|Entry||Database: PDB / ID: 6a70|
|Title||Structure of the human PKD1/PKD2 complex|
|Keywords||MEMBRANE PROTEIN / Asymmetric complex / polycystic kidney disease|
|Function / homology||Leucine-rich repeat domain superfamily / Polycystic kidney disease type 1 protein / PKD/REJ-like domain / EF-hand domain / Leucine-rich repeat / C-type lectin-like / PLAT/LH2 domain / PKD domain / Cysteine-rich flanking region, C-terminal / C-type lectin domain profile. ...Leucine-rich repeat domain superfamily / Polycystic kidney disease type 1 protein / PKD/REJ-like domain / EF-hand domain / Leucine-rich repeat / C-type lectin-like / PLAT/LH2 domain / PKD domain / Cysteine-rich flanking region, C-terminal / C-type lectin domain profile. / Leucine-rich repeat N-terminal domain / Leucine-rich repeat, typical subtype / Leucine rich repeat / Polycystin cation channel / GPS motif / REJ domain / PLAT/LH2 domain / PKD domain / PKD domain superfamily / Lectin C-type domain / PLAT/LH2 domain superfamily / Carbohydrate-binding WSC / WSC domain / Polycystic kidney disease (PKD) domain profile. / C-type lectin-like/link domain superfamily / C-type lectin fold / REJ domain / PKD/Chitinase domain / VxPx cargo-targeting to cilium / Polycystin cation channel, PKD1/PKD2 / EF-hand domain pair / Polycystin cation channel / Polycystic kidney disease type 2 protein / Voltage-dependent channel domain superfamily / Leucine-rich repeat profile. / WSC domain profile. / REJ domain profile. / EF-hand calcium-binding domain profile. / PLAT domain profile. / GPS domain profile. / Immunoglobulin-like fold / metanephric proximal tubule development / metanephric distal tubule morphogenesis / metanephric collecting duct development / metanephric smooth muscle tissue development / metanephric cortical collecting duct development / metanephric distal tubule development / detection of nodal flow / metanephric cortex development / cellular response to hydrostatic pressure / mesonephric tubule development / mesonephric duct development / polycystin complex / go:0030814: / metanephric part of ureteric bud development / metanephric ascending thin limb development / determination of liver left/right asymmetry / integral component of cytoplasmic side of endoplasmic reticulum membrane / lung epithelium development / renal tubule morphogenesis / calcium-induced calcium release activity / positive regulation of inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity / basal cortex / renal artery morphogenesis / lymph vessel morphogenesis / outward rectifier potassium channel activity / metanephric mesenchyme development / metanephric S-shaped body morphogenesis / non-motile cilium / cellular response to osmotic stress / genitalia development / HLH domain binding / calcium-independent cell-matrix adhesion / Golgi-associated vesicle membrane / placenta blood vessel development / voltage-gated sodium channel activity / regulation of calcium ion import / response to fluid shear stress / detection of mechanical stimulus / motile cilium / sodium ion transmembrane transport / cytoplasmic sequestering of transcription factor / voltage-gated cation channel activity / aorta development / actinin binding / voltage-gated ion channel activity / neural tube development / muscle alpha-actinin binding / ciliary membrane / determination of left/right symmetry / negative regulation of G1/S transition of mitotic cell cycle / digestive tract development / regulation of mitotic spindle organization / JAK-STAT cascade / protein export from nucleus / skin development / potassium channel activity / cartilage development / spinal cord development / potassium ion transmembrane transport|
Function and homology information
|Specimen source||Homo sapiens (human)|
|Method||ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 3.6 Å resolution|
|Authors||Su, Q. / Hu, F. / Ge, X. / Lei, J. / Yu, S. / Wang, T. / Zhou, Q. / Mei, C. / Shi, Y.|
|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.
SummaryFull reportAbout validation report
|Date||Deposition: Jun 29, 2018 / Release: Aug 15, 2018|
|Structure viewer||Molecule: |
Downloads & links
Mass: 66623.406 Da / Num. of mol.: 3 / Source: (gene. exp.) Homo sapiens (human) / Gene: PKD2, TRPP2Polycystin 2 / Cell line (production host): 293F cells / Production host: Mammalian expression vector pCK9 (others) / References: UniProt: Q13563
Mass: 127024.836 Da / Num. of mol.: 1 / Source: (gene. exp.) Homo sapiens (human) / Gene: PKD1 / Cell line (production host): 293F cells / Production host: Mammalian expression vector pCK9 (others) / References: UniProt: P98161
|Experiment||Method: ELECTRON MICROSCOPY|
|EM experiment||Aggregation state: PARTICLE / Reconstruction method: single particle reconstruction|
|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: 1,
|Molecular weight||Value: 0.31 MDa / Experimental value: NO||Source (natural)||Organism: Homo sapiens (human)||Source (recombinant)||Cell: 293F cells / Organism: Mammalian expression vector pCK9 (others)||Buffer solution||pH: 7.5||Buffer component|
|Specimen||Conc.: 10 mg/ml / Details: This sample was monodisperse. / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES||Specimen support||Grid material: GOLD / Grid mesh size: 300 / Grid type: Quantifoil R1.2/1.3||Vitrification||Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 281 kelvins|
-Electron microscopy imaging
Model: Titan Krios / Image courtesy: FEI Company
|Microscopy||Microscope 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)|
|Software||Name: PHENIX / Version: 1.13_2998: / Classification: refinement|
|CTF correction||Type: PHASE FLIPPING AND AMPLITUDE CORRECTION|
|3D reconstruction||Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 27296 / Symmetry type: POINT|
-Jul 12, 2017. Major update of PDB
Major update of PDB
- wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary. This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated. See below links for details.
- In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software). Now, EM Navigator and Yorodumi are based on the updated data.
-Jun 16, 2017. Omokage search with filter
Omokage search with filter
- Result of Omokage search can be filtered by keywords and the database types
Related info.: Omokage search
+Sep 15, 2016. EM Navigator & Yorodumi renewed
EM Navigator & Yorodumi renewed
- New versions of EM Navigator and Yorodumi started
Related info.: Changes in new EM Navigator and Yorodumi
+Aug 31, 2016. New EM Navigator & Yorodumi
New EM Navigator & Yorodumi
- In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
- Current version will continue as 'legacy version' for some time.
Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi
+Apr 13, 2016. Omokage search got faster
Omokage search got faster
- The computation time became ~1/2 compared to the previous version by re-optimization of data accession
- Enjoy "shape similarity" of biomolecules, more!
Related info.: Omokage search
Thousand views of thousand structures
- Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
- This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
Related info.: EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi