6UR8

CryoEM structure of human alpha4beta2 nicotinic acetylcholine receptor in complex with varenicline

External Resource: Annotation

Domain Annotation: ECOD Classification
Domain Annotation: CATH
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	e6ur8A2	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	e6ur8A1	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	e6ur8D2	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	e6ur8D1	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	e6ur8B2	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	e6ur8B1	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	e6ur8C2	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	e6ur8C1	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	e6ur8E2	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	e6ur8E1	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)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.70.170.10	Mainly Beta	Distorted Sandwich	Acetylcholine Binding Protein	Chain: A,	CATH (utative)
D	2.70.170.10	Mainly Beta	Distorted Sandwich	Acetylcholine Binding Protein	Chain: A,	CATH (utative)
B	2.70.170.10	Mainly Beta	Distorted Sandwich	Acetylcholine Binding Protein	Chain: A,	CATH (utative)
C	2.70.170.10	Mainly Beta	Distorted Sandwich	Acetylcholine Binding Protein	Chain: A,	CATH (utative)
E	2.70.170.10	Mainly Beta	Distorted Sandwich	Acetylcholine Binding Protein	Chain: A,	CATH (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, D	PF02932	Neurotransmitter-gated ion-channel transmembrane region (Neur_chan_memb)	Neurotransmitter-gated ion-channel transmembrane region	-	Family
A, D	PF02931	Neurotransmitter-gated ion-channel ligand binding domain (Neur_chan_LBD)	Neurotransmitter-gated ion-channel ligand binding domain	-	Family
B, C, E	PF02932	Neurotransmitter-gated ion-channel transmembrane region (Neur_chan_memb)	Neurotransmitter-gated ion-channel transmembrane region	-	Family
B, C, 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, D	Chimera of soluble cytochrome b562 (BRIL) and neuronal acetylcholine receptor subunit alpha-4	binding organic cyclic compound binding tetrapyrrole binding heme binding electron transfer activity cation binding transition metal ion binding iron ion binding ion binding metal ion binding small molecule binding ligand-gated channel activity ligand-gated monoatomic ion channel activity passive transmembrane transporter activity binding organic cyclic compound binding tetrapyrrole binding heme binding electron transfer activity cation binding transition metal ion binding iron ion binding ion binding metal ion binding small molecule binding ligand-gated channel activity ligand-gated monoatomic ion channel activity passive transmembrane transporter activity gated channel activity monoatomic ion channel activity channel activity monoatomic ion transmembrane transporter activity transporter activity transmembrane transporter activity neurotransmitter receptor activity postsynaptic neurotransmitter receptor activity molecular transducer activity signaling receptor activity transmembrane signaling receptor activity acetylcholine receptor activity acetylcholine binding transmitter-gated monoatomic ion channel activity monoatomic cation transmembrane transporter activity transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential acetylcholine-gated monoatomic cation-selective channel activity ligand-gated monoatomic cation channel activity excitatory extracellular ligand-gated monoatomic ion channel activity extracellular ligand-gated monoatomic ion channel activity monoatomic cation channel activity neurotransmitter receptor activity involved in regulation of postsynaptic membrane potential transmitter-gated channel activity	electron transport chain metabolic process cellular process generation of precursor metabolites and energy biological regulation action potential regulation of biological quality regulation of membrane potential localization transport monoatomic ion transport establishment of localization monoamine transport regulation of localization electron transport chain metabolic process cellular process generation of precursor metabolites and energy biological regulation action potential regulation of biological quality regulation of membrane potential localization transport monoatomic ion transport establishment of localization monoamine transport regulation of localization nitrogen compound transport regulation of cellular process signaling regulation of catecholamine secretion organic hydroxy compound transport dopamine transport cell communication secretion by cell regulation of secretion by cell catecholamine transport signal release regulation of biological process secretion regulation of transport export from cell cell-cell signaling dopamine secretion regulation of secretion catecholamine secretion amine transport regulation of amine transport regulation of dopamine secretion multicellular organismal process immune system process B cell activation cell activation lymphocyte activation leukocyte activation system process nervous system process cognition cellular response to stimulus response to stimulus signal transduction primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process cellular response to stress DNA damage response response to stress macromolecule metabolic process DNA repair trans-synaptic signaling synaptic signaling anterograde trans-synaptic signaling chemical synaptic transmission regulation of postsynaptic membrane potential chemical synaptic transmission, postsynaptic cell surface receptor signaling pathway inhibitory postsynaptic potential response to decreased oxygen levels response to hypoxia response to oxygen levels response to abiotic stimulus membrane depolarization behavior adult behavior response to chemical response to nicotine behavioral response to nicotine monoatomic cation transport calcium ion transport metal ion transport sensory perception sensory perception of pain response to oxidative stress cellular response to nitrogen compound cellular response to acetylcholine response to oxygen-containing compound response to nitrogen compound acetylcholine receptor signaling pathway postsynaptic signal transduction cellular response to oxygen-containing compound cellular response to chemical stimulus response to acetylcholine synaptic transmission, cholinergic	cellular anatomical structure periplasmic space cell periphery postsynapse postsynaptic membrane synapse cell junction membrane plasma membrane plasma membrane region synaptic membrane cell surface external side of plasma membrane side of membrane cellular anatomical structure periplasmic space cell periphery postsynapse postsynaptic membrane synapse cell junction membrane plasma membrane plasma membrane region synaptic membrane cell surface external side of plasma membrane side of membrane somatodendritic compartment cell projection dendrite dendritic tree neuron projection plasma membrane bounded cell projection protein-containing complex plasma membrane protein complex membrane protein complex transporter complex receptor complex acetylcholine-gated channel complex transmembrane transporter complex plasma membrane signaling receptor complex monoatomic ion channel complex cell body neuronal cell body
B, C, E	Neuronal acetylcholine receptor subunit beta-2	ligand-gated channel activity ligand-gated monoatomic ion channel activity passive transmembrane transporter activity gated channel activity monoatomic ion channel activity channel activity monoatomic ion transmembrane transporter activity transporter activity transmembrane transporter activity neurotransmitter receptor activity postsynaptic neurotransmitter receptor activity molecular transducer activity signaling receptor activity transmembrane signaling receptor activity ligand-gated channel activity ligand-gated monoatomic ion channel activity passive transmembrane transporter activity gated channel activity monoatomic ion channel activity channel activity monoatomic ion transmembrane transporter activity transporter activity transmembrane transporter activity neurotransmitter receptor activity postsynaptic neurotransmitter receptor activity molecular transducer activity signaling receptor activity transmembrane signaling receptor activity acetylcholine receptor activity binding quaternary ammonium group binding small molecule binding protein-containing complex binding cation binding acetylcholine binding ion binding heterocyclic compound binding transmitter-gated monoatomic ion channel activity monoatomic cation transmembrane transporter activity transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential acetylcholine-gated monoatomic cation-selective channel activity ligand-gated monoatomic cation channel activity excitatory extracellular ligand-gated monoatomic ion channel activity extracellular ligand-gated monoatomic ion channel activity monoatomic cation channel activity neurotransmitter receptor activity involved in regulation of postsynaptic membrane potential transmitter-gated channel activity	behavior multicellular organismal process system process learning learning or memory nervous system process cognition regulation of biological process regulation of cellular process regulation of amine metabolic process organic hydroxy compound metabolic process biological regulation dopamine metabolic process primary metabolic process behavior multicellular organismal process system process learning learning or memory nervous system process cognition regulation of biological process regulation of cellular process regulation of amine metabolic process organic hydroxy compound metabolic process biological regulation dopamine metabolic process primary metabolic process catechol-containing compound metabolic process regulation of primary metabolic process amine metabolic process catecholamine metabolic process phenol-containing compound metabolic process metabolic process cellular process regulation of catecholamine metabolic process regulation of metabolic process biogenic amine metabolic process regulation of dopamine metabolic process localization transport monoatomic ion transport establishment of localization immune system process B cell activation cell activation lymphocyte activation leukocyte activation memory trans-synaptic signaling regulation of signaling signaling modulation of chemical synaptic transmission regulation of synaptic transmission, dopaminergic cell-cell signaling chemical synaptic transmission cell communication synaptic signaling regulation of trans-synaptic signaling anterograde trans-synaptic signaling regulation of cell communication synaptic transmission, dopaminergic axonogenesis cellular developmental process cell projection organization plasma membrane bounded cell projection morphogenesis cell development central nervous system neuron development neuron projection development cell morphogenesis cellular component organization neurogenesis multicellular organism development central nervous system neuron differentiation cell projection morphogenesis neuron differentiation neuron projection morphogenesis cell differentiation anatomical structure development cellular component organization or biogenesis system development developmental process central nervous system projection neuron axonogenesis central nervous system neuron axonogenesis plasma membrane bounded cell projection organization nervous system development axon development cell morphogenesis involved in neuron differentiation generation of neurons anatomical structure morphogenesis central nervous system development neuron development sensory perception sensory perception of sound sensory perception of mechanical stimulus response to decreased oxygen levels response to stimulus response to hypoxia response to stress response to oxygen levels response to abiotic stimulus regulation of cellular component organization cellular component biogenesis cellular component assembly cell junction assembly regulation of synapse structure or activity regulation of synapse assembly synapse organization regulation of biological quality regulation of cellular component biogenesis regulation of cell junction assembly regulation of synapse organization cell junction organization synapse assembly positive regulation of cell population proliferation positive regulation of B cell proliferation regulation of leukocyte activation positive regulation of biological process regulation of cell activation leukocyte proliferation positive regulation of lymphocyte activation positive regulation of cell activation regulation of B cell proliferation lymphocyte proliferation regulation of B cell activation positive regulation of leukocyte activation positive regulation of mononuclear cell proliferation regulation of multicellular organismal process regulation of immune system process positive regulation of immune system process positive regulation of cellular process regulation of lymphocyte proliferation regulation of leukocyte proliferation cell population proliferation positive regulation of lymphocyte proliferation B cell proliferation positive regulation of B cell activation regulation of cell population proliferation mononuclear cell proliferation positive regulation of leukocyte proliferation regulation of mononuclear cell proliferation positive regulation of multicellular organismal process regulation of lymphocyte activation cellular response to nitrogen compound cellular response to stimulus cellular response to acetylcholine response to oxygen-containing compound response to nitrogen compound acetylcholine receptor signaling pathway postsynaptic signal transduction cellular response to oxygen-containing compound cellular response to chemical stimulus response to chemical response to acetylcholine signal transduction excretion micturition renal system process synaptic transmission involved in micturition neuromuscular synaptic transmission nerve development vestibulocochlear nerve development cranial nerve development circadian sleep/wake cycle, sleep rhythmic process circadian sleep/wake cycle rhythmic behavior regulation of circadian sleep/wake cycle, REM sleep circadian rhythm regulation of circadian sleep/wake cycle regulation of circadian rhythm regulation of behavior circadian behavior circadian sleep/wake cycle, REM sleep sleep regulation of circadian sleep/wake cycle, sleep circadian sleep/wake cycle process locomotory behavior cranial nerve morphogenesis optic nerve morphogenesis optic nerve development smooth muscle contraction muscle contraction muscle system process monoamine transport regulation of localization nitrogen compound transport regulation of catecholamine secretion organic hydroxy compound transport dopamine transport secretion by cell regulation of secretion by cell catecholamine transport signal release secretion regulation of transport export from cell dopamine secretion regulation of secretion catecholamine secretion amine transport regulation of amine transport regulation of dopamine secretion positive regulation of secretion by cell positive regulation of amine transport positive regulation of secretion positive regulation of catecholamine secretion positive regulation of dopamine secretion positive regulation of transport response to light stimulus visual learning visual behavior associative learning response to radiation response to alcohol response to ethanol head development forebrain development animal organ development brain development diencephalon development lateral geniculate nucleus development thalamus development neural nucleus development regulation of action potential negative regulation of action potential negative regulation of biological process action potential regulation of membrane potential biological process involved in intraspecies interaction between organisms social behavior sensory perception of light stimulus visual perception regulation of neuron projection development regulation of developmental process dendrite development regulation of dendrite morphogenesis regulation of anatomical structure morphogenesis regulation of cell projection organization dendrite morphogenesis regulation of dendrite development regulation of plasma membrane bounded cell projection organization membrane depolarization adult behavior response to nicotine behavioral response to nicotine monoatomic cation transport calcium ion transport metal ion transport sensory perception of pain synaptic transmission, cholinergic response to organic cyclic compound response to cocaine response to alkaloid	cell periphery cellular anatomical structure cell surface membrane plasma membrane external side of plasma membrane side of membrane presynapse synapse cell junction presynaptic membrane plasma membrane region synaptic membrane cholinergic synapse cell periphery cellular anatomical structure cell surface membrane plasma membrane external side of plasma membrane side of membrane presynapse synapse cell junction presynaptic membrane plasma membrane region synaptic membrane cholinergic synapse cell projection neuron projection plasma membrane bounded cell projection postsynaptic specialization membrane postsynaptic specialization postsynapse organelle postsynaptic membrane protein-containing complex plasma membrane protein complex membrane protein complex transporter complex receptor complex acetylcholine-gated channel complex transmembrane transporter complex plasma membrane signaling receptor complex monoatomic ion channel complex membrane microdomain membrane raft plasma membrane raft

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, D	IPR010980	Cytochrome c/b562	Homologous Superfamily
A, D	IPR009155	Cytochrome b562	Family
A, D	IPR006202	Neurotransmitter-gated ion-channel ligand-binding domain	Domain
A, D	IPR036719	Neurotransmitter-gated ion-channel transmembrane domain superfamily	Homologous Superfamily
A, D	IPR002394	Nicotinic acetylcholine receptor	Family
A, D	IPR006029	Neurotransmitter-gated ion-channel transmembrane domain	Domain
A, D	IPR036734	Neurotransmitter-gated ion-channel ligand-binding domain superfamily	Homologous Superfamily
A, D	IPR018000	Neurotransmitter-gated ion-channel, conserved site	Conserved Site
A, D	IPR038050	Neuronal acetylcholine receptor	Homologous Superfamily
A, D	IPR006201	Neurotransmitter-gated ion-channel	Family
B, C, E	IPR002394	Nicotinic acetylcholine receptor	Family
B, C, E	IPR036734	Neurotransmitter-gated ion-channel ligand-binding domain superfamily	Homologous Superfamily
B, C, E	IPR018000	Neurotransmitter-gated ion-channel, conserved site	Conserved Site
B, C, E	IPR038050	Neuronal acetylcholine receptor	Homologous Superfamily
B, C, E	IPR006202	Neurotransmitter-gated ion-channel ligand-binding domain	Domain
B, C, E	IPR036719	Neurotransmitter-gated ion-channel transmembrane domain superfamily	Homologous Superfamily
B, C, E	IPR006029	Neurotransmitter-gated ion-channel transmembrane domain	Domain
B, C, E	IPR006201	Neurotransmitter-gated ion-channel	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, D	Pharos: P43681	autosomal dominant nocturnal frontal lobe epilepsy 1 nicotine dependence frontal lobe epilepsy Inflammation nervous system disorder dystonic disorder autosomal dominant nocturnal frontal lobe epilepsy visual epilepsy developmental disability psoriasis epilepsy episodic kinesigenic dyskinesia 1 autism chronic obstructive pulmonary disease depressive disorder autosomal dominant nocturnal frontal lobe epilepsy 1 nicotine dependence frontal lobe epilepsy Inflammation nervous system disorder dystonic disorder autosomal dominant nocturnal frontal lobe epilepsy visual epilepsy developmental disability psoriasis epilepsy episodic kinesigenic dyskinesia 1 autism chronic obstructive pulmonary disease depressive disorder schizophrenia sleep-wake disorder intellectual disability cocaine abuse pellagra attention deficit hyperactivity disorder, inattentive type
B, C, E	Pharos: P17787	autosomal dominant nocturnal frontal lobe epilepsy 3 Alzheimer disease Sudden infant death syndrome substance withdrawal syndrome nicotine dependence frontal lobe epilepsy hyperreflexia autosomal dominant nocturnal frontal lobe epilepsy pellagra glioblastoma malignant ependymoma autism osteosarcoma sleep-wake disorder pilocytic astrocytoma autosomal dominant nocturnal frontal lobe epilepsy 3 Alzheimer disease Sudden infant death syndrome substance withdrawal syndrome nicotine dependence frontal lobe epilepsy hyperreflexia autosomal dominant nocturnal frontal lobe epilepsy pellagra glioblastoma malignant ependymoma autism osteosarcoma sleep-wake disorder pilocytic astrocytoma anxiety disorder lung adenocarcinoma attention deficit hyperactivity disorder, inattentive type malignant glioma schizophrenia epilepsy intellectual disability lung carcinoma atypical teratoid rhabdoid tumor

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	Nicotinic Acetylcholine α4β2 Receptor with varenicline in complex with anti-BRIL synthetic antibody BAK5

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.