+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-8356 | |||||||||
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Title | Cryo-EM structure of Polycystic Kidney Disease protein 2 (PKD2) | |||||||||
Map data | map of hPKD2:53-792 in amphipols generated from RELION auto-refinement and postprocessing | |||||||||
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 / 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 / centrosome duplication / 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 / outward rectifier potassium channel activity / cellular response to fluid shear stress / voltage-gated monoatomic cation channel activity / non-motile cilium / cellular response to osmotic stress / actinin binding / motile cilium / transcription regulator inhibitor activity / determination of left/right symmetry / aorta development / inorganic cation transmembrane transport / neural tube development / ciliary membrane / voltage-gated sodium channel activity / protein heterotetramerization / embryonic placenta development / 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 / voltage-gated potassium channel activity / cytoplasmic side of endoplasmic reticulum membrane / cell surface receptor signaling pathway via JAK-STAT / potassium channel activity / sodium ion transmembrane transport / voltage-gated calcium channel activity / monoatomic cation channel activity / basal plasma membrane / cellular response to cAMP / release of sequestered calcium ion into cytosol / potassium ion transmembrane transport / cellular response to calcium ion / cytoskeletal protein binding / ciliary basal body / liver development / establishment of localization in cell / lumenal side of endoplasmic reticulum membrane / phosphoprotein binding / calcium ion transmembrane transport / protein tetramerization / cellular response to reactive oxygen species / cytoplasmic vesicle membrane / cilium / mitotic spindle / Wnt signaling pathway / intracellular calcium ion homeostasis / calcium ion transport / positive regulation of nitric oxide biosynthetic process / cell-cell junction / lamellipodium / ATPase binding / heart development / regulation of cell population proliferation / positive regulation of cytosolic calcium ion concentration / 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 / positive regulation of transcription by RNA polymerase II / protein homodimerization activity / extracellular exosome Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.0 Å | |||||||||
Authors | Shen PS / Yang X / DeCaen PG / Liu X / Bulkley D / Clapham DE / Cao E | |||||||||
Citation | Journal: Cell / Year: 2016 Title: The Structure of the Polycystic Kidney Disease Channel PKD2 in Lipid Nanodiscs. Authors: Peter S Shen / Xiaoyong Yang / Paul G DeCaen / Xiaowen Liu / David Bulkley / David E Clapham / Erhu Cao / Abstract: The Polycystic Kidney Disease 2 (Pkd2) gene is mutated in autosomal dominant polycystic kidney disease (ADPKD), one of the most common human monogenic disorders. Here, we present the cryo-EM ...The Polycystic Kidney Disease 2 (Pkd2) gene is mutated in autosomal dominant polycystic kidney disease (ADPKD), one of the most common human monogenic disorders. Here, we present the cryo-EM structure of PKD2 in lipid bilayers at 3.0 Å resolution, which establishes PKD2 as a homotetrameric ion channel and provides insight into potential mechanisms for its activation. The PKD2 voltage-sensor domain retains two of four gating charges commonly found in those of voltage-gated ion channels. The PKD2 ion permeation pathway is constricted at the selectivity filter and near the cytoplasmic end of S6, suggesting that two gates regulate ion conduction. The extracellular domain of PKD2, a hotspot for ADPKD pathogenic mutations, contributes to channel assembly and strategically interacts with the transmembrane core, likely serving as a physical substrate for extracellular stimuli to allosterically gate the channel. Finally, our structure establishes the molecular basis for the majority of pathogenic mutations in Pkd2-related ADPKD. | |||||||||
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_8356.map.gz | 3.5 MB | EMDB map data format | |
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Header (meta data) | emd-8356-v30.xml emd-8356.xml | 13.7 KB 13.7 KB | Display Display | EMDB header |
Images | emd_8356.png | 74 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-8356 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-8356 | HTTPS FTP |
-Validation report
Summary document | emd_8356_validation.pdf.gz | 78.6 KB | Display | EMDB validaton report |
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Full document | emd_8356_full_validation.pdf.gz | 77.7 KB | Display | |
Data in XML | emd_8356_validation.xml.gz | 494 B | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-8356 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-8356 | HTTPS FTP |
-Related 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_8356.map.gz / Format: CCP4 / Size: 27 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | map of hPKD2:53-792 in amphipols generated from RELION auto-refinement and postprocessing | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.193 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : hPKD2:53-792 tetramer
Entire | Name: hPKD2:53-792 tetramer |
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Components |
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-Supramolecule #1: hPKD2:53-792 tetramer
Supramolecule | Name: hPKD2:53-792 tetramer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Homo sapiens (human) / Recombinant cell: HEK293S GnTI-/- / Recombinant plasmid: pFastbac1 |
-Macromolecule #1: hPKD2:53-792 tetramer
Macromolecule | Name: hPKD2:53-792 tetramer / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: GAMGSFEIEM QRIRQAAARD PPAGAAASPS PPLSSCSRQA WSRDNPGFEA EEEEEEVEGE EGGMVVEMDV EWRPGSRRSA ASSAVSSVGA RSRGLGGYHG AGHPSGRRRR REDQGPPCPS PVGGGDPLHR HLPLEGQPPR VAWAERLVRG LRGLWGTRLM EESSTNREKY ...String: GAMGSFEIEM QRIRQAAARD PPAGAAASPS PPLSSCSRQA WSRDNPGFEA EEEEEEVEGE EGGMVVEMDV EWRPGSRRSA ASSAVSSVGA RSRGLGGYHG AGHPSGRRRR REDQGPPCPS PVGGGDPLHR HLPLEGQPPR VAWAERLVRG LRGLWGTRLM EESSTNREKY LKSVLRELVT YLLFLIVLCI LTYGMMSSNV YYYTRMMSQL FLDTPVSKTE KTNFKTLSSM EDFWKFTEGS LLDGLYWKMQ PSNQTEADNR SFIFYENLLL GVPRIRQLRV RNGSCSIPQD LRDEIKECYD VYSVSSEDRA PFGPRNGTAW IYTSEKDLNG SSHWGIIATY SGAGYYLDLS RTREETAAQV ASLKKNVWLD RGTRATFIDF SVYNANINLF CVVRLLVEFP ATGGVIPSWQ FQPLKLIRYV TTFDFFLAAC EIIFCFFIFY YVVEEILEIR IHKLHYFRSF WNCLDVVIVV LSVVAIGINI YRTSNVEVLL QFLEDQNTFP NFEHLAYWQI QFNNIAAVTV FFVWIKLFKF INFNRTMSQL STTMSRCAKD LFGFAIMFFI IFLAYAQLAY LVFGTQVDDF STFQECIFTQ FRIILGDINF AEIEEANRVL GPIYFTTFVF FMFFILLNMF LAIINDTYSE VKSDLAQQKA EMELSDLIRK GYHKALVKLK LKKNTVDDIS ESLRQGGGKL NFDELRQDLK GKGHTDAEIE AIFTKYDQDG DQELTEHEHQ QMRDDLEKER EDLDLD |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 2 mg/mL | |||||||||
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Buffer | pH: 7.4 Component:
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Grid | Model: Quantifoil / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE | |||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 80 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK II / Details: blot for 7 seconds, -1 mm offset before plunging. | |||||||||
Details | Single particles solubilized in amphipols. This sample was monodisperse. |
-Electron microscopy
Microscope | FEI TECNAI F20 |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 794 / Average exposure time: 0.2 sec. / Average electron dose: 1.35 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated magnification: 41911 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal magnification: 29000 |
Sample stage | Specimen holder model: GATAN 626 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Tecnai F20 / Image courtesy: FEI Company |