5WPT

Cryo-EM structure of mammalian endolysosomal TRPML1 channel in nanodiscs in closed II conformation at 3.75 Angstrom resolution

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: 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)
A	PF08016	e5wptA1	A: alpha complex topology	X: Voltage-gated ion channels (From Topology)	H: Voltage-gated ion channels (From Topology)	T: Voltage-gated ion channels	F: PF08016	ECOD (1.6)
A	PF21381	e5wptA2	A: a+b two layers	X: Polycystin-mucolipin domain (From Topology)	H: Polycystin-mucolipin domain (From Topology)	T: Polycystin-mucolipin domain	F: PF21381	ECOD (1.6)
B	PF08016	e5wptB2	A: alpha complex topology	X: Voltage-gated ion channels (From Topology)	H: Voltage-gated ion channels (From Topology)	T: Voltage-gated ion channels	F: PF08016	ECOD (1.6)
B	PF21381	e5wptB1	A: a+b two layers	X: Polycystin-mucolipin domain (From Topology)	H: Polycystin-mucolipin domain (From Topology)	T: Polycystin-mucolipin domain	F: PF21381	ECOD (1.6)
C	PF08016	e5wptC2	A: alpha complex topology	X: Voltage-gated ion channels (From Topology)	H: Voltage-gated ion channels (From Topology)	T: Voltage-gated ion channels	F: PF08016	ECOD (1.6)
C	PF21381	e5wptC1	A: a+b two layers	X: Polycystin-mucolipin domain (From Topology)	H: Polycystin-mucolipin domain (From Topology)	T: Polycystin-mucolipin domain	F: PF21381	ECOD (1.6)
D	PF08016	e5wptD2	A: alpha complex topology	X: Voltage-gated ion channels (From Topology)	H: Voltage-gated ion channels (From Topology)	T: Voltage-gated ion channels	F: PF08016	ECOD (1.6)
D	PF21381	e5wptD1	A: a+b two layers	X: Polycystin-mucolipin domain (From Topology)	H: Polycystin-mucolipin domain (From Topology)	T: Polycystin-mucolipin domain	F: PF21381	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF08016	Polycystin cation channel (PKD_channel)	Polycystin cation channel	-	Family
A, B, C, D	PF21381	Mucolipin, extracytosolic domain (MCLN_ECD)	Mucolipin, extracytosolic domain	Mucolipins 1-3 are ion channel proteins that belong to the transient receptor potential (TRP) superfamily of cation channels and are the major Ca2+-permeable channels on late endosomes and lysosomes (LEL). This entry represents the extracytosolic dom ...	Mucolipins 1-3 are ion channel proteins that belong to the transient receptor potential (TRP) superfamily of cation channels and are the major Ca2+-permeable channels on late endosomes and lysosomes (LEL). This entry represents the extracytosolic domain (ECD) which consists of two beta sheets and two extracytosolic helices that tetramerize into a ring that caps the extracytosolic side of the channel [1-5].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	Mucolipin-1	monoatomic cation transmembrane transporter activity intracellularly ligand-gated monoatomic ion channel 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 intracellularly phosphatidylinositol-3,5-bisphosphate-gated monatomic cation channel activity monoatomic ion transmembrane transporter activity transporter activity ligand-gated monoatomic cation channel activity transmembrane transporter activity monoatomic cation transmembrane transporter activity intracellularly ligand-gated monoatomic ion channel 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 intracellularly phosphatidylinositol-3,5-bisphosphate-gated monatomic cation 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 inorganic molecular entity transmembrane transporter activity ligand-gated calcium channel activity inorganic cation transmembrane transporter activity metal ion transmembrane transporter activity binding lipid binding NAADP-sensitive calcium-release channel activity intracellularly gated calcium channel activity identical protein binding protein binding	response to stimulus immune response immune system process adaptive immune response cellular component disassembly catabolic process macroautophagy protein-containing complex organization cellular metabolic process autophagy protein-containing complex disassembly cellular catabolic process cellular component organization autophagosome maturation response to stimulus immune response immune system process adaptive immune response cellular component disassembly catabolic process macroautophagy protein-containing complex organization cellular metabolic process autophagy protein-containing complex disassembly cellular catabolic process cellular component organization autophagosome maturation cellular process metabolic process cellular component organization or biogenesis process utilizing autophagic mechanism localization protein homotetramerization cellular component biogenesis cellular component assembly protein complex oligomerization protein tetramerization protein-containing complex assembly protein homooligomerization cellular response to stimulus response to pH cellular response to pH response to abiotic stimulus cellular response to abiotic stimulus cellular response to environmental stimulus organelle organization phagosome maturation cellular response to inorganic substance cellular response to metal ion response to inorganic substance cellular response to chemical stimulus response to metal ion response to chemical cellular response to calcium ion response to calcium ion 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 monoatomic ion transport monoatomic cation transport calcium ion transmembrane transport cellular localization establishment of localization in cell intracellular transport vesicle-mediated transport endosomal transport regulation of localization regulation of cellular process inorganic ion homeostasis intracellular calcium ion homeostasis homeostatic process negative regulation of biological process calcium ion homeostasis negative regulation of sequestering of calcium ion maintenance of location in cell intracellular monoatomic cation homeostasis monoatomic ion homeostasis negative regulation of cellular process intracellular chemical homeostasis monoatomic cation homeostasis regulation of sequestering of calcium ion intracellular monoatomic ion homeostasis regulation of biological process calcium ion transmembrane import into cytosol sequestering of calcium ion biological regulation maintenance of location release of sequestered calcium ion into cytosol cellular homeostasis chemical homeostasis calcium ion export positive regulation of organelle organization regulation of cellular component organization positive regulation of cellular component organization vacuole organization lytic vacuole organization positive regulation of vacuole organization positive regulation of biological process regulation of vacuole organization regulation of organelle organization lysosome organization regulation of lysosome organization positive regulation of lysosome organization positive regulation of cellular process	membrane cellular anatomical entity cell periphery plasma membrane membrane-bounded organelle intracellular organelle intracellular anatomical structure organelle intracellular membrane-bounded organelle endosome membrane endosome intracellular vesicle late endosome membrane endomembrane system membrane cellular anatomical entity cell periphery plasma membrane membrane-bounded organelle intracellular organelle intracellular anatomical structure organelle intracellular membrane-bounded organelle endosome membrane endosome intracellular vesicle late endosome membrane endomembrane system cytoplasmic vesicle membrane bounding membrane of organelle cytoplasmic vesicle vesicle membrane late endosome cytoplasm vesicle organelle membrane nucleus membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen lytic vacuole vacuole lysosome protein-containing complex receptor complex phagocytic vesicle phagocytic vesicle membrane endocytic vesicle membrane endocytic vesicle vacuolar membrane lytic vacuole membrane lysosomal membrane Golgi apparatus phagocytic cup cell projection

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR047316	Mucolipin-1, extracytosolic/lumenal domain	Domain
A, B, C, D	IPR049134	Mucolipin, extracytosolic domain	Domain
A, B, C, D	IPR039031	Mucolipin	Family
A, B, C, D	IPR013122	Polycystin cation channel, PKD1/PKD2	Domain

Membrane Protein Annotation: OPM OPM Database Homepage

Chains	External Link	Type	Class	Superfamily	Family
A, B, C, D	OPM	Transmembrane	Alpha-helical polytopic	Ion channel (VIC) superfamily	Polycystin cation channel

Membrane Protein Annotation: PDBTM PDBTM Database Homepage

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

Membrane Protein Annotation: MemProtMD MemProtMD Database Homepage

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

Membrane Protein Annotation: mpstruc mpstruc Database Homepage

Chains	Resource Link	Group	Subgroup	Protein
A, B, C, D	mpstruc	TRANSMEMBRANE PROTEINS: ALPHA-HELICAL	Channels: Transient Receptor Potential (TRP)	Endolysosomal TRPML1 channel in nanodiscs

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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.