auth D], I [auth E], J [auth A]	IPR006028	Gamma-aminobutyric acid A receptor/Glycine receptor alpha	Family
A [auth B], G [auth C], H [auth D], I [auth E], J [auth A]	IPR002289	Gamma-aminobutyric-acid A receptor, beta subunit	Family
A [auth B], G [auth C], H [auth D], I [auth E], J [auth A]	IPR006029	Neurotransmitter-gated ion-channel transmembrane domain	Domain
A [auth B], G [auth C], H [auth D], I [auth E], J [auth A]	IPR036734	Neurotransmitter-gated ion-channel ligand-binding domain superfamily	Homologous Superfamily
A [auth B], G [auth C], H [auth D], I [auth E], J [auth A]	IPR018000	Neurotransmitter-gated ion-channel, conserved site	Conserved Site
A [auth B], G [auth C], H [auth D], I [auth E], J [auth A]	IPR038050	Neuronal acetylcholine receptor	Homologous Superfamily
A [auth B], G [auth C], H [auth D], I [auth E], J [auth A]	IPR006201	Neurotransmitter-gated ion-channel	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A [auth B], G [auth C], H [auth D], I [auth E], J [auth A]	Pharos: P28472	Angelman syndrome epilepsy 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 Angelman syndrome epilepsy 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 pilocytic astrocytoma gastric carcinoma glioblastoma primitive neuroectodermal tumor bipolar disorder brain injury interstitial cystitis juvenile absence epilepsy Sjogren syndrome malignant glioma mixed anxiety and depressive disorder oligodendroglioma epilepsy with generalized tonic-clonic seizures pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia epilepsy, childhood absence, susceptibility to, 1 peptic ulcer disease pituitary cancer psoriasis schizoaffective disorder irritable bowel syndrome large cell medulloblastoma Crohn disease lung carcinoma alcohol withdrawal delirium medulloblastoma early myoclonic encephalopathy tetanus panic disorder atypical teratoid rhabdoid tumor Pick disease Prader-Willi syndrome generalized anxiety disorder

Membrane Protein Annotation: OPM OPM Database Homepage

Chains	External Link	Type	Class	Superfamily	Family
A [auth B], B [auth K], C [auth O], D [auth N], E [auth M] A [auth B], B [auth K], C [auth O], D [auth N], E [auth M], F [auth L], G [auth C], H [auth D], I [auth E], J [auth A]	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 [auth B], B [auth K], C [auth O], D [auth N], E [auth M] A [auth B], B [auth K], C [auth O], D [auth N], E [auth M], F [auth L], G [auth C], H [auth D], I [auth E], J [auth A]	PDBTM	Annotated as membrane protein by PDBTM

Membrane Protein Annotation: MemProtMD MemProtMD Database Homepage

Chains	External Link	Comment
A [auth B], B [auth K], C [auth O], D [auth N], E [auth M] A [auth B], B [auth K], C [auth O], D [auth N], E [auth M], F [auth L], G [auth C], H [auth D], I [auth E], J [auth A]	MemProtMD	Annotated as membrane protein by MemProtMD

Membrane Protein Annotation: mpstruc mpstruc Database Homepage

Chains	Resource Link	Group	Subgroup	Protein
A [auth B], B [auth K], C [auth O], D [auth N], E [auth M] A [auth B], B [auth K], C [auth O], D [auth N], E [auth M], F [auth L], G [auth C], H [auth D], I [auth E], J [auth A]	mpstruc	TRANSMEMBRANE PROTEINS: ALPHA-HELICAL	Cys-Loop Receptor Family	GABA_A receptor (β3 homopentamer) in complex with histamine and megabody Mb25

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.