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Open data
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Basic information
Entry | Database: PDB / ID: 6cv9 | |||||||||
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Title | Cytoplasmic domain of mTRPC6 | |||||||||
![]() | Short transient receptor potential channel 6 | |||||||||
![]() | TRANSPORT PROTEIN / Ion Channel / Membrane Protein / TRP Channel / TRPC6 / focal segmental glomerulosclerosis | |||||||||
Function / homology | ![]() Elevation of cytosolic Ca2+ levels / Effects of PIP2 hydrolysis / positive regulation of ion transmembrane transporter activity / manganese ion transport / negative regulation of dendrite morphogenesis / slit diaphragm / : / store-operated calcium channel activity / cation channel complex / TRP channels ...Elevation of cytosolic Ca2+ levels / Effects of PIP2 hydrolysis / positive regulation of ion transmembrane transporter activity / manganese ion transport / negative regulation of dendrite morphogenesis / slit diaphragm / : / store-operated calcium channel activity / cation channel complex / TRP channels / inositol 1,4,5 trisphosphate binding / positive regulation of calcium ion transport / actinin binding / clathrin binding / plasma membrane => GO:0005886 / single fertilization / monoatomic cation channel activity / regulation of cytosolic calcium ion concentration / positive regulation of neuron differentiation / positive regulation of peptidyl-threonine phosphorylation / calcium ion transmembrane transport / calcium channel activity / neuron differentiation / cellular response to hydrogen peroxide / monoatomic ion channel activity / actin binding / positive regulation of cytosolic calcium ion concentration / ATPase binding / cellular response to hypoxia / protein homodimerization activity / membrane / plasma membrane / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.8 Å | |||||||||
![]() | Azumaya, C.M. / Sierra-Valdez, F.J. / Cordero-Morales, J.F. / Nakagawa, T. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Cryo-EM structure of the cytoplasmic domain of murine transient receptor potential cation channel subfamily C member 6 (TRPC6). Authors: Caleigh M Azumaya / Francisco Sierra-Valdez / Julio F Cordero-Morales / Terunaga Nakagawa / ![]() Abstract: The kidney maintains the internal milieu by regulating the retention and excretion of proteins, ions, and small molecules. The glomerular podocyte forms the slit diaphragm of the ultrafiltration ...The kidney maintains the internal milieu by regulating the retention and excretion of proteins, ions, and small molecules. The glomerular podocyte forms the slit diaphragm of the ultrafiltration filter, whose damage leads to progressive kidney failure and focal segmental glomerulosclerosis (FSGS). The canonical transient receptor potential 6 (TRPC6) ion channel is expressed in the podocyte, and mutations in its cytoplasmic domain cause FSGS in humans. evaluation of disease-causing mutations in TRPC6 has revealed that these genetic alterations result in abnormal ion channel gating. However, the mechanism whereby the cytoplasmic domain modulates TRPC6 function is largely unknown. Here, we report a cryo-EM structure of the cytoplasmic domain of murine TRPC6 at 3.8 Å resolution. The cytoplasmic fold of TRPC6 is characterized by an inverted dome-like chamber pierced by four radial horizontal helices that converge into a vertical coiled-coil at the central axis. Unlike other TRP channels, TRPC6 displays a unique domain swap that occurs at the junction of the horizontal helices and coiled-coil. Multiple FSGS mutations converge at the buried interface between the vertical coiled-coil and the ankyrin repeats, which form the dome, suggesting these regions are critical for allosteric gating modulation. This functionally critical interface is a potential target for drug design. Importantly, dysfunction in other family members leads to learning deficits (TRPC1/4/5) and ataxia (TRPC3). Our data provide a structural framework for the mechanistic investigation of the TRPC family. | |||||||||
History |
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Structure visualization
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 264.9 KB | Display | ![]() |
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PDB format | ![]() | 190 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 994.2 KB | Display | ![]() |
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Full document | ![]() | 1003.5 KB | Display | |
Data in XML | ![]() | 46.9 KB | Display | |
Data in CIF | ![]() | 63.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7637MC 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
#1: Protein | Mass: 96671.375 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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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: cytoplasmic domain of TRPC6 / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT | ||||||||||||||||||||
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Molecular weight | Value: 0.144 MDa / Experimental value: YES | ||||||||||||||||||||
Source (natural) | Organism: ![]() ![]() | ||||||||||||||||||||
Source (recombinant) | Organism: ![]() ![]() | ||||||||||||||||||||
Buffer solution | pH: 7.4 | ||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 0.3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: Monodisperse | ||||||||||||||||||||
Specimen support | Details: 25 mA / Grid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: C-flat-2/1 | ||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 281.15 K Details: blotted for 8 seconds, 3 filter papers on each side |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 89000 X / Nominal defocus max: 3000 nm / Nominal defocus min: 1200 nm / Cs: 0.001 mm |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 9 sec. / Electron dose: 46.8 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 2 / Num. of real images: 2618 |
EM imaging optics | Energyfilter name: GIF Bioquantum / Energyfilter upper: 20 eV / Energyfilter lower: 0 eV Spherical aberration corrector: Microscope was modified with a Cs aberration corrector |
Image scans | Width: 3838 / Height: 3710 / Movie frames/image: 30 / Used frames/image: 1-30 |
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Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 663034 | ||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C4 (4 fold cyclic) | ||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 67280 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||
Atomic model building | B value: 113 / Protocol: AB INITIO MODEL / Space: REAL / Target criteria: Correlation coefficient |