+
Open data
-
Basic information
Entry | Database: PDB / ID: 7d7e | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Structure of PKD1L3-CTD/PKD2L1 in apo state | |||||||||
![]() |
| |||||||||
![]() | TRANSPORT PROTEIN / Heterotetrameric TRP channel / Calcium / Primary cilia / PKD | |||||||||
Function / homology | ![]() detection of chemical stimulus involved in sensory perception of sour taste / detection of chemical stimulus involved in sensory perception of taste / sensory perception of sour taste / response to water / calcium-activated potassium channel activity / cellular response to pH / detection of mechanical stimulus / cation channel complex / muscle alpha-actinin binding / cellular response to acidic pH ...detection of chemical stimulus involved in sensory perception of sour taste / detection of chemical stimulus involved in sensory perception of taste / sensory perception of sour taste / response to water / calcium-activated potassium channel activity / cellular response to pH / detection of mechanical stimulus / cation channel complex / muscle alpha-actinin binding / cellular response to acidic pH / sodium channel activity / non-motile cilium / inorganic cation transmembrane transport / ciliary membrane / smoothened signaling pathway / monoatomic cation transport / monoatomic cation channel activity / potassium ion transmembrane transport / calcium channel complex / protein tetramerization / calcium channel activity / actin cytoskeleton / cytoplasmic vesicle / carbohydrate binding / protein homotetramerization / transmembrane transporter binding / receptor complex / calcium ion binding / endoplasmic reticulum / identical protein binding / membrane / plasma membrane / cytosol Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å | |||||||||
![]() | Su, Q. / Chen, M. / Li, B. / Wang, Y. / Jing, D. / Zhan, X. / Yu, Y. / Shi, Y. | |||||||||
Funding support | ![]()
| |||||||||
![]() | ![]() Title: Structural basis for Ca activation of the heteromeric PKD1L3/PKD2L1 channel. Authors: Qiang Su / Mengying Chen / Yan Wang / Bin Li / Dan Jing / Xiechao Zhan / Yong Yu / Yigong Shi / ![]() ![]() Abstract: The heteromeric complex between PKD1L3, a member of the polycystic kidney disease (PKD) protein family, and PKD2L1, also known as TRPP2 or TRPP3, has been a prototype for mechanistic characterization ...The heteromeric complex between PKD1L3, a member of the polycystic kidney disease (PKD) protein family, and PKD2L1, also known as TRPP2 or TRPP3, has been a prototype for mechanistic characterization of heterotetrametric TRP-like channels. Here we show that a truncated PKD1L3/PKD2L1 complex with the C-terminal TRP-fold fragment of PKD1L3 retains both Ca and acid-induced channel activities. Cryo-EM structures of this core heterocomplex with or without supplemented Ca were determined at resolutions of 3.1 Å and 3.4 Å, respectively. The heterotetramer, with a pseudo-symmetric TRP architecture of 1:3 stoichiometry, has an asymmetric selectivity filter (SF) guarded by Lys2069 from PKD1L3 and Asp523 from the three PKD2L1 subunits. Ca-entrance to the SF vestibule is accompanied by a swing motion of Lys2069 on PKD1L3. The S6 of PKD1L3 is pushed inward by the S4-S5 linker of the nearby PKD2L1 (PKD2L1-III), resulting in an elongated intracellular gate which seals the pore domain. Comparison of the apo and Ca-loaded complexes unveils an unprecedented Ca binding site in the extracellular cleft of the voltage-sensing domain (VSD) of PKD2L1-III, but not the other three VSDs. Structure-guided mutagenic studies support this unconventional site to be responsible for Ca-induced channel activation through an allosteric mechanism. | |||||||||
History |
|
-
Structure visualization
Movie |
![]() |
---|---|
Structure viewer | Molecule: ![]() ![]() |
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 346.7 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 286.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 872.3 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 905.3 KB | Display | |
Data in XML | ![]() | 53.9 KB | Display | |
Data in CIF | ![]() | 80.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 30606MC ![]() 7d7fC M: map data used to model this data C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
|
---|---|
1 |
|
-
Components
#1: Protein | Mass: 69234.734 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein | | Mass: 62541.914 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #3: Sugar | ChemComp-NAG / #4: Chemical | Has ligand of interest | N | |
---|
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-
Sample preparation
Component | Name: Heterotetrameric TRP channel of PKD1L3/PKD2L1 complex / Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT |
---|---|
Source (natural) | Organism: ![]() ![]() |
Source (recombinant) | Organism: ![]() |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-
Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
---|---|
Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
-
Processing
Software | Name: PHENIX / Version: 1.17.1_3660: / Classification: refinement | ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
CTF correction | Type: NONE | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 549716 / Symmetry type: POINT | ||||||||||||||||||||||||
Refinement | Highest resolution: 3.4 Å | ||||||||||||||||||||||||
Refine LS restraints |
|