+Open data
-Basic information
Entry | Database: PDB / ID: 6a70 | ||||||||||||
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Title | Structure of the human PKD1/PKD2 complex | ||||||||||||
Components |
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Keywords | MEMBRANE PROTEIN / Asymmetric complex / polycystic kidney disease | ||||||||||||
Function / homology | Function and homology information metanephric distal tubule morphogenesis / 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 distal tubule morphogenesis / 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 / lung epithelium development / metanephric proximal tubule development / lymph vessel morphogenesis / 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 / mitocytosis / migrasome / calcium-independent cell-matrix adhesion / cilium organization / Wnt receptor activity / VxPx cargo-targeting to cilium / establishment of epithelial cell polarity / genitalia development / detection of mechanical stimulus / regulation of calcium ion import / response to fluid shear stress / cation channel complex / calcium-induced calcium release activity / muscle alpha-actinin binding / placenta blood vessel development / Golgi-associated vesicle membrane / voltage-gated monoatomic ion channel activity / cellular response to hydrostatic pressure / outward rectifier potassium channel activity / voltage-gated monoatomic cation channel activity / non-motile cilium / digestive tract development / cellular response to fluid shear stress / metanephric collecting duct development / cellular response to osmotic stress / voltage-gated sodium channel activity / actinin binding / motile cilium / inorganic cation transmembrane transport / transcription regulator inhibitor activity / cartilage development / determination of left/right symmetry / neural tube development / aorta development / protein heterotetramerization / ciliary membrane / skin development / branching involved in ureteric bud morphogenesis / cartilage condensation / negative regulation of G1/S transition of mitotic cell cycle / spinal cord development / branching morphogenesis of an epithelial tube / heart looping / homophilic cell adhesion via plasma membrane adhesion molecules / regulation of G1/S transition of mitotic cell cycle / cytoplasmic side of endoplasmic reticulum membrane / voltage-gated potassium channel activity / cell surface receptor signaling pathway via JAK-STAT / potassium channel activity / centrosome duplication / sodium ion transmembrane transport / negative regulation of ryanodine-sensitive calcium-release channel activity / lateral plasma membrane / anatomical structure morphogenesis / voltage-gated calcium channel activity / embryonic placenta development / regulation of proteasomal protein catabolic process / regulation of cell adhesion / regulation of mitotic spindle organization / monoatomic cation channel activity / cellular response to cAMP / release of sequestered calcium ion into cytosol / potassium ion transmembrane transport / calcium channel complex / cellular response to calcium ion / protein export from nucleus / cytoskeletal protein binding / basal plasma membrane / cell-matrix adhesion / ciliary basal body / liver development / kidney development / establishment of localization in cell / lumenal side of endoplasmic reticulum membrane / calcium ion transmembrane transport / protein tetramerization / phosphoprotein binding Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å | ||||||||||||
Authors | Su, Q. / Hu, F. / Ge, X. / Lei, J. / Yu, S. / Wang, T. / Zhou, Q. / Mei, C. / Shi, Y. | ||||||||||||
Funding support | China, 3items
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Citation | Journal: Science / Year: 2018 Title: Structure of the human PKD1-PKD2 complex. Authors: Qiang Su / Feizhuo Hu / Xiaofei Ge / Jianlin Lei / Shengqiang Yu / Tingliang Wang / Qiang Zhou / Changlin Mei / Yigong Shi / Abstract: Mutations in two genes, and , account for most cases of autosomal dominant polycystic kidney disease, one of the most common monogenetic disorders. Here we report the 3.6-angstrom cryo-electron ...Mutations in two genes, and , account for most cases of autosomal dominant polycystic kidney disease, one of the most common monogenetic disorders. Here we report the 3.6-angstrom cryo-electron microscopy structure of truncated human PKD1-PKD2 complex assembled in a 1:3 ratio. PKD1 contains a voltage-gated ion channel (VGIC) fold that interacts with PKD2 to form the domain-swapped, yet noncanonical, transient receptor potential (TRP) channel architecture. The S6 helix in PKD1 is broken in the middle, with the extracellular half, S6a, resembling pore helix 1 in a typical TRP channel. Three positively charged, cavity-facing residues on S6b may block cation permeation. In addition to the VGIC, a five-transmembrane helix domain and a cytosolic PLAT domain were resolved in PKD1. The PKD1-PKD2 complex structure establishes a framework for dissecting the function and disease mechanisms of the PKD proteins. | ||||||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6a70.cif.gz | 374.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6a70.ent.gz | 281.1 KB | Display | PDB format |
PDBx/mmJSON format | 6a70.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a7/6a70 ftp://data.pdbj.org/pub/pdb/validation_reports/a7/6a70 | HTTPS FTP |
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-Related structure data
Related structure data | 6991MC 6992C M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | |
EM raw data | EMPIAR-10262 (Title: Structure of the human PKD1-PKD2 complex / Data size: 209.8 Data #1: Autopicked particles of PKD1/PKD2 complex [picked particles - multiframe - unprocessed]) |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 66623.406 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PKD2, TRPP2 / Cell line (production host): HEK293F / Production host: HOMO SAPIENS (human) / References: UniProt: Q13563 #2: Protein | | Mass: 127024.836 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PKD1 / Cell line (production host): HEK293F / Production host: HOMO SAPIENS (human) / References: UniProt: P98161 |
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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 |
-Sample preparation
Component | Name: the structure of an asymmetric complex / Type: COMPLEX Details: Samples were obtained by co-expression in 293F cells. A complex contains one PKD1 subunit and three PKD2 subunits. Entity ID: all / Source: RECOMBINANT | ||||||||||||||||||||
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Molecular weight | Value: 0.31 MDa / Experimental value: NO | ||||||||||||||||||||
Source (natural) | Organism: Homo sapiens (human) | ||||||||||||||||||||
Source (recombinant) | Organism: HOMO SAPIENS (human) / Cell: HEK293F | ||||||||||||||||||||
Buffer solution | pH: 7.5 | ||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 10 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: This sample was monodisperse. | ||||||||||||||||||||
Specimen support | Grid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3 | ||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 281 K |
-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: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: DARK FIELD |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.13_2998: / Classification: refinement |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
3D reconstruction | Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 27296 / Symmetry type: POINT |