Annotations: 5Z1W

Cryo-EM structure of polycystic kidney disease-like channel PKD2L1

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	V-set	e5z1wA1	A: beta barrels	X: FAD-linked reductases, C-terminal domain-like	H: FAD-linked reductases-C	T: FAD-linked reductases-C	F: V-set	ECOD (v294.2)
B	V-set	e5z1wB1	A: beta barrels	X: FAD-linked reductases, C-terminal domain-like	H: FAD-linked reductases-C	T: FAD-linked reductases-C	F: V-set	ECOD (v294.2)
C	V-set	e5z1wC1	A: beta barrels	X: FAD-linked reductases, C-terminal domain-like	H: FAD-linked reductases-C	T: FAD-linked reductases-C	F: V-set	ECOD (v294.2)
D	V-set	e5z1wD1	A: beta barrels	X: FAD-linked reductases, C-terminal domain-like	H: FAD-linked reductases-C	T: FAD-linked reductases-C	F: V-set	ECOD (v294.2)

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	PF20519	Polycystin domain (Polycystin_dom)	Polycystin domain	This domain represents the polycystin domain from group II of Transient receptor potential (TRP) channels (TRPP) including PKD1, PKD2, PKD2L and mucolipins. The polycystin domain display a sandwich-like shape with five beta-sheets in the tilted middl ...	This domain represents the polycystin domain from group II of Transient receptor potential (TRP) channels (TRPP) including PKD1, PKD2, PKD2L and mucolipins. The polycystin domain display a sandwich-like shape with five beta-sheets in the tilted middle layer, three alpha-helices on one side and a large loop with two short antiparallel beta-sheets on the other [3].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	Polycystic kidney disease 2-like 1 protein	cation binding ion binding binding calcium ion binding metal ion binding small molecule binding 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 cation binding ion binding binding calcium ion binding metal ion binding small molecule binding 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 ligand-gated channel activity ligand-gated monoatomic ion channel activity pH-gated monoatomic ion channel activity gated channel activity cytoskeletal protein binding protein binding alpha-actinin binding actinin binding muscle alpha-actinin binding calcium-activated cation channel activity potassium ion transmembrane transporter activity potassium channel activity monoatomic ion-gated channel activity calcium-activated potassium channel activity ligand-gated monoatomic cation channel activity metal ion transmembrane transporter activity transmembrane transporter binding sodium channel activity sodium ion transmembrane transporter activity molecular transducer activity molecular sensor activity signaling receptor activity osmolarity-sensing monoatomic cation channel activity transmembrane signaling receptor activity molecular function regulator activity osmosensor activity calcium channel activity calcium ion transmembrane transporter activity identical protein binding	cellular response to stimulus regulation of biological process regulation of cellular process cell surface receptor signaling pathway response to stimulus signaling biological regulation smoothened signaling pathway cell communication cellular process signal transduction transport monoatomic ion transmembrane transport potassium ion transmembrane transport cellular response to stimulus regulation of biological process regulation of cellular process cell surface receptor signaling pathway response to stimulus signaling biological regulation smoothened signaling pathway cell communication cellular process signal transduction transport monoatomic ion transmembrane transport potassium ion transmembrane transport establishment of localization metal ion transport monoatomic cation transmembrane transport transmembrane transport localization monoatomic ion transport potassium ion transport monoatomic cation transport multicellular organismal process system process sensory perception of chemical stimulus sensory perception nervous system process sensory perception of taste sensory perception of sour taste cellular component organization cellular component biogenesis cellular component assembly protein-containing complex organization protein complex oligomerization protein tetramerization protein-containing complex assembly cellular component organization or biogenesis protein homotetramerization protein homooligomerization detection of external stimulus detection of stimulus detection of mechanical stimulus response to mechanical stimulus response to external stimulus response to abiotic stimulus detection of abiotic stimulus response to acid chemical response to chemical response to oxygen-containing compound response to water response to pH cellular response to pH cellular response to acidic pH response to acidic pH cellular response to abiotic stimulus cellular response to environmental stimulus detection of chemical stimulus involved in sensory perception of taste detection of chemical stimulus detection of stimulus involved in sensory perception detection of chemical stimulus involved in sensory perception sodium ion transmembrane transport sodium ion transport detection of chemical stimulus involved in sensory perception of sour taste	cellular anatomical structure membrane intracellular organelle intracellular anatomical structure cytoskeleton organelle membraneless organelle intracellular membraneless organelle actin cytoskeleton cytoplasm cytosol cell periphery plasma membrane protein-containing complex cellular anatomical structure membrane intracellular organelle intracellular anatomical structure cytoskeleton organelle membraneless organelle intracellular membraneless organelle actin cytoskeleton cytoplasm cytosol cell periphery plasma membrane protein-containing complex transmembrane transporter complex membrane protein complex cation channel complex transporter complex calcium channel complex monoatomic ion channel complex membrane-bounded organelle non-motile cilium cell projection cilium plasma membrane bounded cell projection ciliary membrane bounding membrane of organelle plasma membrane region organelle membrane cell projection membrane signaling receptor complex cytoplasmic vesicle intracellular vesicle intracellular membrane-bounded organelle vesicle endoplasmic reticulum endomembrane system

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR046791	Polycystin domain	Domain
A, B, C, D	IPR002048	EF-hand domain	Domain
A, B, C, D	IPR011992	EF-hand domain pair	Homologous Superfamily
A, B, C, D	IPR003915	Polycystic kidney disease type 2 protein	Family
A, B, C, D	IPR051223	Polycystin	Family
A, B, C, D	IPR027359	Voltage-dependent channel domain superfamily	Homologous Superfamily
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)	PKD2L1 polycystic kidney disease channel (residues 64-629)

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

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.