|Entry||Database: PDB / ID: 6x2j|
|Title||Structure of human TRPA1 in complex with agonist GNE551|
|Components||Transient receptor potential cation channel subfamily A member 1|
|Keywords||MEMBRANE PROTEIN/Agonist / TRPA1 / channel / agonist / MEMBRANE PROTEIN / MEMBRANE PROTEIN-Agonist complex|
|Function / homology|
Function and homology information
temperature-gated cation channel activity / thermoception / detection of chemical stimulus involved in sensory perception of pain / stereocilium bundle / channel activity / calcium-release channel activity / response to pain / response to organic substance / detection of mechanical stimulus involved in sensory perception of pain / ion transport ...temperature-gated cation channel activity / thermoception / detection of chemical stimulus involved in sensory perception of pain / stereocilium bundle / channel activity / calcium-release channel activity / response to pain / response to organic substance / detection of mechanical stimulus involved in sensory perception of pain / ion transport / calcium ion transmembrane transport / sensory perception of pain / response to cold / response to organic cyclic compound / response to hydrogen peroxide / protein homotetramerization / cell surface receptor signaling pathway / response to drug / integral component of plasma membrane / identical protein binding / plasma membrane
Ankyrin repeat-containing domain / Ankyrin repeat / Ion transport domain / Ankyrin repeat-containing domain superfamily
Transient receptor potential cation channel subfamily A member 1
|Biological species||Homo sapiens (human)|
|Method||ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3 Å|
|Authors||Rohou, A. / Rouge, L. / Chen, H.|
|Citation||Journal: Neuron / Year: 2020|
Title: A Non-covalent Ligand Reveals Biased Agonism of the TRPA1 Ion Channel.
Authors: Chang Liu / Rebecca Reese / Simon Vu / Lionel Rougé / Shannon D Shields / Satoko Kakiuchi-Kiyota / Huifen Chen / Kevin Johnson / Yu Patrick Shi / Tania Chernov-Rogan / Demi Maria Zabala ...Authors: Chang Liu / Rebecca Reese / Simon Vu / Lionel Rougé / Shannon D Shields / Satoko Kakiuchi-Kiyota / Huifen Chen / Kevin Johnson / Yu Patrick Shi / Tania Chernov-Rogan / Demi Maria Zabala Greiner / Pawan Bir Kohli / David Hackos / Bobby Brillantes / Christine Tam / Tianbo Li / Jianyong Wang / Brian Safina / Steve Magnuson / Matthew Volgraf / Jian Payandeh / Jie Zheng / Alexis Rohou / Jun Chen /
Abstract: The TRPA1 ion channel is activated by electrophilic compounds through the covalent modification of intracellular cysteine residues. How non-covalent agonists activate the channel and whether covalent ...The TRPA1 ion channel is activated by electrophilic compounds through the covalent modification of intracellular cysteine residues. How non-covalent agonists activate the channel and whether covalent and non-covalent agonists elicit the same physiological responses are not understood. Here, we report the discovery of a non-covalent agonist, GNE551, and determine a cryo-EM structure of the TRPA1-GNE551 complex, revealing a distinct binding pocket and ligand-interaction mechanism. Unlike the covalent agonist allyl isothiocyanate, which elicits channel desensitization, tachyphylaxis, and transient pain, GNE551 activates TRPA1 into a distinct conducting state without desensitization and induces persistent pain. Furthermore, GNE551-evoked pain is relatively insensitive to antagonist treatment. Thus, we demonstrate the biased agonism of TRPA1, a finding that has important implications for the discovery of effective drugs tailored to different disease etiologies.
SummaryFull reportAbout validation report
|Structure viewer||Molecule: |
Downloads & links
A: Transient receptor potential cation channel subfamily A member 1
B: Transient receptor potential cation channel subfamily A member 1
C: Transient receptor potential cation channel subfamily A member 1
D: Transient receptor potential cation channel subfamily A member 1
Mass: 72622.125 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRPA1, ANKTM1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: O75762
Mass: 450.262 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C18H17BrFN5O3 / Feature type: SUBJECT OF INVESTIGATION
|Has ligand of interest||Y|
|Experiment||Method: ELECTRON MICROSCOPY|
|EM experiment||Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction|
|Component||Name: TRPA1 bound by agonist GNE551 / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT|
|Molecular weight||Units: MEGADALTONS / Experimental value: NO|
|Source (natural)||Organism: Homo sapiens (human)|
|Source (recombinant)||Organism: Spodoptera frugiperda (fall armyworm)|
|Buffer solution||pH: 8.2|
|Specimen||Conc.: 0.33 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES|
|Specimen support||Details: Solarus plasma cleaner / Grid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R0.6/1|
|Vitrification||Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K|
Details: Triple blot. Put blot in vitroblot Apply 3.5ul to grid, wait 30sec, blot manually Apply 3.5ul to grid, wait 30sec, blot manually, apply final 3.5ul, final blot by vitrobot (3.5s)
-Electron microscopy imaging
Model: Titan Krios / Image courtesy: FEI Company
|Microscopy||Model: FEI TITAN KRIOS|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM|
|Electron lens||Mode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 165000 X / Cs: 2.7 mm / C2 aperture diameter: 70 µm / Alignment procedure: COMA FREE|
|Specimen holder||Cryogen: NITROGEN / Model: FEI TITAN KRIOS AUTOGRID HOLDER|
|Image recording||Average exposure time: 1.6 sec. / Electron dose: 41.8 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 11063|
|EM imaging optics||Energyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV|
|Image scans||Sampling size: 5 µm / Movie frames/image: 40 / Used frames/image: 1-40|
|CTF correction||Type: PHASE FLIPPING AND AMPLITUDE CORRECTION|
|Particle selection||Num. of particles selected: 505112|
|Symmetry||Point symmetry: C4 (4 fold cyclic)|
|3D reconstruction||Resolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 58837 / Algorithm: FOURIER SPACE|
Details: Data at spatial frequencies higher than 1/4.0 A-1 were not used during any part of the refinement. The final map was density-modified using Phenix.
Symmetry type: POINT
|Atomic model building||Protocol: AB INITIO MODEL / Space: REAL|
|Atomic model building||PDB-ID: 6PQQ|
-Aug 12, 2020. New: Covid-19 info
New: Covid-19 info
Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data
-Mar 5, 2020. Novel coronavirus structure data
Novel coronavirus structure data
- International Committee on Taxonomy of Viruses (ICTV) defined the short name of the 2019 coronavirus as "SARS-CoV-2".
The species Severe acute respiratory syndrome-related coronavirus: classifying 2019-nCoV and naming it SARS-CoV-2 - nature microbiology
- In the structure databanks used in Yorodumi, some data are registered as the other names, "COVID-19 virus" and "2019-nCoV". Here are the details of the virus and the list of structure data.
Related info.:Yorodumi Speices / Aug 12, 2020. New: Covid-19 info
+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)
EMDB accession codes are about to change! (news from PDBe EMDB page)
- The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force. (see PDBe EMDB page)
- The EM Navigator/Yorodumi systems omit the EMD- prefix.
Related info.:Q: What is "EMD"? / ID/Accession-code notation in Yorodumi/EM Navigator
+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
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