5WPV | pdb_00005wpv

Cryo-EM structure of mammalian endolysosomal TRPML1 channel in nanodiscs at 3.59 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)
B	3Beta_HSD, Polysacc_synt_2	e5wpvB1	A: alpha bundles	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: 3Beta_HSD, Polysacc_synt_2	ECOD (develop294)
D	3Beta_HSD, Polysacc_synt_2	e5wpvD1	A: alpha bundles	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: 3Beta_HSD, Polysacc_synt_2	ECOD (develop294)
C	3Beta_HSD, Polysacc_synt_2	e5wpvC1	A: alpha bundles	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: 3Beta_HSD, Polysacc_synt_2	ECOD (develop294)
A	3Beta_HSD, Polysacc_synt_2	e5wpvA1	A: alpha bundles	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: 3Beta_HSD, Polysacc_synt_2	ECOD (develop294)

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 monoatomic cation channel activity passive transmembrane transporter activity monoatomic ion channel activity channel activity monoatomic ion transmembrane transporter activity transporter activity transmembrane transporter activity potassium ion transmembrane transporter activity potassium channel activity metal ion transmembrane transporter activity calcium channel activity gated channel activity ligand-gated channel activity monoatomic cation transmembrane transporter activity monoatomic cation channel activity passive transmembrane transporter activity monoatomic ion channel activity channel activity monoatomic ion transmembrane transporter activity transporter activity transmembrane transporter activity potassium ion transmembrane transporter activity potassium channel activity metal ion transmembrane transporter activity calcium channel activity gated channel activity ligand-gated channel activity ligand-gated monoatomic ion channel activity calcium ion transmembrane transporter activity ligand-gated calcium channel activity ligand-gated monoatomic cation channel activity monoatomic anion transmembrane transporter activity monoatomic anion channel activity iron ion transmembrane transporter activity transition metal ion transmembrane transporter activity binding lipid binding sodium channel activity sodium ion transmembrane transporter activity intracellularly ligand-gated monoatomic ion channel activity NAADP-sensitive calcium-release channel activity intracellularly gated calcium channel activity intracellularly phosphatidylinositol-3,5-bisphosphate-gated monatomic cation channel activity identical protein binding protein binding	regulation of localization regulation of biological process regulation of protein localization positive regulation of protein localization to nucleus biological regulation positive regulation of biological process regulation of protein localization to nucleus protein localization to nucleus localization macromolecule localization protein localization to organelle positive regulation of protein localization intracellular protein localization response to stimulus regulation of localization regulation of biological process regulation of protein localization positive regulation of protein localization to nucleus biological regulation positive regulation of biological process regulation of protein localization to nucleus protein localization to nucleus localization macromolecule localization protein localization to organelle positive regulation of protein localization intracellular protein localization response to stimulus immune response immune system process adaptive immune response cellular component disassembly catabolic process protein-containing complex organization macroautophagy autophagy protein-containing complex disassembly cellular component organization autophagosome maturation cellular process metabolic process cellular component organization or biogenesis process utilizing autophagic mechanism protein homotetramerization cellular component biogenesis cellular component assembly protein complex oligomerization protein tetramerization protein-containing complex assembly protein homooligomerization regulation of defense response regulation of response to biotic stimulus biological process involved in interspecies interaction between organisms negative regulation of response to biotic stimulus regulation of response to external stimulus negative regulation of biological process response to biotic stimulus response to stress regulation of response to stress innate immune response regulation of immune system process response to external biotic stimulus negative regulation of response to stimulus response to other organism defense response regulation of innate immune response negative regulation of immune response defense response to symbiont response to external stimulus regulation of response to stimulus negative regulation of immune system process defense response to other organism negative regulation of response to external stimulus negative regulation of defense response regulation of immune response negative regulation of innate immune response 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 lysosome organization vacuole organization lytic vacuole organization cellular response to metal ion 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 establishment of localization calcium ion transport metal ion transport monoatomic cation transmembrane transport 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 calcium ion transmembrane import into cytosol release of sequestered calcium ion into cytosol iron ion transport iron ion transmembrane transport transition metal ion transport calcium ion export negative regulation of protein localization to nucleus negative regulation of protein localization positive regulation of organelle organization regulation of cellular component organization regulation of cellular process positive regulation of cellular component organization positive regulation of vacuole organization regulation of vacuole organization regulation of organelle organization regulation of lysosome organization positive regulation of lysosome organization positive regulation of cellular process antibacterial innate immune response defense response to bacterium response to bacterium	cellular anatomical structure membrane cell periphery plasma membrane membrane-bounded organelle endosome membrane intracellular anatomical structure endosome intracellular vesicle late endosome membrane intracellular membrane-bounded organelle endomembrane system intracellular organelle cytoplasmic vesicle membrane cellular anatomical structure membrane cell periphery plasma membrane membrane-bounded organelle endosome membrane intracellular anatomical structure endosome intracellular vesicle late endosome membrane intracellular membrane-bounded organelle endomembrane system intracellular organelle cytoplasmic vesicle membrane bounding membrane of organelle cytoplasmic vesicle vesicle membrane organelle 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

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 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.

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