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- PDB-8ed8: cryo-EM structure of TRPM3 ion channel in the presence of PIP2 an... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8ed8 | ||||||
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Title | cryo-EM structure of TRPM3 ion channel in the presence of PIP2 and PregS, state 1 | ||||||
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![]() | MEMBRANE PROTEIN / TRPM3 / ion channel / PIP2 | ||||||
Function / homology | ![]() metal ion transport / monoatomic cation transmembrane transport / monoatomic cation transport / monoatomic cation channel activity / protein tetramerization / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å | ||||||
![]() | Zhao, C. / MacKinnon, R. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structural and functional analyses of a GPCR-inhibited ion channel TRPM3. Authors: Chen Zhao / Roderick MacKinnon / ![]() Abstract: G-protein coupled receptors (GPCRs) govern the physiological response to stimuli by modulating the activity of downstream effectors, including ion channels. TRPM3 is an ion channel inhibited by GPCRs ...G-protein coupled receptors (GPCRs) govern the physiological response to stimuli by modulating the activity of downstream effectors, including ion channels. TRPM3 is an ion channel inhibited by GPCRs through direct interaction with G protein (Gβγ) released upon their activation. This GPCR-TRPM3 signaling pathway contributes to the analgesic effect of morphine. Here, we characterized Gβγ inhibition of TRPM3 using electrophysiology and single particle cryo-electron microscopy (cryo-EM). From electrophysiology, we obtained a half inhibition constant (IC50) of ∼240 nM. Using cryo-EM, we determined structures of mouse TRPM3 expressed in human cells with and without Gβγ and with and without PIP, a lipid required for TRPM3 activity, at resolutions of 2.7-4.7 Å. Gβγ-TRPM3 interfaces vary depending on PIP occupancy; however, in all cases, Gβγ appears loosely attached to TRPM3. The IC50 in electrophysiology experiments raises the possibility that additional unknown factors may stabilize the TRPM3-Gβγ complex. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 717.8 KB | Display | ![]() |
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PDB format | ![]() | 580 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 28032MC ![]() 8ddqC ![]() 8ddrC ![]() 8ddsC ![]() 8ddtC ![]() 8dduC ![]() 8ddvC ![]() 8ddwC ![]() 8ddxC ![]() 8ed7C ![]() 8ed9C C: citing same article ( M: map data used to model this data |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Components
-Protein / Protein/peptide , 2 types, 8 molecules ABCDEFGH
#1: Protein | Mass: 154780.516 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein/peptide | Mass: 1464.797 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 4 types, 13 molecules ![](data/chem/img/3PH.gif)
![](data/chem/img/9Z9.gif)
![](data/chem/img/PIO.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/9Z9.gif)
![](data/chem/img/PIO.gif)
![](data/chem/img/NA.gif)
#3: Chemical | ChemComp-3PH / #4: Chemical | ChemComp-9Z9 / ( #5: Chemical | ChemComp-PIO / [( #6: Chemical | ChemComp-NA / | |
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-Details
Has ligand of interest | Y |
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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 |
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Sample preparation
Component | Name: TRPM3 / Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: ![]() ![]() |
Source (recombinant) | Organism: ![]() |
Buffer solution | pH: 8.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
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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: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm |
Image recording | Electron dose: 51.44 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
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Processing
Software | Name: PHENIX / Version: 1.20.1_4487: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
Symmetry | Point symmetry: C4 (4 fold cyclic) | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 224116 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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