[English] 日本語
Yorodumi- PDB-7x6c: Cryo-EM structure of the human TRPC5 ion channel in lipid nanodis... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7x6c | ||||||
---|---|---|---|---|---|---|---|
Title | Cryo-EM structure of the human TRPC5 ion channel in lipid nanodiscs, class1 | ||||||
Components | Short transient receptor potential channel 5 | ||||||
Keywords | METAL TRANSPORT / TRP / transient receptor potential | ||||||
Function / homology | Function and homology information regulation of membrane hyperpolarization / phosphatidylserine exposure on apoptotic cell surface / negative regulation of dendrite morphogenesis / Role of second messengers in netrin-1 signaling / store-operated calcium channel activity / cation channel complex / inositol 1,4,5 trisphosphate binding / actinin binding / TRP channels / clathrin binding ...regulation of membrane hyperpolarization / phosphatidylserine exposure on apoptotic cell surface / negative regulation of dendrite morphogenesis / Role of second messengers in netrin-1 signaling / store-operated calcium channel activity / cation channel complex / inositol 1,4,5 trisphosphate binding / actinin binding / TRP channels / clathrin binding / positive regulation of axon extension / regulation of cytosolic calcium ion concentration / calcium channel complex / positive regulation of neuron differentiation / positive regulation of peptidyl-threonine phosphorylation / calcium ion transmembrane transport / calcium channel activity / neuron differentiation / calcium ion transport / ATPase binding / nervous system development / actin binding / positive regulation of cytosolic calcium ion concentration / growth cone / neuron apoptotic process / neuronal cell body / positive regulation of cell population proliferation / dendrite / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.15 Å | ||||||
Authors | Won, J. / Jeong, H. / Lee, H.H. | ||||||
Funding support | Korea, Republic Of, 1items
| ||||||
Citation | Journal: Nat Commun / Year: 2023 Title: Molecular architecture of the Gα-bound TRPC5 ion channel. Authors: Jongdae Won / Jinsung Kim / Hyeongseop Jeong / Jinhyeong Kim / Shasha Feng / Byeongseok Jeong / Misun Kwak / Juyeon Ko / Wonpil Im / Insuk So / Hyung Ho Lee / Abstract: G-protein coupled receptors (GPCRs) and ion channels serve as key molecular switches through which extracellular stimuli are transformed into intracellular effects, and it has long been postulated ...G-protein coupled receptors (GPCRs) and ion channels serve as key molecular switches through which extracellular stimuli are transformed into intracellular effects, and it has long been postulated that ion channels are direct effector molecules of the alpha subunit of G-proteins (Gα). However, no complete structural evidence supporting the direct interaction between Gα and ion channels is available. Here, we present the cryo-electron microscopy structures of the human transient receptor potential canonical 5 (TRPC5)-Gα complexes with a 4:4 stoichiometry in lipid nanodiscs. Remarkably, Gα binds to the ankyrin repeat edge of TRPC5 ~ 50 Å away from the cell membrane. Electrophysiological analysis shows that Gα increases the sensitivity of TRPC5 to phosphatidylinositol 4,5-bisphosphate (PIP), thereby rendering TRPC5 more easily opened in the cell membrane, where the concentration of PIP is physiologically regulated. Our results demonstrate that ion channels are one of the direct effector molecules of Gα proteins triggered by GPCR activation-providing a structural framework for unraveling the crosstalk between two major classes of transmembrane proteins: GPCRs and ion channels. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 7x6c.cif.gz | 484.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7x6c.ent.gz | 407.5 KB | Display | PDB format |
PDBx/mmJSON format | 7x6c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7x6c_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 7x6c_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 7x6c_validation.xml.gz | 82.1 KB | Display | |
Data in CIF | 7x6c_validation.cif.gz | 117.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x6/7x6c ftp://data.pdbj.org/pub/pdb/validation_reports/x6/7x6c | HTTPS FTP |
-Related structure data
Related structure data | 33021MC 7x6iC 8gvwC 8gvxC M: map data used to model this data C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
|
---|---|
1 |
|
-Components
-Protein , 1 types, 4 molecules CABD
#1: Protein | Mass: 89951.891 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: reisdues 766,777(SR) restriction enzyme site, XbaI, residues 768-773(LEVLFQ) protease cleavage site, HRV-3C Source: (gene. exp.) Homo sapiens (human) / Gene: TRPC5, TRP5 / Production host: Homo sapiens (human) / References: UniProt: Q9UL62 |
---|
-Non-polymers , 6 types, 24 molecules
#2: Chemical | ChemComp-PTY / #3: Chemical | ChemComp-POV / ( #4: Chemical | ChemComp-Y01 / #5: Chemical | ChemComp-ZN / #6: Chemical | ChemComp-CA / #7: Chemical | ChemComp-YZY / ( |
---|
-Details
Has ligand of interest | Y |
---|
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Transient receptor potential / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT |
---|---|
Molecular weight | Experimental value: NO |
Source (natural) | Organism: Homo sapiens (human) |
Source (recombinant) | Organism: Homo sapiens (human) |
Buffer solution | pH: 8 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Microscopy | Model: TFS GLACIOS |
---|---|
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm |
Image recording | Electron dose: 40 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.19.2_4158: / Classification: refinement | ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.15 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 105020 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
|