5YDZ | pdb_00005ydz

structure of endo-lysosomal TRPML1 channel inserting into amphipol: state 1

External Resource: Annotation

Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Membrane Protein Annotation: PDBTM
Membrane Protein Annotation: MemProtMD

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
D	F_UNCLASSIFIED	e5ydzD1	A: alpha complex topology	X: Voltage-gated ion channels (From Topology)	H: Voltage-gated ion channels (From Topology)	T: Voltage-gated ion channels	F: F_UNCLASSIFIED	ECOD (1.6)
D	KOG3733	e5ydzD2	A: a+b two layers	X: Polycystin-mucolipin domain (From Topology)	H: Polycystin-mucolipin domain (From Topology)	T: Polycystin-mucolipin domain	F: KOG3733	ECOD (1.6)
C	F_UNCLASSIFIED	e5ydzC1	A: alpha complex topology	X: Voltage-gated ion channels (From Topology)	H: Voltage-gated ion channels (From Topology)	T: Voltage-gated ion channels	F: F_UNCLASSIFIED	ECOD (1.6)
C	KOG3733	e5ydzC2	A: a+b two layers	X: Polycystin-mucolipin domain (From Topology)	H: Polycystin-mucolipin domain (From Topology)	T: Polycystin-mucolipin domain	F: KOG3733	ECOD (1.6)
B	F_UNCLASSIFIED	e5ydzB1	A: alpha complex topology	X: Voltage-gated ion channels (From Topology)	H: Voltage-gated ion channels (From Topology)	T: Voltage-gated ion channels	F: F_UNCLASSIFIED	ECOD (1.6)
B	KOG3733	e5ydzB2	A: a+b two layers	X: Polycystin-mucolipin domain (From Topology)	H: Polycystin-mucolipin domain (From Topology)	T: Polycystin-mucolipin domain	F: KOG3733	ECOD (1.6)
A	F_UNCLASSIFIED	e5ydzA2	A: alpha complex topology	X: Voltage-gated ion channels (From Topology)	H: Voltage-gated ion channels (From Topology)	T: Voltage-gated ion channels	F: F_UNCLASSIFIED	ECOD (1.6)
A	KOG3733	e5ydzA1	A: a+b two layers	X: Polycystin-mucolipin domain (From Topology)	H: Polycystin-mucolipin domain (From Topology)	T: Polycystin-mucolipin domain	F: KOG3733	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
A, B, 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, B, C, D	mammalian endo-lysosomal TRPML1 channel	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 monoatomic anion transmembrane transporter activity monoatomic anion channel activity iron ion transmembrane transporter 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 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 calcium channel activity intracellularly ligand-gated monoatomic ion channel activity gated channel activity NAADP-sensitive calcium-release channel activity intracellularly gated calcium 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 intracellularly phosphatidylinositol-3,5-bisphosphate-gated monatomic cation channel activity identical protein binding protein binding	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 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 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 metal ion cellular response to chemical stimulus response to metal ion response to chemical cellular response to calcium ion response to calcium ion localization cellular localization transport establishment of localization in cell intracellular transport establishment of localization vesicle-mediated transport endosomal transport regulation of localization regulation of cellular process inorganic ion homeostasis intracellular calcium ion homeostasis homeostatic process monoatomic ion transmembrane transport negative regulation of biological process calcium ion homeostasis negative regulation of sequestering of calcium ion calcium ion transport metal ion transport maintenance of location in cell monoatomic cation transmembrane transport intracellular monoatomic cation homeostasis monoatomic ion homeostasis negative regulation of cellular process monoatomic ion transport intracellular chemical homeostasis monoatomic cation homeostasis monoatomic cation transport 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 transmembrane transport release of sequestered calcium ion into cytosol cellular homeostasis chemical homeostasis calcium ion transmembrane transport iron ion transport iron ion transmembrane transport transition metal ion transport 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	cellular anatomical structure 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 cellular anatomical structure 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 cell periphery plasma membrane 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: 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

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.