+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-21586 | |||||||||
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Title | Cryo-EM structure of PKD2 C331S disease variant | |||||||||
Map data | Sharpened map | |||||||||
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 ...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 / cellular response to reactive oxygen species / intracellular calcium ion homeostasis / 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 | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.24 Å | |||||||||
Authors | Cao E / Wang J / Decaen PG | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Proc Natl Acad Sci U S A / Year: 2020 Title: Molecular dysregulation of ciliary polycystin-2 channels caused by variants in the TOP domain. Authors: Thuy N Vien / Jinliang Wang / Leo C T Ng / Erhu Cao / Paul G DeCaen / Abstract: Genetic variants in which encodes for the polycystin-2 ion channel are responsible for many clinical cases of autosomal dominant polycystic kidney disease (ADPKD). Despite our strong understanding ...Genetic variants in which encodes for the polycystin-2 ion channel are responsible for many clinical cases of autosomal dominant polycystic kidney disease (ADPKD). Despite our strong understanding of the genetic basis of ADPKD, we do not know how most variants impact channel function. Polycystin-2 is found in organelle membranes, including the primary cilium-an antennae-like structure on the luminal side of the collecting duct. In this study, we focus on the structural and mechanistic regulation of polycystin-2 by its TOP domain-a site with unknown function that is commonly altered by missense variants. We use direct cilia electrophysiology, cryogenic electron microscopy, and superresolution imaging to determine that variants of the TOP domain finger 1 motif destabilizes the channel structure and impairs channel opening without altering cilia localization and channel assembly. Our findings support the channelopathy classification of variants associated with ADPKD, where polycystin-2 channel dysregulation in the primary cilia may contribute to cystogenesis. | |||||||||
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_21586.map.gz | 4.7 MB | EMDB map data format | |
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Header (meta data) | emd-21586-v30.xml emd-21586.xml | 12.3 KB 12.3 KB | Display Display | EMDB header |
Images | emd_21586.png | 80.2 KB | ||
Others | emd_21586_additional.map.gz | 26.3 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-21586 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-21586 | HTTPS FTP |
-Validation report
Summary document | emd_21586_validation.pdf.gz | 355.4 KB | Display | EMDB validaton report |
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Full document | emd_21586_full_validation.pdf.gz | 355 KB | Display | |
Data in XML | emd_21586_validation.xml.gz | 5.9 KB | Display | |
Data in CIF | emd_21586_validation.cif.gz | 6.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-21586 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-21586 | HTTPS FTP |
-Related structure data
Related structure data | 6wb8MC 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_21586.map.gz / Format: CCP4 / Size: 38.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Sharpened map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.05 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Additional map: Unsharpened map
File | emd_21586_additional.map | ||||||||||||
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Annotation | Unsharpened map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : PKD2
Entire | Name: PKD2 |
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Components |
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-Supramolecule #1: PKD2
Supramolecule | Name: PKD2 / type: cell / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Homo sapiens (human) |
-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: 86.517031 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: GMGSAAPGGL CEQRGLEIEM QRIRQAAARD PPAGAAASPS PPLSSCSRQA WSRDNPGFEA EEEEEEVEGE EGGMVVEMDV EWRPGSRRS AASSAVSSVG ARSRGLGGYH GAGHPSGRRR RREDQGPPCP SPVGGGDPLH RHLPLEGQPP RVAWAERLVR G LRGLWGTR ...String: GMGSAAPGGL CEQRGLEIEM QRIRQAAARD PPAGAAASPS PPLSSCSRQA WSRDNPGFEA EEEEEEVEGE EGGMVVEMDV EWRPGSRRS AASSAVSSVG ARSRGLGGYH GAGHPSGRRR RREDQGPPCP SPVGGGDPLH RHLPLEGQPP RVAWAERLVR G LRGLWGTR LMEESSTNRE KYLKSVLREL VTYLLFLIVL CILTYGMMSS NVYYYTRMMS QLFLDTPVSK TEKTNFKTLS SM EDFWKFT EGSLLDGLYW KMQPSNQTEA DNRSFIFYEN LLLGVPRIRQ LRVRNGSSSI PQDLRDEIKE CYDVYSVSSE DRA PFGPRN GTAWIYTSEK DLNGSSHWGI IATYSGAGYY LDLSRTREET AAQVASLKKN VWLDRGTRAT FIDFSVYNAN INLF CVVRL LVEFPATGGV IPSWQFQPLK LIRYVTTFDF FLAACEIIFC FFIFYYVVEE ILEIRIHKLH YFRSFWNCLD VVIVV LSVV AIGINIYRTS NVEVLLQFLE DQNTFPNFEH LAYWQIQFNN IAAVTVFFVW IKLFKFINFN RTMSQLSTTM SRCAKD LFG FAIMFFIIFL AYAQLAYLVF GTQVDDFSTF QECIFTQFRI ILGDINFAEI EEANRVLGPI YFTTFVFFMF FILLNMF LA IINDTYSEVK SDLAQQKAEM ELSDLIRKGY HKALVKLKLK KNTVDDISES LRQGGGKLNF DELRQDLKGK GHTDAEIE A IFTKYDQDGD QELTEHEHQQ MRDDLEKERE DLDLD |
-Macromolecule #2: 2-acetamido-2-deoxy-beta-D-glucopyranose
Macromolecule | Name: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 2 / Number of copies: 12 / 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 | 2 mg/mL |
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Buffer | pH: 7.4 |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 IS (4k x 4k) / Average electron dose: 1.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: DARK FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.24 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 74302 |
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Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: OTHER / Overall B value: 100 |
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Output model | PDB-6wb8: |