Annotations: 25IJ

Cryo-EM structure of human Nav1.6 in complex with delta-paraponeritoxin-Pc1a

External Resource: Annotation

Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Protein Modification Annotation

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
A	PF00520	Ion transport protein (Ion_trans)	Ion transport protein	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C	Sodium channel regulatory 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 animal gross anatomical part developmental process 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 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
B	Delta-paraponeritoxin-Pc1a	channel regulator activity ion channel regulator activity molecular function regulator activity sodium channel regulator activity transporter regulator activity toxin activity	-	host cellular component cellular anatomical structure host cell part host cell synapse host cell membrane host cell presynaptic membrane other organism part extracellular region host cell postsynaptic membrane
A	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 membrane depolarization during action potential membrane depolarization 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 animal gross anatomical part developmental process system development myelination axon ensheathment ensheathment of neurons	cellular anatomical structure membrane intracellular anatomical structure intracellular membraneless organelle Z disc sarcomere intracellular organelle I band organelle membraneless organelle contractile muscle fiber cytoplasm supramolecular fiber myofibril cellular anatomical structure 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 actin cytoskeleton podosome actin-based cell projection cytoskeleton 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

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
C	IPR013106	Immunoglobulin V-set domain	Domain
C	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
C	IPR027098	Sodium channel subunit beta-1/beta-3	Family
A	IPR024583	Voltage-gated Na+ ion channel, cytoplasmic domain	Domain
A	IPR001696	Voltage gated sodium channel, alpha subunit	Family
A	IPR058542	SCN5A-like, C-terminal IQ motif	Domain
A	IPR000048	IQ motif, EF-hand binding site	Binding Site
A	IPR010526	Sodium ion transport-associated domain	Domain
A	IPR005821	Ion transport domain	Domain
A	IPR008054	Voltage gated sodium channel, alpha-8 subunit	Family
A	IPR044564	Voltage-gated sodium channel alpha subunit, inactivation gate	Domain
A	IPR043203	Voltage-gated cation channel calcium and sodium	Family
A	IPR027359	Voltage-dependent channel domain superfamily	Homologous Superfamily

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
B	NH2	: AA0081 , AA0083 , AA0084 , AA0086 , AA0087 , AA0088 , AA0090 , AA0091 , AA0092 , AA0093 , AA0095 , AA0096 , AA0097 , AA0098 , AA0099 , AA0100 : L-alanine amide MOD:00090 , L-asparagine amide MOD:00092 , L-aspartic acid 1-amide MOD:00093 , L-glutamine amide MOD:00095 , L-glutamic acid 1-amide MOD:00096 , glycine amide MOD:00097 , L-isoleucine amide MOD:00099 , L-leucine amide MOD:00100 , L-lysine amide MOD:00101 , L-methionine amide MOD:00102 , L-proline amide MOD:00104 , L-serine amide MOD:00105 , L-threonine amide MOD:00106 , L-tryptophan amide MOD:00107 , L-tyrosine amide MOD:00108 , L-valine amide MOD:00109

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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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.

25IJ | pdb_000025ij

Cryo-EM structure of human Nav1.6 in complex with delta-paraponeritoxin-Pc1a

External Resource: Annotation

Protein Family Annotation Pfam Database Homepage

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

InterPro: Protein Family Classification InterPro Database Homepage

Protein Modification Annotation