8GZ2 | pdb_00008gz2

Cryo-EM structure of human NaV1.6/beta1/beta2-4,9-anhydro-tetrodotoxin

External Resource: Annotation

Domain Annotation: ECOD Classification
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)
C	V-set_9	e8gz2C1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_9	ECOD (1.6)
B	Ion_trans	e8gz2B3	A: alpha complex topology	X: Voltage-gated ion channels (From Topology)	H: Voltage-gated ion channels (From Topology)	T: Voltage-gated ion channels	F: Ion_trans	ECOD (1.6)
A [auth D]	V-set_9	e8gz2D1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_9	ECOD (1.6)
A [auth D]	F_UNCLASSIFIED	e8gz2D2	A: extended segments	X: Fibroblast growth factor receptor 3 transmembrane domain (From Topology)	H: Fibroblast growth factor receptor 3 transmembrane domain (From Topology)	T: Fibroblast growth factor receptor 3 transmembrane domain	F: F_UNCLASSIFIED	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
C	PF07686	Immunoglobulin V-set domain (V-set)	Immunoglobulin V-set domain	This domain is found in antibodies as well as neural protein P0 and CTL4 amongst others.	Domain
B	PF00520	Ion transport protein (Ion_trans)	Ion transport protein	-	Family
A [auth D]	PF07686	Immunoglobulin V-set domain (V-set)	Immunoglobulin V-set domain	This domain is found in antibodies as well as neural protein P0 and CTL4 amongst others.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C	Sodium channel subunit beta-2	monoatomic cation transmembrane transporter activity gated channel activity voltage-gated potassium channel activity involved in cardiac muscle cell action potential repolarization monoatomic ion channel activity potassium ion transmembrane transporter activity voltage-gated channel activity voltage-gated monoatomic ion channel activity potassium channel activity voltage-gated monoatomic cation channel activity voltage-gated potassium channel activity involved in ventricular cardiac muscle cell action potential repolarization monoatomic cation channel activity passive transmembrane transporter activity voltage-gated potassium channel activity channel activity monoatomic ion transmembrane transporter activity monoatomic cation transmembrane transporter activity gated channel activity voltage-gated potassium channel activity involved in cardiac muscle cell action potential repolarization monoatomic ion channel activity potassium ion transmembrane transporter activity voltage-gated channel activity voltage-gated monoatomic ion channel activity potassium channel activity voltage-gated monoatomic cation channel activity voltage-gated potassium channel activity involved in ventricular cardiac muscle cell action potential repolarization monoatomic cation channel activity passive transmembrane transporter activity voltage-gated potassium channel activity channel activity monoatomic ion transmembrane transporter activity transporter activity metal ion transmembrane transporter activity transmembrane transporter activity channel regulator activity ion channel regulator activity molecular function regulator activity sodium channel regulator activity transporter regulator activity voltage-gated sodium channel activity involved in cardiac muscle cell action potential voltage-gated sodium channel activity sodium channel activity sodium ion transmembrane transporter activity	membrane depolarization during action potential membrane depolarization biological regulation membrane depolarization during cardiac muscle cell action potential action potential regulation of biological quality cardiac muscle cell action potential regulation of membrane potential heart process cardiac muscle cell contraction multicellular organismal process system process cardiac muscle cell action potential involved in contraction actin filament-based movement membrane depolarization during action potential membrane depolarization biological regulation membrane depolarization during cardiac muscle cell action potential action potential regulation of biological quality cardiac muscle cell action potential regulation of membrane potential heart process cardiac muscle cell contraction multicellular organismal process system process cardiac muscle cell action potential involved in contraction actin filament-based movement cardiac muscle contraction muscle contraction muscle system process striated muscle contraction circulatory system process actin filament-based process cellular process actin-mediated cell contraction heart contraction blood circulation regulation of biological process regulation of cellular process regulation of membrane depolarization regulation of atrial cardiac muscle cell membrane depolarization biosynthetic process metabolic process macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of heart contraction regulation of system process regulation of blood circulation cardiac conduction regulation of multicellular organismal process developmental process multicellular organism development anatomical structure development nervous system development system development trans-synaptic signaling synaptic signaling signaling anterograde trans-synaptic signaling cell-cell signaling chemical synaptic transmission cell communication regulation of localization transport regulation of transport regulation of monoatomic ion transport positive regulation of biological process regulation of sodium ion transport establishment of localization metal ion transport positive regulation of sodium ion transport localization positive regulation of transport positive regulation of monoatomic ion transport monoatomic ion transport monoatomic cation transport regulation of metal ion transport sodium ion transport response to stimulus response to stress response to heat response to abiotic stimulus response to temperature stimulus response to chemical response to pyrethroid response to insecticide response to toxic substance regulation of heart rate by cardiac conduction regulation of heart rate	cell periphery cellular anatomical structure sarcolemma plasma membrane membrane T-tubule axon cell projection main axon neuron projection node of Ranvier plasma membrane bounded cell projection axon initial segment protein-containing complex cell periphery cellular anatomical structure sarcolemma plasma membrane membrane T-tubule axon cell projection main axon neuron projection node of Ranvier plasma membrane bounded cell projection axon initial segment protein-containing complex sodium channel complex voltage-gated sodium channel complex plasma membrane protein complex membrane protein complex cation channel complex transporter complex transmembrane transporter complex monoatomic ion channel complex synapse cell junction
B	Sodium channel protein type 8 subunit alpha	monoatomic cation transmembrane transporter activity voltage-gated sodium channel activity monoatomic ion channel activity sodium channel activity sodium ion transmembrane transporter activity monoatomic cation channel activity passive transmembrane transporter activity channel activity monoatomic ion transmembrane transporter activity transporter activity metal ion transmembrane transporter activity transmembrane transporter activity cation binding ion binding monoatomic cation transmembrane transporter activity voltage-gated sodium channel activity monoatomic ion channel activity sodium channel activity sodium ion transmembrane transporter activity monoatomic cation channel activity passive transmembrane transporter activity channel activity monoatomic ion transmembrane transporter activity transporter activity metal ion transmembrane transporter activity transmembrane transporter activity cation binding ion binding binding alkali metal ion binding sodium ion binding metal ion binding small molecule binding	heart process cardiac muscle cell contraction multicellular organismal process system process cardiac muscle cell action potential involved in contraction biological regulation action potential actin filament-based movement cardiac muscle contraction muscle contraction muscle system process striated muscle contraction circulatory system process actin filament-based process heart process cardiac muscle cell contraction multicellular organismal process system process cardiac muscle cell action potential involved in contraction biological regulation action potential actin filament-based movement cardiac muscle contraction muscle contraction muscle system process striated muscle contraction circulatory system process actin filament-based process cellular process regulation of biological quality actin-mediated cell contraction heart contraction cardiac muscle cell action potential blood circulation regulation of membrane potential transport monoatomic ion transmembrane transport sodium ion transmembrane transport establishment of localization metal ion transport monoatomic cation transmembrane transport transmembrane transport localization monoatomic ion transport monoatomic cation transport sodium ion transport developmental process multicellular organism development anatomical structure development peripheral nervous system development nervous system development system development myelination axon ensheathment ensheathment of neurons	cellular anatomical structure cell junction membrane intracellular anatomical structure intracellular membraneless organelle Z disc sarcomere intracellular organelle I band organelle membraneless organelle contractile muscle fiber cytoplasm supramolecular fiber cellular anatomical structure cell junction membrane intracellular anatomical structure intracellular membraneless organelle Z disc sarcomere intracellular organelle I band organelle membraneless organelle contractile muscle fiber cytoplasm supramolecular fiber myofibril supramolecular polymer supramolecular complex axon cell projection main axon neuron projection node of Ranvier plasma membrane bounded cell projection podosome cytoskeleton actin cytoskeleton anchoring junction cell periphery plasma membrane axon initial segment membrane-bounded organelle cytoplasmic vesicle intracellular vesicle intracellular membrane-bounded organelle vesicle protein-containing complex sodium channel complex voltage-gated sodium channel complex plasma membrane protein complex membrane protein complex cation channel complex transporter complex transmembrane transporter complex monoatomic ion channel complex
A [auth D]	Sodium channel subunit beta-1	molecular function inhibitor activity sodium channel inhibitor activity channel regulator activity transporter inhibitor activity ion channel regulator activity ion channel inhibitor activity molecular function regulator activity sodium channel regulator activity transporter regulator activity channel inhibitor activity protein binding binding transmembrane transporter binding	membrane depolarization during action potential membrane depolarization biological regulation membrane depolarization during cardiac muscle cell action potential action potential regulation of biological quality cardiac muscle cell action potential regulation of membrane potential heart process cardiac muscle cell contraction multicellular organismal process system process cardiac muscle cell action potential involved in contraction actin filament-based movement membrane depolarization during action potential membrane depolarization biological regulation membrane depolarization during cardiac muscle cell action potential action potential regulation of biological quality cardiac muscle cell action potential regulation of membrane potential heart process cardiac muscle cell contraction multicellular organismal process system process cardiac muscle cell action potential involved in contraction actin filament-based movement cardiac muscle contraction muscle contraction muscle system process striated muscle contraction circulatory system process actin filament-based process cellular process actin-mediated cell contraction heart contraction blood circulation regulation of biological process regulation of cellular process regulation of membrane depolarization regulation of atrial cardiac muscle cell membrane depolarization cardiac muscle cell membrane repolarization membrane repolarization regulation of membrane repolarization ventricular cardiac muscle cell membrane repolarization regulation of cardiac muscle cell membrane repolarization regulation of ventricular cardiac muscle cell membrane repolarization 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 corticospinal neuron axon guidance system development developmental process central nervous system projection neuron axonogenesis central nervous system neuron axonogenesis plasma membrane bounded cell projection organization axon guidance nervous system development axon development cell morphogenesis involved in neuron differentiation generation of neurons anatomical structure morphogenesis central nervous system development neuron projection guidance neuron development corticospinal tract morphogenesis transport monoatomic ion transmembrane transport sodium ion transmembrane transport establishment of localization metal ion transport monoatomic cation transmembrane transport transmembrane transport localization monoatomic ion transport monoatomic cation transport sodium ion transport regulation of neuron projection development regulation of cellular component organization positive regulation of cellular component organization positive regulation of biological process positive regulation of neuron projection development positive regulation of cell projection organization positive regulation of cellular process regulation of cell projection organization regulation of plasma membrane bounded cell projection organization regulation of localization regulation of monoatomic ion transmembrane transport regulation of sodium ion transport regulation of sodium ion transmembrane transport regulation of metal ion transport regulation of transport regulation of monoatomic ion transport regulation of transmembrane transport regulation of monoatomic cation transmembrane transport locomotion positive regulation of cation transmembrane transport positive regulation of sodium ion transmembrane transporter activity regulation of transmembrane transporter activity positive regulation of sodium ion transport positive regulation of molecular function regulation of sodium ion transmembrane transporter activity positive regulation of monoatomic ion transport positive regulation of transmembrane transport positive regulation of sodium ion transmembrane transport positive regulation of monoatomic ion transmembrane transport regulation of voltage-gated sodium channel activity positive regulation of cation channel activity regulation of molecular function positive regulation of transport positive regulation of transporter activity positive regulation of ion transmembrane transporter activity positive regulation of voltage-gated sodium channel activity regulation of heart contraction regulation of system process regulation of blood circulation cardiac conduction regulation of multicellular organismal process cell adhesion Purkinje myocyte to ventricular cardiac muscle cell communication membrane depolarization during Purkinje myocyte cell action potential signaling cell-cell signaling involved in cardiac conduction cell communication Purkinje myocyte action potential cell communication involved in cardiac conduction cell-cell signaling Purkinje myocyte to ventricular cardiac muscle cell signaling nervous system process action potential propagation transmission of nerve impulse neuronal action potential propagation regulation of heart rate by cardiac conduction regulation of heart rate	cell periphery cellular anatomical structure sarcolemma plasma membrane membrane T-tubule somatodendritic compartment cell body perikaryon neuronal cell body axon cell projection main axon neuron projection cell periphery cellular anatomical structure sarcolemma plasma membrane membrane T-tubule somatodendritic compartment cell body perikaryon neuronal cell body axon cell projection main axon neuron projection node of Ranvier plasma membrane bounded cell projection extracellular region protein-containing complex sodium channel complex voltage-gated sodium channel complex plasma membrane protein complex membrane protein complex cation channel complex transporter complex transmembrane transporter complex monoatomic ion channel complex cell-cell junction intercalated disc anchoring junction cell junction cell-cell contact zone

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
C	IPR000920	Myelin P0 protein-related	Family
C	IPR013106	Immunoglobulin V-set domain	Domain
C	IPR003599	Immunoglobulin domain subtype	Domain
C	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
C	IPR007110	Immunoglobulin-like domain	Domain
B	IPR024583	Voltage-gated Na+ ion channel, cytoplasmic domain	Domain
B	IPR001696	Voltage gated sodium channel, alpha subunit	Family
B	IPR000048	IQ motif, EF-hand binding site	Binding Site
B	IPR010526	Sodium ion transport-associated domain	Domain
B	IPR005821	Ion transport domain	Domain
B	IPR008054	Voltage gated sodium channel, alpha-8 subunit	Family
B	IPR044564	Voltage-gated sodium channel alpha subunit, inactivation gate	Domain
B	IPR043203	Voltage-gated cation channel calcium and sodium	Family
B	IPR027359	Voltage-dependent channel domain superfamily	Homologous Superfamily
A [auth D]	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
A [auth D]	IPR013106	Immunoglobulin V-set domain	Domain
A [auth D]	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
A [auth D]	IPR027098	Sodium channel subunit beta-1/beta-3	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
C	Pharos: O60939	Brugada syndrome familial atrial fibrillation atrial fibrillation, familial, 14 lung adenocarcinoma pituitary cancer astrocytic tumor glioblastoma lung carcinoma medulloblastoma Pick disease primitive neuroectodermal tumor atrial fibrillation atypical teratoid rhabdoid tumor Epileptic encephalopathy large cell medulloblastoma Brugada syndrome familial atrial fibrillation atrial fibrillation, familial, 14 lung adenocarcinoma pituitary cancer astrocytic tumor glioblastoma lung carcinoma medulloblastoma Pick disease primitive neuroectodermal tumor atrial fibrillation atypical teratoid rhabdoid tumor Epileptic encephalopathy large cell medulloblastoma malignant ependymoma non-small cell lung carcinoma pilocytic astrocytoma subependymal giant cell astrocytoma atrial fibrillation, familial, 1 breast cancer malignant glioma oligodendroglioma
B	Pharos: Q9UQD0	epilepsy developmental and epileptic encephalopathy, 13 cognitive impairment with or without cerebellar ataxia status epilepticus cerebellar ataxia seizures, benign familial infantile, 5 intellectual disability nervous system disorder Tremor infantile convulsions and choreoathetosis Lennox-Gastaut syndrome primitive neuroectodermal tumor malignant mesothelioma developmental and epileptic encephalopathy astrocytic tumor epilepsy developmental and epileptic encephalopathy, 13 cognitive impairment with or without cerebellar ataxia status epilepticus cerebellar ataxia seizures, benign familial infantile, 5 intellectual disability nervous system disorder Tremor infantile convulsions and choreoathetosis Lennox-Gastaut syndrome primitive neuroectodermal tumor malignant mesothelioma developmental and epileptic encephalopathy astrocytic tumor subependymal giant cell astrocytoma pancreatic ductal adenocarcinoma bipolar disorder malignant ependymoma glioblastoma oligodendroglioma tinea pedis Herpesviridae infectious disease pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia atypical teratoid rhabdoid tumor pilocytic astrocytoma psoriasis lung carcinoma malignant glioma medulloblastoma epilepsy with generalized tonic-clonic seizures tinea corporis partial epilepsy benign familial infantile epilepsy large cell medulloblastoma postherpetic neuralgia
A [auth D]	Pharos: Q07699	Brugada syndrome Sudden infant death syndrome Brugada syndrome 5 familial atrial fibrillation generalized epilepsy with febrile seizures plus, type 1 atrial fibrillation, familial, 13 developmental and epileptic encephalopathy, 52 epilepsy generalized epilepsy with febrile seizures plus intellectual disability atrial fibrillation autosomal dominant cardiac arrhythmia (Kuhn) developmental and epileptic encephalopathy, 6 progressive familial heart block atrial fibrillation, familial, 1 Brugada syndrome Sudden infant death syndrome Brugada syndrome 5 familial atrial fibrillation generalized epilepsy with febrile seizures plus, type 1 atrial fibrillation, familial, 13 developmental and epileptic encephalopathy, 52 epilepsy generalized epilepsy with febrile seizures plus intellectual disability atrial fibrillation autosomal dominant cardiac arrhythmia (Kuhn) developmental and epileptic encephalopathy, 6 progressive familial heart block atrial fibrillation, familial, 1 dilated cardiomyopathy Hodgkins lymphoma progressive familial heart block, type 1A Dravet syndrome

Membrane Protein Annotation: OPM OPM Database Homepage

Chains	External Link	Type	Class	Superfamily	Family
A [auth D], B, C	OPM	Transmembrane	Alpha-helical polytopic	Ion channel (VIC) superfamily	Voltage-gated calcium and sodium channels

Membrane Protein Annotation: PDBTM PDBTM Database Homepage

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

Membrane Protein Annotation: MemProtMD MemProtMD Database Homepage

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

Membrane Protein Annotation: mpstruc mpstruc Database Homepage

Chains	Resource Link	Group	Subgroup	Protein
A [auth D], B, C	mpstruc	TRANSMEMBRANE PROTEINS: ALPHA-HELICAL	Channels: Potassium, Sodium, & Proton Ion-Selective	Na_V1.6 with β1 and β2 subunits, apo state

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.