6PKW | pdb_00006pkw

Cryo-EM structure of the zebrafish TRPM2 channel in the apo conformation, processed with C2 symmetry (pseudo C4 symmetry)

External Resource: Annotation

Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Membrane Protein Annotation: OPM
Membrane Protein Annotation: PDBTM
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)
D	AAA_9	e6pkwD1	A: a/b three-layered sandwiches	X: CNF1/YfiH-like putative cysteine hydrolases	H: Bromodomain	T: Bromodomain	F: AAA_9	ECOD (v294.1)
C [auth B]	AAA_9	e6pkwB1	A: a/b three-layered sandwiches	X: CNF1/YfiH-like putative cysteine hydrolases	H: Bromodomain	T: Bromodomain	F: AAA_9	ECOD (v294.1)
B [auth C]	AAA_9	e6pkwC1	A: a/b three-layered sandwiches	X: CNF1/YfiH-like putative cysteine hydrolases	H: Bromodomain	T: Bromodomain	F: AAA_9	ECOD (v294.1)
A	AAA_9	e6pkwA1	A: a/b three-layered sandwiches	X: CNF1/YfiH-like putative cysteine hydrolases	H: Bromodomain	T: Bromodomain	F: AAA_9	ECOD (v294.1)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B [auth C], C [auth B], 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, B [auth C], C [auth B], 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, B [auth C], C [auth B], 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, B [auth C], C [auth B], D	Transient receptor potential cation channel subfamily M member 2	cation binding ion binding binding calcium ion binding metal ion binding small molecule binding nucleoside phosphate binding ADP-D-ribose binding anion binding heterocyclic compound binding carbohydrate derivative binding monoatomic cation transmembrane transporter activity gated channel activity monoatomic ion channel activity cation binding ion binding binding calcium ion binding metal ion binding small molecule binding nucleoside phosphate binding ADP-D-ribose binding anion binding heterocyclic compound binding carbohydrate derivative binding monoatomic cation transmembrane transporter activity gated channel activity monoatomic ion channel activity ligand-gated channel activity ligand-gated monoatomic ion channel activity monoatomic cation channel activity passive transmembrane transporter activity channel activity monoatomic ion transmembrane transporter activity transporter activity ligand-gated monoatomic cation channel activity transmembrane transporter activity calcium channel activity calcium ion transmembrane transporter activity ligand-gated calcium channel activity metal ion transmembrane transporter activity mono-ADP-D-ribose binding	transport monoatomic ion transmembrane transport establishment of localization calcium ion transport metal ion transport monoatomic cation transmembrane transport transmembrane transport localization monoatomic ion transport cellular process monoatomic cation transport calcium ion transmembrane transport protein-containing complex organization protein homotetramerization transport monoatomic ion transmembrane transport establishment of localization calcium ion transport metal ion transport monoatomic cation transmembrane transport transmembrane transport localization monoatomic ion transport cellular process monoatomic cation transport calcium ion transmembrane transport 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	cell periphery cellular anatomical structure plasma membrane membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B [auth C], C [auth B], D	IPR005821	Ion transport domain	Domain
A, B [auth C], C [auth B], D	IPR057366	TRPM-like domain	Domain
A, B [auth C], C [auth B], D	IPR041491	TRPM, SLOG domain	Domain
A, B [auth C], C [auth B], D	IPR015797	NUDIX hydrolase-like domain superfamily	Homologous Superfamily
A, B [auth C], C [auth B], D	IPR050927	Transient receptor potential cation channel M	Family

Membrane Protein Annotation: OPM OPM Database Homepage

Chains	External Link	Type	Class	Superfamily	Family
A, B [auth C], C [auth B], D	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, B [auth C], C [auth B], D	PDBTM	Annotated as membrane protein by PDBTM

Membrane Protein Annotation: mpstruc mpstruc Database Homepage

Chains	Resource Link	Group	Subgroup	Protein
A, B [auth C], C [auth B], D	mpstruc	TRANSMEMBRANE PROTEINS: ALPHA-HELICAL	Channels: Transient Receptor Potential (TRP)	TRPM2 ion channel in apo state processed with C4 symmetry

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.