3J5Q

Structure of TRPV1 ion channel in complex with DkTx and RTX determined by single particle electron cryo-microscopy

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Membrane Protein Annotation: OPM
Membrane Protein Annotation: PDBTM
Membrane Protein Annotation: MemProtMD
Membrane Protein Annotation: mpstruc

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
E [auth A]	SCOP2B Superfamily	omega toxin-like	8082259	3000255	SCOP2B (2022-06-29)
F [auth C]	SCOP2B Superfamily	omega toxin-like	8082259	3000255	SCOP2B (2022-06-29)
G [auth F]	SCOP2B Superfamily	omega toxin-like	8082259	3000255	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	omega toxin-like	8082259	3000255	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A [auth D]	PF12796	e3j5qD1	A: alpha superhelices	X: Repetitive alpha hairpins	H: Ankyrin repeat (From Topology)	T: Ankyrin repeat	F: PF12796	ECOD (1.6)
A [auth D]	PF00520	e3j5qD2	A: alpha complex topology	X: Voltage-gated ion channels (From Topology)	H: Voltage-gated ion channels (From Topology)	T: Voltage-gated ion channels	F: PF00520	ECOD (1.6)
B	PF12796	e3j5qB1	A: alpha superhelices	X: Repetitive alpha hairpins	H: Ankyrin repeat (From Topology)	T: Ankyrin repeat	F: PF12796	ECOD (1.6)
B	PF00520	e3j5qB2	A: alpha complex topology	X: Voltage-gated ion channels (From Topology)	H: Voltage-gated ion channels (From Topology)	T: Voltage-gated ion channels	F: PF00520	ECOD (1.6)
D [auth G]	PF12796	e3j5qG1	A: alpha superhelices	X: Repetitive alpha hairpins	H: Ankyrin repeat (From Topology)	T: Ankyrin repeat	F: PF12796	ECOD (1.6)
D [auth G]	PF00520	e3j5qG2	A: alpha complex topology	X: Voltage-gated ion channels (From Topology)	H: Voltage-gated ion channels (From Topology)	T: Voltage-gated ion channels	F: PF00520	ECOD (1.6)
C [auth E]	PF12796	e3j5qE1	A: alpha superhelices	X: Repetitive alpha hairpins	H: Ankyrin repeat (From Topology)	T: Ankyrin repeat	F: PF12796	ECOD (1.6)
C [auth E]	PF00520	e3j5qE2	A: alpha complex topology	X: Voltage-gated ion channels (From Topology)	H: Voltage-gated ion channels (From Topology)	T: Voltage-gated ion channels	F: PF00520	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A [auth D]	1.25.40.20	Mainly Alpha	Alpha Horseshoe	Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat	Ankyrin repeat-containing domain	CATH (4.3.0)
B	1.25.40.20	Mainly Alpha	Alpha Horseshoe	Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat	Ankyrin repeat-containing domain	CATH (4.3.0)
D [auth G]	1.25.40.20	Mainly Alpha	Alpha Horseshoe	Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat	Ankyrin repeat-containing domain	CATH (4.3.0)
C [auth E]	1.25.40.20	Mainly Alpha	Alpha Horseshoe	Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat	Ankyrin repeat-containing domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
E [auth A], F [auth C], G [auth F], H	PF07740	Ion channel inhibitory toxin (Toxin_12)	Ion channel inhibitory toxin	This is a family of potent toxins that function as ion-channel inhibitors for several different ions. Omega-Grammotoxin SIA is a VSCC antagonist that inhibits neuronal N- and P-type VSCC responses [1]. Huwentoxin-IV, from the Chinese bird spider, is ...	This is a family of potent toxins that function as ion-channel inhibitors for several different ions. Omega-Grammotoxin SIA is a VSCC antagonist that inhibits neuronal N- and P-type VSCC responses [1]. Huwentoxin-IV, from the Chinese bird spider, is a highly potent neurotoxin that specifically inhibits the neuronal tetrodotoxin-sensitive voltage-gated sodium channel in rat dorsal root ganglion neurons [2]. Hainantoxin-4, from the venom of spider Selenocosmia hainana, adopts an inhibitor cystine knot structural motif like huwentoin-IV, and is a potent antagonist that acts at site 1 on tetrodotoxin-sensitive (TTX-S) sodium channels [3]. Study of the molecular nature of toxin-receptor interactions has helped elucidate the functioning of many ion-channels [4].	Domain
A [auth D], B, C [auth E], D [auth G]	PF00023	Ankyrin repeat (Ank)	Ankyrin repeat	-	Repeat
A [auth D], B, C [auth E], D [auth G]	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
E [auth A], F [auth C], G [auth F], H	Kappa-theraphotoxin-Cg1a 1	molecular function inhibitor activity channel regulator activity transporter inhibitor activity ion channel inhibitor activity ion channel regulator activity molecular function regulator activity transporter regulator activity channel inhibitor activity potassium channel regulator activity sodium channel regulator activity toxin activity	-	extracellular region cellular anatomical entity
A [auth D], B, C [auth E], D [auth G]	Transient receptor potential cation channel subfamily V member 1	binding phospholipid binding lipid binding phosphatidylinositol 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 monoatomic cation transmembrane transporter activity binding phospholipid binding lipid binding phosphatidylinositol 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 monoatomic cation transmembrane transporter activity monoatomic cation channel activity phosphoprotein binding protein binding temperature-gated ion channel activity adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding excitatory extracellular ligand-gated monoatomic ion channel activity extracellular ligand-gated monoatomic ion channel activity channel regulator activity ion channel regulator activity molecular function regulator activity transporter regulator activity chloride channel regulator activity calmodulin binding calcium channel activity calcium ion transmembrane transporter activity inorganic molecular entity transmembrane transporter activity inorganic cation transmembrane transporter activity metal ion transmembrane transporter activity cation binding metal ion binding identical protein binding molecular transducer activity transmembrane signaling receptor activity signaling receptor activity intracellularly ligand-gated monoatomic ion channel activity intracellularly gated calcium channel activity ligand-gated calcium channel activity ligand-gated monoatomic cation channel activity	regulation of biosynthetic process regulation of nitric oxide biosynthetic process regulation of biological process biological regulation positive regulation of biological process reactive nitrogen species metabolic process positive regulation of nitric oxide metabolic process nitric oxide metabolic process positive regulation of metabolic process nitric oxide biosynthetic process biosynthetic process positive regulation of biosynthetic process metabolic process regulation of nitric oxide metabolic process regulation of biosynthetic process regulation of nitric oxide biosynthetic process regulation of biological process biological regulation positive regulation of biological process reactive nitrogen species metabolic process positive regulation of nitric oxide metabolic process nitric oxide metabolic process positive regulation of metabolic process nitric oxide biosynthetic process biosynthetic process positive regulation of biosynthetic process metabolic process regulation of nitric oxide metabolic process positive regulation of nitric oxide biosynthetic process regulation of metabolic process multicellular organismal process response to nutrient levels multicellular organismal-level homeostasis response to stimulus response to dietary excess homeostatic process diet induced thermogenesis energy homeostasis adaptive thermogenesis negative regulation of membrane potential regulation of mitochondrial membrane potential negative regulation of mitochondrial membrane potential regulation of biological quality regulation of membrane potential cellular response to stimulus cellular response to heat cellular response to stress response to stress response to heat response to abiotic stimulus cellular process response to temperature stimulus system process thermoception sensory perception nervous system process sensory perception of temperature stimulus detection of stimulus involved in sensory perception of pain sensory perception of pain detection of stimulus sensory perception of chemical stimulus response to chemical detection of chemical stimulus detection of chemical stimulus involved in sensory perception of pain detection of stimulus involved in sensory perception detection of chemical stimulus involved in sensory perception positive regulation of programmed cell death regulation of cellular process regulation of apoptotic process regulation of programmed cell death cell death positive regulation of apoptotic process apoptotic process programmed cell death positive regulation of cellular process cellular response to nitrogen compound response to organic substance response to organonitrogen compound response to endogenous stimulus response to nitrogen compound response to alkaloid cellular response to endogenous stimulus cellular response to chemical stimulus cellular response to organonitrogen compound cellular response to organic substance cellular response to alkaloid cellular response to growth factor stimulus cellular response to nerve growth factor stimulus response to nerve growth factor response to growth factor excretion micturition renal system process smooth muscle contraction involved in micturition urinary bladder smooth muscle contraction muscle contraction muscle system process smooth muscle contraction urinary tract smooth muscle contraction behavior multicellular organismal response to stress response to pain behavioral response to pain transport monoatomic ion transmembrane transport inorganic ion transmembrane transport establishment of localization calcium ion transport metal ion transport inorganic cation transmembrane transport transmembrane transport monoatomic cation transmembrane transport localization monoatomic ion transport monoatomic cation transport calcium ion transmembrane transport peptide transport peptide secretion nitrogen compound transport secretion amide transport organic substance transport detection of external stimulus response to external stimulus detection of temperature stimulus involved in sensory perception detection of abiotic stimulus detection of temperature stimulus detection of temperature stimulus involved in sensory perception of pain cellular response to ATP response to organophosphorus cellular response to organic cyclic compound response to oxygen-containing compound response to ATP response to purine-containing compound cellular response to oxygen-containing compound response to organic cyclic compound negative regulation of biological process negative regulation of cellular metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription regulation of RNA metabolic process transcription by RNA polymerase II organic substance biosynthetic process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process regulation of transcription by RNA polymerase II negative regulation of DNA-templated transcription negative regulation of transcription by RNA polymerase II cellular metabolic process negative regulation of metabolic process primary metabolic process regulation of cellular metabolic process negative regulation of cellular biosynthetic process organic cyclic compound metabolic process regulation of gene expression negative regulation of macromolecule biosynthetic process organic cyclic compound biosynthetic process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of DNA-templated transcription negative regulation of RNA metabolic process cellular biosynthetic process RNA metabolic process RNA biosynthetic process nucleic acid biosynthetic process organic substance metabolic process negative regulation of cellular process regulation of RNA biosynthetic process negative regulation of macromolecule metabolic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of cellular biosynthetic process negative regulation of biosynthetic process detection of temperature stimulus involved in thermoception defense response cell activation myeloid leukocyte activation leukocyte activation macrophage activation immune system process leukocyte activation involved in inflammatory response microglial cell activation inflammatory response glial cell activation neuroinflammatory response cellular response to temperature stimulus positive regulation of cytosolic calcium ion concentration response to hormone response to peptide hormone organic anion transport carboxylic acid transport export from cell organic acid transport amino acid transport acidic amino acid transport secretion by cell dicarboxylic acid transport glutamate secretion protein-containing complex organization protein homotetramerization cellular component organization cellular component biogenesis cellular component assembly protein complex oligomerization protein tetramerization protein-containing complex assembly protein homooligomerization cellular component organization or biogenesis response to pH cellular response to pH cellular response to acidic pH cellular response to abiotic stimulus response to acidic pH cellular response to environmental stimulus lipid metabolic process fever generation acute-phase response heat generation temperature homeostasis acute inflammatory response regulation of developmental process cellular developmental process regulation of establishment of blood-brain barrier cell development regulation of cell differentiation regulation of cell development multicellular organism development cell differentiation anatomical structure development negative regulation of cell differentiation system development developmental process establishment of blood-brain barrier negative regulation of developmental process nervous system development negative regulation of cell development central nervous system development negative regulation of establishment of blood-brain barrier import into cell calcium ion transmembrane import into cytosol import across plasma membrane inorganic cation import across plasma membrane calcium ion import across plasma membrane inorganic ion import across plasma membrane calcium ion import calcium ion import into cytosol response to cytokine cellular response to tumor necrosis factor cellular response to cytokine stimulus response to tumor necrosis factor regulation of systemic arterial blood pressure circulatory system process regulation of blood pressure negative regulation of systemic arterial blood pressure blood circulation negative regulation of blood pressure sensory perception of mechanical stimulus heart process negative regulation of heart rate regulation of heart contraction regulation of system process negative regulation of blood circulation negative regulation of heart contraction regulation of blood circulation regulation of multicellular organismal process heart contraction negative regulation of multicellular organismal process regulation of heart rate response to capsazepine	cell periphery postsynapse postsynaptic membrane synapse cell junction membrane plasma membrane plasma membrane region cellular anatomical entity synaptic membrane cell surface external side of plasma membrane side of membrane somatodendritic compartment cell periphery postsynapse postsynaptic membrane synapse cell junction membrane plasma membrane plasma membrane region cellular anatomical entity 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 dendritic spine neuron projection membrane dendrite membrane cell leading edge neuron spine leading edge membrane dendritic spine membrane cell projection membrane cell body neuronal cell body

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
E [auth A], F [auth C], G [auth F], H	IPR011696	Huwentoxin-1 family	Family
A [auth D], B, C [auth E], D [auth G]	IPR002110	Ankyrin repeat	Repeat
A [auth D], B, C [auth E], D [auth G]	IPR024862	Transient receptor potential cation channel subfamily V	Family
A [auth D], B, C [auth E], D [auth G]	IPR008347	Transient receptor potential cation channel subfamily V member 1-4	Family
A [auth D], B, C [auth E], D [auth G]	IPR036770	Ankyrin repeat-containing domain superfamily	Homologous Superfamily
A [auth D], B, C [auth E], D [auth G]	IPR005821	Ion transport domain	Domain

Membrane Protein Annotation: OPM OPM Database Homepage

Chains	External Link	Type	Class	Superfamily	Family
A [auth D], B, C [auth E], D [auth G], E [auth A] A [auth D], B, C [auth E], D [auth G], E [auth A], F [auth C], G [auth F], H	OPM	Transmembrane	Alpha-helical polytopic	Ion channel (VIC) superfamily	Transient receptor potential channels

Membrane Protein Annotation: PDBTM PDBTM Database Homepage

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

Membrane Protein Annotation: MemProtMD MemProtMD Database Homepage

Chains	External Link	Comment
A [auth D], B, C [auth E], D [auth G], E [auth A] A [auth D], B, C [auth E], D [auth G], E [auth A], F [auth C], G [auth F], H	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 [auth E], D [auth G], E [auth A] A [auth D], B, C [auth E], D [auth G], E [auth A], F [auth C], G [auth F], H	mpstruc	TRANSMEMBRANE PROTEINS: ALPHA-HELICAL	Channels: Transient Receptor Potential (TRP)	TRPV1 transient receptor potential channel in complex with vanilloid agonist RTX

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 R01GM133198.