Journal: Nat Struct Mol Biol / Year: 2017 Title: Structure of the polycystic kidney disease TRP channel Polycystin-2 (PC2). Authors: Mariana Grieben / Ashley C W Pike / Chitra A Shintre / Elisa Venturi / Sam El-Ajouz / Annamaria Tessitore / Leela Shrestha / Shubhashish Mukhopadhyay / Pravin Mahajan / Rod Chalk / Nicola A ...Authors: Mariana Grieben / Ashley C W Pike / Chitra A Shintre / Elisa Venturi / Sam El-Ajouz / Annamaria Tessitore / Leela Shrestha / Shubhashish Mukhopadhyay / Pravin Mahajan / Rod Chalk / Nicola A Burgess-Brown / Rebecca Sitsapesan / Juha T Huiskonen / Elisabeth P Carpenter / Abstract: Mutations in either polycystin-1 (PC1 or PKD1) or polycystin-2 (PC2, PKD2 or TRPP1) cause autosomal-dominant polycystic kidney disease (ADPKD) through unknown mechanisms. Here we present the ...Mutations in either polycystin-1 (PC1 or PKD1) or polycystin-2 (PC2, PKD2 or TRPP1) cause autosomal-dominant polycystic kidney disease (ADPKD) through unknown mechanisms. Here we present the structure of human PC2 in a closed conformation, solved by electron cryomicroscopy at 4.2-Å resolution. The structure reveals a novel polycystin-specific 'tetragonal opening for polycystins' (TOP) domain tightly bound to the top of a classic transient receptor potential (TRP) channel structure. The TOP domain is formed from two extensions to the voltage-sensor-like domain (VSLD); it covers the channel's endoplasmic reticulum lumen or extracellular surface and encloses an upper vestibule, above the pore filter, without blocking the ion-conduction pathway. The TOP-domain fold is conserved among the polycystins, including the homologous channel-like region of PC1, and is the site of a cluster of ADPKD-associated missense variants. Extensive contacts among the TOP-domain subunits, the pore and the VSLD provide ample scope for regulation through physical and chemical stimuli.
History
Deposition
Jun 21, 2016
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Header (metadata) release
Aug 24, 2016
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Map release
Aug 24, 2016
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Update
Oct 21, 2020
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Current status
Oct 21, 2020
Processing site: PDBe / Status: Released
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Structure visualization
Movie
Surface view with section colored by density value
Model: C-flat / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR
Vitrification
Cryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 85 K / Instrument: FEI VITROBOT MARK IV Details: 3 microlitres were applied to the grid and blotted for 3secs prior to plunge in liquid ethane.
Details
Sample was monodisperse after size exclusion chromatography
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Electron microscopy
Microscope
FEI POLARA 300
Specialist optics
Energy filter - Name: GIF Quantum / Energy filter - Lower energy threshold: 0 eV / Energy filter - Upper energy threshold: 20 eV
Image recording
Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Frames/image: 1-22 / Number grids imaged: 1 / Number real images: 758 / Average exposure time: 8.8 sec. / Average electron dose: 45.1 e/Å2 Details: Images were collected in movie-mode at 2.5 frames per second for a duration of 8.8secs
Electron beam
Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Model: Tecnai Polara / Image courtesy: FEI Company
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Image processing
Particle selection
Number selected: 161965 Details: Particles were autopicked using CTF-corrected template based picking algorithm in RELION using selected 2D class averages based on manually picked particles.
CTF correction
Software: (Name: CTFFIND (ver. 4.0.8), RELION (ver. 1.3)) / Details: CTF correction as implemented in CTTFIND4/RELION
Startup model
Type of model: OTHER Details: Initial model generated from a projection of a side view 2D class average
Final reconstruction
Number classes used: 1 / Applied symmetry - Point group: C4 (4 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 4.22 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 1.3) Details: Resolution determined by gold-standard FSC procedure as implemented in RELION Number images used: 19546
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