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- PDB-5mkf: cryoEM Structure of Polycystin-2 in complex with calcium and lipids -
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Basic information
Entry | Database: PDB / ID: 5mkf | |||||||||
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Title | cryoEM Structure of Polycystin-2 in complex with calcium and lipids | |||||||||
![]() | Polycystin-2 | |||||||||
![]() | TRANSPORT PROTEIN / Ca2+ signaling / cryoEM / membrane protein structure / Polycystin-2 / TRP channel | |||||||||
Function / homology | ![]() detection of nodal flow / metanephric smooth muscle tissue development / metanephric cortex development / metanephric cortical collecting duct development / metanephric distal tubule development / polycystin complex / mesonephric tubule development / mesonephric duct development / : / metanephric part of ureteric bud development ...detection of nodal flow / metanephric smooth muscle tissue development / metanephric cortex development / metanephric cortical collecting duct development / metanephric distal tubule development / polycystin complex / mesonephric tubule development / mesonephric duct development / : / metanephric part of ureteric bud development / determination of liver left/right asymmetry / renal tubule morphogenesis / metanephric ascending thin limb development / HLH domain binding / basal cortex / metanephric mesenchyme development / metanephric S-shaped body morphogenesis / renal artery morphogenesis / positive regulation of inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity / migrasome / cilium organization / VxPx cargo-targeting to cilium / detection of mechanical stimulus / calcium-induced calcium release activity / regulation of calcium ion import / cation channel complex / muscle alpha-actinin binding / placenta blood vessel development / voltage-gated monoatomic ion channel activity / cellular response to hydrostatic pressure / voltage-gated monoatomic cation channel activity / cellular response to fluid shear stress / cellular response to osmotic stress / non-motile cilium / outward rectifier potassium channel activity / actinin binding / motile cilium / transcription regulator inhibitor activity / aorta development / determination of left/right symmetry / inorganic cation transmembrane transport / neural tube development / protein heterotetramerization / ciliary membrane / voltage-gated sodium channel activity / branching involved in ureteric bud morphogenesis / negative regulation of G1/S transition of mitotic cell cycle / spinal cord development / heart looping / voltage-gated potassium channel activity / potassium channel activity / cytoplasmic side of endoplasmic reticulum membrane / cell surface receptor signaling pathway via JAK-STAT / centrosome duplication / sodium ion transmembrane transport / negative regulation of ryanodine-sensitive calcium-release channel activity / voltage-gated calcium channel activity / embryonic placenta development / monoatomic cation channel activity / release of sequestered calcium ion into cytosol / cellular response to cAMP / potassium ion transmembrane transport / cytoskeletal protein binding / cellular response to calcium ion / basal plasma membrane / ciliary basal body / liver development / establishment of localization in cell / lumenal side of endoplasmic reticulum membrane / calcium ion transmembrane transport / phosphoprotein binding / protein tetramerization / cytoplasmic vesicle membrane / mitotic spindle / Wnt signaling pathway / cilium / intracellular calcium ion homeostasis / cellular response to reactive oxygen species / calcium ion transport / positive regulation of nitric oxide biosynthetic process / cell-cell junction / lamellipodium / heart development / regulation of cell population proliferation / positive regulation of cytosolic calcium ion concentration / ATPase binding / basolateral plasma membrane / protein homotetramerization / transmembrane transporter binding / regulation of cell cycle / negative regulation of cell population proliferation / signaling receptor binding / calcium ion binding / positive regulation of gene expression / endoplasmic reticulum membrane / Golgi apparatus / endoplasmic reticulum / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / extracellular exosome Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.2 Å | |||||||||
![]() | Wilkes, M. / Madej, M.G. / Ziegler, C. | |||||||||
![]() | ![]() Title: Molecular insights into lipid-assisted Ca regulation of the TRP channel Polycystin-2. Authors: Martin Wilkes / M Gregor Madej / Lydia Kreuter / Daniel Rhinow / Veronika Heinz / Silvia De Sanctis / Sabine Ruppel / Rebecca M Richter / Friederike Joos / Marina Grieben / Ashley C W Pike / ...Authors: Martin Wilkes / M Gregor Madej / Lydia Kreuter / Daniel Rhinow / Veronika Heinz / Silvia De Sanctis / Sabine Ruppel / Rebecca M Richter / Friederike Joos / Marina Grieben / Ashley C W Pike / Juha T Huiskonen / Elisabeth P Carpenter / Werner Kühlbrandt / Ralph Witzgall / Christine Ziegler / ![]() ![]() Abstract: Polycystin-2 (PC2), a calcium-activated cation TRP channel, is involved in diverse Ca signaling pathways. Malfunctioning Ca regulation in PC2 causes autosomal-dominant polycystic kidney disease. Here ...Polycystin-2 (PC2), a calcium-activated cation TRP channel, is involved in diverse Ca signaling pathways. Malfunctioning Ca regulation in PC2 causes autosomal-dominant polycystic kidney disease. Here we report two cryo-EM structures of distinct channel states of full-length human PC2 in complex with lipids and cations. The structures reveal conformational differences in the selectivity filter and in the large exoplasmic domain (TOP domain), which displays differing N-glycosylation. The more open structure has one cation bound below the selectivity filter (single-ion mode, PC2), whereas multiple cations are bound along the translocation pathway in the second structure (multi-ion mode, PC2). Ca binding at the entrance of the selectivity filter suggests Ca blockage in PC2, and we observed density for the Ca-sensing C-terminal EF hand in the unblocked PC2 state. The states show altered interactions of lipids with the pore loop and TOP domain, thus reflecting the functional diversity of PC2 at different locations, owing to different membrane compositions. | |||||||||
History |
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Structure visualization
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PDBx/mmCIF format | ![]() | 413.8 KB | Display | ![]() |
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PDB format | ![]() | 321.3 KB | Display | ![]() |
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-Validation report
Summary document | ![]() | 1.6 MB | Display | ![]() |
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Full document | ![]() | 1.7 MB | Display | |
Data in XML | ![]() | 79.3 KB | Display | |
Data in CIF | ![]() | 109.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3524MC ![]() 3523C ![]() 5mkeC M: map data used to model this data C: citing same article ( |
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Similar structure data |
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Assembly
Deposited unit | ![]()
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Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 109820.086 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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-Sugars , 2 types, 16 molecules ![](data/chem/img/NAG.gif)
#2: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source #3: Sugar | ChemComp-NAG / |
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-Non-polymers , 4 types, 29 molecules ![](data/chem/img/PX6.gif)
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![](data/chem/img/CHS.gif)
![](data/chem/img/CA.gif)
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#4: Chemical | ChemComp-PX6 / #5: Chemical | ChemComp-PLM / #6: Chemical | ChemComp-CHS / #7: Chemical | ChemComp-CA / |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: Polycystin-2 / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT |
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Source (natural) | Organism: ![]() |
Source (recombinant) | Organism: ![]() |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
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Electron microscopy imaging
Microscopy | Model: JEOL 3200FSC |
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Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Cs: 4.1 mm |
Image recording | Electron dose: 1.8 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
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Processing
Software | Name: PHENIX / Version: 1.10.1_2155: / Classification: refinement | ||||||||||||||||||||||||
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EM software | Name: PHENIX / Category: model fitting | ||||||||||||||||||||||||
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
Symmetry | Point symmetry: C4 (4 fold cyclic) | ||||||||||||||||||||||||
3D reconstruction | Resolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 35318 / Symmetry type: POINT | ||||||||||||||||||||||||
Atomic model building | Space: REAL Details: we used for comparative structure modeling TRPA1 (pdb entry code 3J9P) as template for S1 and S3-S5, TRPV1 (pdb entry code 3J5Q) for S5-S6, and the TRPV2 (pdb entry code 5AN8) fitted best ...Details: we used for comparative structure modeling TRPA1 (pdb entry code 3J9P) as template for S1 and S3-S5, TRPV1 (pdb entry code 3J5Q) for S5-S6, and the TRPV2 (pdb entry code 5AN8) fitted best for S2-S3 to obtain an initial model. The soluble domain was build based on pdbID: 5K47. But we had no search model for molecular replacement. Although we had a good idea what the architecture would be like, we build the model de novo with COOT. | ||||||||||||||||||||||||
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