6BCJ | pdb_00006bcj

cryo-EM structure of TRPM4 in apo state with short coiled coil at 3.1 angstrom resolution

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Membrane Protein Annotation: PDBTM
Membrane Protein Annotation: MemProtMD
Membrane Protein Annotation: mpstruc

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
D	d6bcjd1	Alpha and beta proteins (a/b)	MCP/YpsA-like	MCP/YpsA-like	SMF/DprA-LOG (SLOG) domain from TPRM channels	Calcium-activated non-selective cation channel TRPM4	Mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
D	d6bcjd2	Membrane and cell surface proteins and peptides	Gated ion channels	Voltage-gated ion channels	TRPM-like (melastatin-like transient receptor potential) channels	Calcium-activated non-selective cation channel TRPM4	Mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
C	d6bcjc1	Alpha and beta proteins (a/b)	MCP/YpsA-like	MCP/YpsA-like	SMF/DprA-LOG (SLOG) domain from TPRM channels	Calcium-activated non-selective cation channel TRPM4	Mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
C	d6bcjc2	Membrane and cell surface proteins and peptides	Gated ion channels	Voltage-gated ion channels	TRPM-like (melastatin-like transient receptor potential) channels	Calcium-activated non-selective cation channel TRPM4	Mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
B [auth A]	d6bcja1	Alpha and beta proteins (a/b)	MCP/YpsA-like	MCP/YpsA-like	SMF/DprA-LOG (SLOG) domain from TPRM channels	Calcium-activated non-selective cation channel TRPM4	Mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
B [auth A]	d6bcja2	Membrane and cell surface proteins and peptides	Gated ion channels	Voltage-gated ion channels	TRPM-like (melastatin-like transient receptor potential) channels	Calcium-activated non-selective cation channel TRPM4	Mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
A [auth B]	d6bcjb1	Alpha and beta proteins (a/b)	MCP/YpsA-like	MCP/YpsA-like	SMF/DprA-LOG (SLOG) domain from TPRM channels	Calcium-activated non-selective cation channel TRPM4	Mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
A [auth B]	d6bcjb2	Membrane and cell surface proteins and peptides	Gated ion channels	Voltage-gated ion channels	TRPM-like (melastatin-like transient receptor potential) channels	Calcium-activated non-selective cation channel TRPM4	Mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A [auth B], B [auth A], C, D	PF18139	SLOG in TRPM (LSDAT_euk)	SLOG in TRPM	Family in the SLOG superfamily, found in several eukaryotic channels including diverse ciliate channels and the TRPM class of animal ion channels. Positioned near the N-terminus of all TRPM channels, it is predicted to play a regulatory role for the ...	Family in the SLOG superfamily, found in several eukaryotic channels including diverse ciliate channels and the TRPM class of animal ion channels. Positioned near the N-terminus of all TRPM channels, it is predicted to play a regulatory role for the channel in potentially recognizing a universal nucleotide or nucleotide-derived ligand [1].	Domain
A [auth B], B [auth A], C, D	PF25508	TRPM2-like domain (TRPM2)	TRPM2-like domain	This domain is found in human Transient receptor potential cation channel subfamily M member 2 (TRPM2) and similar proteins. TRPM2 is a nonselective, voltage-independent cation channel that mediates Na+ and Ca2+ influx, leading to increased cytoplasm ...	This domain is found in human Transient receptor potential cation channel subfamily M member 2 (TRPM2) and similar proteins. TRPM2 is a nonselective, voltage-independent cation channel that mediates Na+ and Ca2+ influx, leading to increased cytoplasmic Ca2+ levels. It plays a role in mediating behavioural and physiological responses to moderate heat, insulin secretion, dendritic cell differentiation and maturation and the the regulation of the reorganisation of the actin cytoskeleton and filopodia formation. This domain is found associated with Pfam:PF00520 and adopts an all-alpha configuration.	Domain
A [auth B], B [auth A], C, D	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
A [auth B], B [auth A], C, D	Transient receptor potential cation channel subfamily M member 4	binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding protein binding calmodulin binding passive transmembrane transporter activity gated channel activity monoatomic ion channel activity channel activity voltage-gated channel activity voltage-gated monoatomic ion channel activity monoatomic ion transmembrane transporter activity transporter activity transmembrane transporter activity calcium channel activity monoatomic cation transmembrane transporter activity monoatomic cation channel activity calcium ion transmembrane transporter activity metal ion transmembrane transporter activity identical protein binding cation binding calcium ion binding metal ion binding calcium-activated cation channel activity monoatomic ion-gated channel activity ligand-gated channel activity ligand-gated monoatomic ion channel activity ligand-gated monoatomic cation channel activity	heart process multicellular organismal process system process regulation of biological process regulation of heart contraction regulation of system process biological regulation positive regulation of biological process positive regulation of heart rate positive regulation of blood circulation positive regulation of heart contraction circulatory system process regulation of blood circulation positive regulation of multicellular organismal process heart process multicellular organismal process system process regulation of biological process regulation of heart contraction regulation of system process biological regulation positive regulation of biological process positive regulation of heart rate positive regulation of blood circulation positive regulation of heart contraction circulatory system process regulation of blood circulation positive regulation of multicellular organismal process regulation of multicellular organismal process regulation of biological quality heart contraction blood circulation regulation of heart rate response to stimulus immune response immune system process adaptive immune response regulation of tube diameter regulation of tube size positive regulation of vasoconstriction vascular process in circulatory system regulation of vasoconstriction blood vessel diameter maintenance vasoconstriction regulation of anatomical structure size peptidyl-lysine modification primary metabolic process protein sumoylation macromolecule modification peptidyl-amino acid modification metabolic process cellular process protein metabolic process macromolecule metabolic process protein modification process post-translational protein modification protein modification by small protein conjugation protein modification by small protein conjugation or removal regulation of actin filament-based process regulation of cellular process cardiac muscle cell action potential involved in contraction regulation of ventricular cardiac muscle cell action potential cardiac muscle contraction striated muscle contraction regulation of cardiac muscle cell action potential actin filament-based process cardiac muscle cell contraction regulation of action potential ventricular cardiac muscle cell action potential regulation of cardiac muscle contraction action potential actin filament-based movement muscle contraction muscle system process regulation of muscle system process regulation of striated muscle contraction regulation of actin filament-based movement regulation of muscle contraction regulation of cardiac muscle cell contraction actin-mediated cell contraction cardiac muscle cell action potential regulation of membrane potential cell chemotaxis cellular response to stimulus chemotaxis dendritic cell chemotaxis response to external stimulus leukocyte migration dendritic cell migration cellular response to chemical stimulus taxis response to chemical mononuclear cell migration cell migration cell motility leukocyte chemotaxis locomotion Purkinje myocyte to ventricular cardiac muscle cell communication membrane depolarization during Purkinje myocyte cell action potential signaling membrane depolarization during cardiac muscle cell action potential cell communication Purkinje myocyte action potential cell communication involved in cardiac conduction membrane depolarization during action potential cell-cell signaling Purkinje myocyte to ventricular cardiac muscle cell signaling membrane depolarization cardiac conduction monoatomic cation transmembrane transport transmembrane transport localization transport monoatomic ion transmembrane transport monoatomic ion transport monoatomic cation transport establishment of localization adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains lymphocyte mediated immunity regulation of immune effector process T cell mediated immunity T cell cytokine production regulation of T cell cytokine production regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains cytokine production regulation of cytokine production leukocyte mediated immunity regulation of immune system process cytokine production involved in immune response regulation of T cell mediated immunity production of molecular mediator of immune response regulation of biosynthetic process regulation of cytokine production involved in immune response regulation of adaptive immune response regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process immune effector process regulation of gene expression regulation of leukocyte mediated immunity biosynthetic process regulation of lymphocyte mediated immunity regulation of response to stimulus regulation of immune response regulation of macromolecule biosynthetic process regulation of production of molecular mediator of immune response regulation of metabolic process cellular response to nitrogen compound cellular response to ATP response to organophosphorus response to oxygen-containing compound response to nitrogen compound response to ATP response to purine-containing compound cellular response to oxygen-containing compound developmental process fat cell differentiation positive regulation of fat cell differentiation regulation of developmental process cellular developmental process regulation of cell differentiation positive regulation of developmental process positive regulation of cell differentiation cell differentiation regulation of fat cell differentiation positive regulation of cellular process positive regulation of membrane depolarization regulation of membrane depolarization regulation of vascular associated smooth muscle cell membrane depolarization positive regulation of regulation of vascular associated smooth muscle cell membrane depolarization regulation of heart rate by cardiac conduction positive regulation of cytosolic calcium ion concentration AV node cell action potential membrane depolarization during AV node cell action potential AV node cell to bundle of His cell signaling AV node cell to bundle of His cell communication connective tissue development adipose tissue development positive regulation of adipose tissue development animal organ development tissue development regulation of adipose tissue development anatomical structure development regulation of osteoblast differentiation negative regulation of osteoblast differentiation negative regulation of developmental process negative regulation of biological process osteoblast differentiation ossification negative regulation of cellular process negative regulation of cell differentiation 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 intracellular signal transduction calcium-mediated signaling intracellular signaling cassette signal transduction behavior learning or memory long-term memory nervous system process cognition memory cell population proliferation positive regulation of cell population proliferation regulation of cell population proliferation positive regulation of atrial cardiac muscle cell action potential regulation of atrial cardiac muscle cell action potential regulation of cardiac conduction atrial cardiac muscle cell to AV node cell signaling atrial cardiac muscle cell to AV node cell communication atrial cardiac muscle cell action potential positive regulation of action potential import into cell import across plasma membrane sodium ion import across plasma membrane sodium ion transmembrane transport inorganic cation import across plasma membrane metal ion transport inorganic ion import across plasma membrane sodium ion transport positive regulation of cell communication regulation of localization establishment of protein localization nitrogen compound transport positive regulation of establishment of protein localization carbohydrate homeostasis establishment of localization in cell positive regulation of insulin secretion involved in cellular response to glucose stimulus positive regulation of insulin secretion intracellular protein localization regulation of peptide hormone secretion regulation of hormone levels positive regulation of peptide hormone secretion establishment of protein localization to extracellular region intracellular glucose homeostasis protein secretion regulation of protein secretion regulation of secretion cellular response to carbohydrate stimulus chemical homeostasis response to glucose glucose homeostasis positive regulation of protein localization insulin secretion involved in cellular response to glucose stimulus cellular localization regulation of hormone secretion regulation of protein localization regulation of peptide secretion homeostatic process positive regulation of secretion by cell hormone secretion protein localization to extracellular region positive regulation of protein transport peptide secretion regulation of secretion by cell secretion by cell positive regulation of hormone secretion response to monosaccharide response to carbohydrate positive regulation of secretion signal release cellular response to hexose stimulus intracellular chemical homeostasis cellular response to monosaccharide stimulus positive regulation of peptide secretion regulation of signaling regulation of transport secretion regulation of peptide transport regulation of establishment of protein localization export from cell cellular response to glucose stimulus regulation of protein transport positive regulation of protein secretion peptide transport response to hexose cellular homeostasis positive regulation of transport regulation of cellular localization protein transport regulation of insulin secretion peptide hormone secretion macromolecule localization regulation of insulin secretion involved in cellular response to glucose stimulus hormone transport regulation of cell communication insulin secretion positive regulation of signaling calcium ion transport bundle of His cell to Purkinje myocyte signaling bundle of His cell to Purkinje myocyte communication bundle of His cell action potential membrane depolarization during bundle of His cell action potential positive regulation of signal transduction regulation of canonical Wnt signaling pathway canonical Wnt signaling pathway regulation of signal transduction positive regulation of response to stimulus positive regulation of Wnt signaling pathway Wnt signaling pathway positive regulation of canonical Wnt signaling pathway cell surface receptor signaling pathway regulation of Wnt signaling pathway negative regulation of biomineral tissue development regulation of biomineral tissue development regulation of bone mineralization negative regulation of bone mineralization multicellular organism development biomineral tissue development regulation of multicellular organismal development bone mineralization negative regulation of ossification negative regulation of multicellular organismal process regulation of ossification	cellular anatomical structure membrane protein-containing complex sodium channel complex transmembrane transporter complex membrane protein complex cation channel complex transporter complex monoatomic ion channel complex membrane-bounded organelle intracellular organelle intracellular anatomical structure Golgi apparatus organelle cellular anatomical structure membrane protein-containing complex sodium channel complex transmembrane transporter complex membrane protein complex cation channel complex transporter complex monoatomic ion channel complex membrane-bounded organelle intracellular organelle intracellular anatomical structure Golgi apparatus organelle cytoplasm intracellular membrane-bounded organelle endomembrane system somatodendritic compartment cell body neuronal cell body cell periphery plasma membrane nucleus membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen endoplasmic reticulum

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A [auth B], B [auth A], C, D	IPR050927	Transient receptor potential cation channel M	Family
A [auth B], B [auth A], C, D	IPR057366	TRPM-like domain	Domain
A [auth B], B [auth A], C, D	IPR005821	Ion transport domain	Domain
A [auth B], B [auth A], C, D	IPR041491	TRPM, SLOG domain	Domain

Membrane Protein Annotation: PDBTM PDBTM Database Homepage

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

Membrane Protein Annotation: MemProtMD MemProtMD Database Homepage

Chains	External Link	Comment
A [auth B], B [auth A], C, D	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 A], C, D	mpstruc	TRANSMEMBRANE PROTEINS: ALPHA-HELICAL	Channels: Transient Receptor Potential (TRP)	TRPM4 Ca²⁺-activated TRP channel, apo state with short coiled-coil

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.