5MKF | pdb_00005mkf

cryoEM Structure of Polycystin-2 in complex with calcium and lipids

External Resource: Annotation

Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations
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		e5mkfA1	A: Immunoglobulin-like beta-sandwich	X: Immunoglobulin-related	H: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	T: Ribosomal_L9_C	F:	ECOD (20:10:01)
B		e5mkfB1	A: Immunoglobulin-like beta-sandwich	X: Immunoglobulin-related	H: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	T: Ribosomal_L9_C	F:	ECOD (20:10:01)
C		e5mkfC1	A: Immunoglobulin-like beta-sandwich	X: Immunoglobulin-related	H: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	T: Ribosomal_L9_C	F:	ECOD (20:10:01)
D		e5mkfD1	A: Immunoglobulin-like beta-sandwich	X: Immunoglobulin-related	H: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	T: Ribosomal_L9_C	F:	ECOD (20:10:01)

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	Polycystin-2	cytoskeletal protein binding protein binding binding alpha-actinin binding actinin binding muscle alpha-actinin binding monoatomic cation transmembrane transporter activity gated channel activity monoatomic ion channel activity potassium ion transmembrane transporter activity voltage-gated channel activity voltage-gated monoatomic ion channel activity potassium channel activity voltage-gated monoatomic cation channel activity cytoskeletal protein binding protein binding binding alpha-actinin binding actinin binding muscle alpha-actinin binding monoatomic cation transmembrane transporter activity gated channel activity monoatomic ion channel activity potassium ion transmembrane transporter activity voltage-gated channel activity voltage-gated monoatomic ion channel activity potassium channel activity voltage-gated monoatomic cation channel activity monoatomic cation channel activity passive transmembrane transporter activity voltage-gated potassium channel activity channel activity monoatomic ion transmembrane transporter activity transporter activity metal ion transmembrane transporter activity transmembrane transporter activity cation binding ion binding calcium ion binding metal ion binding small molecule binding signaling receptor binding voltage-gated sodium channel activity sodium channel activity sodium ion transmembrane transporter activity identical protein binding protein homodimerization activity protein dimerization activity calcium-induced calcium release activity calcium channel activity intracellularly ligand-gated monoatomic ion 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 outward rectifier potassium channel activity molecular function inhibitor activity molecular function regulator activity transcription regulator inhibitor activity phosphoprotein binding HLH domain binding protein domain specific binding ATPase binding enzyme binding voltage-gated calcium channel activity transmembrane transporter binding	multicellular organismal process kidney epithelium development metanephric epithelium development nephron tubule development metanephric distal tubule development renal system development multicellular organism development metanephros development anatomical structure development renal tubule development nephron development metanephric nephron epithelium development nephron epithelium development system development multicellular organismal process kidney epithelium development metanephric epithelium development nephron tubule development metanephric distal tubule development renal system development multicellular organism development metanephros development anatomical structure development renal tubule development nephron development metanephric nephron epithelium development nephron epithelium development system development developmental process epithelium development tube development metanephric nephron tubule development animal organ development tissue development distal tubule development metanephric tubule development kidney development regulation of biosynthetic process regulation of nitric oxide biosynthetic process regulation of biological process regulation of cellular process biological regulation positive regulation of biological process reactive nitrogen species metabolic process nitric oxide metabolic process positive regulation of metabolic process nitric oxide biosynthetic process biosynthetic process positive regulation of biosynthetic process cellular process metabolic process regulation of nitric oxide metabolic process positive regulation of nitric oxide biosynthetic process regulation of metabolic process positive regulation of cellular process mesonephric epithelium development mesonephros development mesonephric tubule development heart development circulatory system development 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 microtubule organizing center organization microtubule cytoskeleton organization cellular component organization centrosome duplication organelle organization centrosome cycle microtubule-based process cell cycle cellular component organization or biogenesis cytoskeleton organization cell cycle process cellular response to stimulus cellular response to metal ion cellular response to chemical stimulus response to stimulus response to metal ion response to chemical cellular response to calcium ion response to calcium ion calcium ion transport calcium ion transmembrane transport cell surface receptor signaling pathway via STAT cell surface receptor signaling pathway signaling cell communication signal transduction cell surface receptor signaling pathway via JAK-STAT cellular response to stress response to stress response to fluid shear stress cellular response to fluid shear stress response to osmotic stress cellular response to chemical stress cellular response to osmotic stress cellular response to environmental stimulus response to abiotic stimulus cellular response to abiotic stimulus spinal cord development central nervous system development nervous system development gland development pattern specification process liver development regionalization determination of liver left/right asymmetry hepaticobiliary system development determination of bilateral symmetry determination of left/right symmetry left/right pattern formation specification of symmetry detection of external stimulus detection of stimulus detection of mechanical stimulus response to mechanical stimulus response to external stimulus detection of abiotic stimulus placenta development chordate embryonic development embryo development in utero embryonic development embryonic placenta development embryo development ending in birth or egg hatching embryonic organ development renal cortex development mesenchyme development metanephric cortex development cellular response to acid chemical response to oxygen-containing compound response to water cellular response to oxygen-containing compound response to acid chemical cellular response to hydrostatic pressure cellular response to water stimulus response to hydrostatic pressure cellular localization establishment of localization in cell sodium ion transmembrane transport sodium ion transport calcium ion transmembrane import into cytosol release of sequestered calcium ion into cytosol cell population proliferation regulation of cell population proliferation Wnt signaling pathway metanephric mesenchyme development kidney mesenchyme development nephron morphogenesis metanephric nephron morphogenesis S-shaped body morphogenesis metanephric S-shaped body morphogenesis kidney morphogenesis anatomical structure morphogenesis metanephros morphogenesis animal organ morphogenesis metanephric nephron development response to endogenous stimulus detection of nodal flow cellular response to endogenous stimulus renal artery morphogenesis blood vessel morphogenesis artery development vasculature development kidney vasculature development tube morphogenesis renal system vasculature development artery morphogenesis kidney vasculature morphogenesis blood vessel development renal system vasculature morphogenesis regulation of calcium ion import regulation of calcium ion transport regulation of localization regulation of transport regulation of monoatomic ion transport calcium ion import regulation of metal ion transport cellular component biogenesis cellular component assembly protein-containing complex organization protein complex oligomerization protein tetramerization protein-containing complex assembly smooth muscle tissue development metanephric smooth muscle tissue development muscle tissue development kidney smooth muscle tissue development regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process positive regulation of macromolecule biosynthetic process regulation of gene expression positive regulation of gene expression regulation of macromolecule biosynthetic process positive regulation of macromolecule metabolic process macromolecule metabolic process nephric duct development mesonephric duct development inorganic ion homeostasis intracellular calcium ion homeostasis homeostatic process calcium ion homeostasis cellular homeostasis chemical homeostasis intracellular monoatomic cation homeostasis monoatomic ion homeostasis intracellular chemical homeostasis monoatomic cation homeostasis intracellular monoatomic ion homeostasis aorta development placenta blood vessel development loop of Henle development metanephric loop of Henle development metanephric ascending thin limb development ascending thin limb development branching morphogenesis of an epithelial tube nephron tubule morphogenesis nephron epithelium morphogenesis ureteric bud morphogenesis branching involved in ureteric bud morphogenesis epithelial tube morphogenesis ureteric bud development morphogenesis of an epithelium tissue morphogenesis morphogenesis of a branching structure mesonephric tubule morphogenesis renal tubule morphogenesis morphogenesis of a branching epithelium positive regulation of DNA-templated transcription RNA metabolic process regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process DNA-templated transcription regulation of RNA metabolic process transcription by RNA polymerase II regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of transcription by RNA polymerase II primary metabolic process positive regulation of transcription by RNA polymerase II nucleobase-containing compound biosynthetic process nucleic acid metabolic process positive regulation of RNA metabolic process positive regulation of RNA biosynthetic process regulation of DNA-templated transcription heart morphogenesis embryonic heart tube development embryonic heart tube morphogenesis heart looping embryonic organ morphogenesis embryonic morphogenesis determination of heart left/right asymmetry protein heterotetramerization protein heterooligomerization protein homotetramerization protein homooligomerization cellular response to nitrogen compound response to organophosphorus response to nitrogen compound response to purine-containing compound response to cAMP cellular response to cAMP cortical collecting duct development metanephric cortical collecting duct development positive regulation of cell communication positive regulation of signal transduction regulation of signal transduction phospholipase C-activating G protein-coupled receptor signaling pathway positive regulation of response to stimulus regulation of G protein-coupled receptor signaling pathway regulation of signaling positive regulation of G protein-coupled receptor signaling pathway positive regulation of phospholipase C-activating G protein-coupled receptor signaling pathway regulation of response to stimulus regulation of cell communication G protein-coupled receptor signaling pathway regulation of phospholipase C-activating G protein-coupled receptor signaling pathway positive regulation of signaling cellular response to oxidative stress response to reactive oxygen species cellular response to reactive oxygen species response to oxidative stress negative regulation of cell population proliferation negative regulation of cellular process negative regulation of biological process regulation of cell cycle phase transition negative regulation of cell cycle cell cycle phase transition regulation of cell cycle G1/S phase transition cell cycle G1/S phase transition mitotic cell cycle negative regulation of mitotic cell cycle regulation of mitotic cell cycle negative regulation of cell cycle phase transition regulation of cell cycle negative regulation of G1/S transition of mitotic cell cycle negative regulation of mitotic cell cycle phase transition regulation of cell cycle process negative regulation of cell cycle G1/S phase transition negative regulation of cell cycle process regulation of mitotic cell cycle phase transition mitotic cell cycle process regulation of G1/S transition of mitotic cell cycle G1/S transition of mitotic cell cycle mitotic cell cycle phase transition plasma membrane bounded cell projection organization cell projection organization cilium organization metanephric part of ureteric bud development neural tube development	cell-cell junction cellular anatomical structure anchoring junction cell junction intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle organelle subcompartment cytoplasmic side of membrane membrane intracellular membrane-bounded organelle endomembrane system side of membrane cell-cell junction cellular anatomical structure anchoring junction cell junction intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle organelle subcompartment cytoplasmic side of membrane membrane intracellular membrane-bounded organelle endomembrane system side of membrane endoplasmic reticulum subcompartment intracellular organelle organelle nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum cytoplasmic side of endoplasmic reticulum membrane organelle membrane endoplasmic reticulum membrane intracellular membraneless organelle cilium plasma membrane bounded cell projection ciliary basal body cell projection microtubule organizing center cytoskeleton membraneless organelle microtubule cytoskeleton cell periphery basal part of cell plasma membrane basal plasma membrane plasma membrane region motile cilium non-motile cilium ciliary membrane bounding membrane of organelle cell projection membrane migrasome intracellular vesicle cytoplasmic vesicle membrane vesicle membrane cytoplasmic vesicle vesicle lumenal side of endoplasmic reticulum membrane lumenal side of membrane cell leading edge lamellipodium extracellular exosome extracellular vesicle extracellular organelle extracellular region extracellular space extracellular membrane-bounded organelle basolateral plasma membrane Golgi apparatus protein-containing complex polycystin complex cell cortex cell cortex region cytoplasmic region basal cortex mitotic spindle spindle transmembrane transporter complex membrane protein complex cation channel complex transporter complex monoatomic ion channel complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR002048	EF-hand domain	Domain
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
A, B, C, D	IPR046791	Polycystin domain	Domain
A, B, C, D	IPR011992	EF-hand domain pair	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B, C, D	Pharos: Q13563	polycystic kidney disease 2 retinal disease autosomal dominant polycystic kidney disease Liver Cirrhosis, Experimental vascular disease ovarian cancer Pick disease cerebrovascular disorder Ehlers-Danlos syndrome neurodegenerative disease pancreatic intraductal papillary-mucinous carcinoma polycystic kidney disease thoracic aortic aneurysm breast cancer Emery-Dreifuss muscular dystrophy polycystic kidney disease 2 retinal disease autosomal dominant polycystic kidney disease Liver Cirrhosis, Experimental vascular disease ovarian cancer Pick disease cerebrovascular disorder Ehlers-Danlos syndrome neurodegenerative disease pancreatic intraductal papillary-mucinous carcinoma polycystic kidney disease thoracic aortic aneurysm breast cancer Emery-Dreifuss muscular dystrophy invasive ductal breast carcinoma malignant mesothelioma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia progressive supranuclear palsy breast carcinoma gout kidney disease nephrolithiasis

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)	PKD2 polycystic kidney disease channel in complex with cations and lipids

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.