+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-8200 | |||||||||
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Title | CryoEM structure of the human Polycystin-2/PKD2 TRP channel | |||||||||
Map data | None | |||||||||
Sample |
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Function / homology | Function and homology information 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 ...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 / metanephric mesenchyme development / metanephric S-shaped body morphogenesis / renal artery morphogenesis / basal cortex / 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 / cation channel complex / calcium-induced calcium release activity / muscle alpha-actinin binding / voltage-gated monoatomic ion channel activity / regulation of calcium ion import / placenta blood vessel development / cellular response to hydrostatic pressure / outward rectifier potassium channel activity / cellular response to fluid shear stress / non-motile cilium / cellular response to osmotic stress / actinin binding / voltage-gated monoatomic cation channel activity / motile cilium / aorta development / transcription regulator inhibitor activity / determination of left/right symmetry / inorganic cation transmembrane transport / neural tube development / voltage-gated sodium channel activity / ciliary membrane / protein heterotetramerization / branching involved in ureteric bud morphogenesis / negative regulation of G1/S transition of mitotic cell cycle / spinal cord development / heart looping / negative regulation of ryanodine-sensitive calcium-release channel activity / cytoplasmic side of endoplasmic reticulum membrane / centrosome duplication / cell surface receptor signaling pathway via JAK-STAT / voltage-gated potassium channel activity / potassium channel activity / embryonic placenta development / voltage-gated calcium channel activity / sodium ion transmembrane transport / 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 / liver development / basal plasma membrane / ciliary basal body / establishment of localization in cell / calcium ion transmembrane transport / lumenal side of endoplasmic reticulum membrane / phosphoprotein binding / protein tetramerization / cytoplasmic vesicle membrane / cilium / mitotic spindle / Wnt signaling pathway / 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 / cell surface receptor signaling pathway / regulation of cell cycle / negative regulation of cell population proliferation / signaling receptor binding / calcium ion binding / endoplasmic reticulum membrane / positive regulation of gene expression / Golgi apparatus / endoplasmic reticulum / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / extracellular exosome Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.22 Å | |||||||||
Authors | Pike ACW / Grieben M / Shintre CA / Tessitore A / Shrestha L / Mukhopadhyay S / Mahajan P / Chalk R / Burgess-Brown NA / Huiskonen JT ...Pike ACW / Grieben M / Shintre CA / Tessitore A / Shrestha L / Mukhopadhyay S / Mahajan P / Chalk R / Burgess-Brown NA / Huiskonen JT / Arrowsmith CH / Edwards AM / Bountra C / Carpenter EP / Structural Genomics Consortium (SGC) | |||||||||
Funding support | United Kingdom, 1 items
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Citation | 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 |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_8200.map.gz | 27.5 MB | EMDB map data format | |
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Header (meta data) | emd-8200-v30.xml emd-8200.xml | 23.5 KB 23.5 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_8200_fsc.xml | 7 KB | Display | FSC data file |
Images | emd_8200.png | 188.8 KB | ||
Others | emd_8200_additional.map.gz emd_8200_half_map_1.map.gz emd_8200_half_map_2.map.gz | 28.4 MB 20.4 MB 20.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-8200 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-8200 | HTTPS FTP |
-Validation report
Summary document | emd_8200_validation.pdf.gz | 455.6 KB | Display | EMDB validaton report |
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Full document | emd_8200_full_validation.pdf.gz | 454.7 KB | Display | |
Data in XML | emd_8200_validation.xml.gz | 12.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-8200 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-8200 | HTTPS FTP |
-Related structure data
Related structure data | 5k47MC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_8200.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | None | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.35 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Additional map: None
File | emd_8200_additional.map | ||||||||||||
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Annotation | None | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: RELION 3D autorefined half map1, unfiltered, unsharpened
File | emd_8200_half_map_1.map | ||||||||||||
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Annotation | RELION 3D autorefined half map1, unfiltered, unsharpened | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: "RELION 3D autorefined half map2, unfiltered, unsharpened"
File | emd_8200_half_map_2.map | ||||||||||||
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Annotation | "RELION 3D autorefined half map2, unfiltered, unsharpened" | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Polycystin-2 channel tetramer (residues 185-723)
Entire | Name: Polycystin-2 channel tetramer (residues 185-723) |
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Components |
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-Supramolecule #1: Polycystin-2 channel tetramer (residues 185-723)
Supramolecule | Name: Polycystin-2 channel tetramer (residues 185-723) / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 256 KDa |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) / Recombinant plasmid: pFB-CT10HF-LIC |
-Macromolecule #1: Polycystin-2
Macromolecule | Name: Polycystin-2 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 63.986668 KDa |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
Sequence | String: MPRVAWAERL VRGLRGLWGT RLMEESSTNR EKYLKSVLRE LVTYLLFLIV LCILTYGMMS SNVYYYTRMM SQLFLDTPVS KTEKTNFKT LSSMEDFWKF TEGSLLDGLY WKMQPSNQTE ADNRSFIFYE NLLLGVPRIR QLRVRNGSCS IPQDLRDEIK E CYDVYSVS ...String: MPRVAWAERL VRGLRGLWGT RLMEESSTNR EKYLKSVLRE LVTYLLFLIV LCILTYGMMS SNVYYYTRMM SQLFLDTPVS KTEKTNFKT LSSMEDFWKF TEGSLLDGLY WKMQPSNQTE ADNRSFIFYE NLLLGVPRIR QLRVRNGSCS IPQDLRDEIK E CYDVYSVS SEDRAPFGPR NGTAWIYTSE KDLNGSSHWG IIATYSGAGY YLDLSRTREE TAAQVASLKK NVWLDRGTRA TF IDFSVYN ANINLFCVVR LLVEFPATGG VIPSWQFQPL KLIRYVTTFD FFLAACEIIF CFFIFYYVVE EILEIRIHKL HYF RSFWNC LDVVIVVLSV VAIGINIYRT SNVEVLLQFL EDQNTFPNFE HLAYWQIQFN NIAAVTVFFV WIKLFKFINF NRTM SQLST TMSRCAKDLF GFAIMFFIIF LAYAQLAYLV FGTQVDDFST FQECIFTQFR IILGDINFAE IEEANRVLGP IYFTT FVFF MFFILLNMFL AIINDTYSEV KSDLAQQKAE MELSDLIRKG YHKALVKLKL KKNTVDAENL YFQ |
-Macromolecule #3: 2-acetamido-2-deoxy-beta-D-glucopyranose
Macromolecule | Name: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 3 / Number of copies: 8 / Formula: NAG |
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Molecular weight | Theoretical: 221.208 Da |
Chemical component information | ChemComp-NAG: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 4.5 mg/mL | |||||||||||||||
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Buffer | pH: 7.5 Component:
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Grid | 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 |
-Electron microscopy
Microscope | FEI POLARA 300 |
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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 |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 4.5 µm / Nominal defocus min: 1.1 µm / Nominal magnification: 37037 |
Sample stage | Specimen holder model: SIDE ENTRY, EUCENTRIC / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Tecnai Polara / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Details | Model was built directly into map de novo |
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Refinement | Space: RECIPROCAL / Protocol: AB INITIO MODEL |
Output model | PDB-5k47: |