|Entry||Database: EMDB / ID: 6267|
|Title||Human TRPA1 ion channel with agonist AITC|
|Map data||Reconstruction of hTRPA1 treated with AITC comprising summed half-maps, unfiltered and unsharpened. Two associated maps are low-pass-filtered and negative-B-factor-sharpened.|
|Sample||Recombinant human TRPA1 treated with AITC:|
|Keywords||TRPA1 / TRP / ion channel|
|Function / homology||Ankyrin repeat-containing domain / Ion transport protein / Transient receptor potential cation channel subfamily A member 1 / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Bacterial extracellular solute-binding protein / Ion transport domain / Ankyrin repeat-containing domain superfamily / Ankyrin repeats (3 copies) / Solute-binding family 1, conserved site / Ankyrin repeat ...Ankyrin repeat-containing domain / Ion transport protein / Transient receptor potential cation channel subfamily A member 1 / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Bacterial extracellular solute-binding protein / Ion transport domain / Ankyrin repeat-containing domain superfamily / Ankyrin repeats (3 copies) / Solute-binding family 1, conserved site / Ankyrin repeat / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding proteins, family 1 signature. / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / TRP channels / temperature-gated cation channel activity / detection of chemical stimulus involved in sensory perception of pain / thermoception / stereocilium bundle / channel activity / detection of mechanical stimulus involved in sensory perception of pain / calcium-release channel activity / response to pain / detection of maltose stimulus / maltose binding / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / maltose transport / maltodextrin transport / carbohydrate transmembrane transporter activity / carbohydrate transport / calcium channel activity / calcium ion transmembrane transport / transporter activity / sensory perception of pain / ATP-binding cassette (ABC) transporter complex / cell chemotaxis / response to cold / ion transport / response to organic substance / response to organic cyclic compound / response to hydrogen peroxide / protein homotetramerization / outer membrane-bounded periplasmic space / periplasmic space / cell surface receptor signaling pathway / cellular response to DNA damage stimulus / integral component of plasma membrane / identical protein binding / plasma membrane / Transient receptor potential cation channel subfamily A member 1 / Maltose-binding periplasmic protein|
Function and homology information
|Source||Homo sapiens (human)|
|Method||single particle reconstruction / cryo EM / 4.24 Å resolution|
|Authors||Paulsen CE / Armache JP / Gao Y / Cheng Y / Julius D|
|Citation||Journal: Nature / Year: 2015|
Title: Structure of the TRPA1 ion channel suggests regulatory mechanisms.
Authors: Candice E Paulsen / Jean-Paul Armache / Yuan Gao / Yifan Cheng / David Julius
Abstract: The TRPA1 ion channel (also known as the wasabi receptor) is a detector of noxious chemical agents encountered in our environment or produced endogenously during tissue injury or drug metabolism. ...The TRPA1 ion channel (also known as the wasabi receptor) is a detector of noxious chemical agents encountered in our environment or produced endogenously during tissue injury or drug metabolism. These include a broad class of electrophiles that activate the channel through covalent protein modification. TRPA1 antagonists hold potential for treating neurogenic inflammatory conditions provoked or exacerbated by irritant exposure. Despite compelling reasons to understand TRPA1 function, structural mechanisms underlying channel regulation remain obscure. Here we use single-particle electron cryo- microscopy to determine the structure of full-length human TRPA1 to ∼4 Å resolution in the presence of pharmacophores, including a potent antagonist. Several unexpected features are revealed, including an extensive coiled-coil assembly domain stabilized by polyphosphate co-factors and a highly integrated nexus that converges on an unpredicted transient receptor potential (TRP)-like allosteric domain. These findings provide new insights into the mechanisms of TRPA1 regulation, and establish a blueprint for structure-based design of analgesic and anti-inflammatory agents.
|Validation Report||PDB-ID: 3j9p|
SummaryFull reportAbout validation report
|Date||Deposition: Feb 14, 2015 / Header (metadata) release: Apr 8, 2015 / Map release: Apr 8, 2015 / Last update: Oct 7, 2015|
|Structure viewer||EM map: |
Downloads & links
|File||emd_6267.map.gz (map file in CCP4 format, 105470 KB)|
|Projections & slices|
Images are generated by Spider.
|Voxel size||X=Y=Z: 1.2156 Å|
CCP4 map header:
-Entire Recombinant human TRPA1 treated with AITC
|Entire||Name: Recombinant human TRPA1 treated with AITC / Details: The sample was monodisperse. / Number of components: 1 / Oligomeric State: tetramer|
|Mass||Theoretical: 688 kDa|
-Component #1: protein, TRPA1
a.k.a: Transient receptor potential cation channel, member A1
Oligomeric Details: tetramer / Recombinant expression: Yes / Number of Copies: 4
|Mass||Theoretical: 172 kDa / Experimental: 172 kDa|
|Source||Species: Homo sapiens (human)|
|Source (engineered)||Expression System: Homo sapiens (human) / Cell of expression system: HEK293 GnTi-|
|External references||UniProt: UniProt:O75762|
|Specimen||Specimen state: particle / Method: cryo EM|
|Sample solution||Specimen conc.: 0.5 mg/ml|
Buffer solution: 20 mM HEPES, 150 mM NaCl, 1 mM DTT, 1 mM IP6
|Support film||400 mesh holey carbon|
|Vitrification||Instrument: FEI VITROBOT MARK I / Cryogen name: ETHANE / Temperature: 120 K / Humidity: 100 % / Method: Blot for 7 seconds before plunging.|
-Electron microscopy imaging
Model: Tecnai Polara / Image courtesy: FEI Company
|Imaging||Microscope: FEI POLARA 300 / Date: Jul 18, 2014|
Details: Gatan K2 Summit in super-resolution counting mode. Motion correction as described in Li et al. (2013) Nature Methods.
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 21 e/Å2 / Illumination mode: FLOOD BEAM|
|Lens||Magnification: 31000 X (nominal), 31000 X (calibrated) / Cs: 2 mm / Imaging mode: BRIGHT FIELD / Defocus: 1500 - 2800 nm|
|Specimen Holder||Model: OTHER|
|Camera||Detector: GATAN K2 (4k x 4k)|
|Image acquisition||Number of digital images: 1160|
Details: Every image is the average of 30 frames recorded using the K2 Summit. The final reconstruction was calculated from images motion-corrected and weighted using the method described in Scheres, 2014.
URL of raw data: http://dx.doi.org/10.6019/EMPIAR-10024
|Raw data||EMPIAR-10024 (Title: Human TRPA1 ion channel with agonist AITC / Data size: 453.0 GB|
Data #1: TRP ion channel dataset [picked particles - multiframe - unprocessed])
|Processing||Method: single particle reconstruction / Applied symmetry: C4 (4 fold cyclic) / Number of projections: 43585|
Details: Particles were selected using an automatic selection program and manually screened. Defocus was calculated using CTFFIND3 and data were processed and refined using RELION 1.3.
|3D reconstruction||Algorithm: Maximum likelihood / Software: RELION / CTF correction: Each particle / Resolution: 4.24 Å / Resolution method: FSC 0.143, gold-standard|
-Atomic model buiding
-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.
- All the functionalities will be ported from the levgacy version.
- 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