|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 / TRP channels / Ankyrin repeat region circular profile. / Ankyrin repeat profile. / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Ankyrin repeat / Ankyrin repeats (3 copies) / Ion transport protein / Ankyrin repeat-containing domain superfamily ...Ankyrin repeat-containing domain / TRP channels / Ankyrin repeat region circular profile. / Ankyrin repeat profile. / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Ankyrin repeat / Ankyrin repeats (3 copies) / Ion transport protein / Ankyrin repeat-containing domain superfamily / Ion transport domain / Bacterial extracellular solute-binding protein / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Transient receptor potential cation channel subfamily A member 1 / thermoception / temperature-gated cation channel activity / detection of chemical stimulus involved in sensory perception of pain / stereocilium bundle / channel activity / response to pain / calcium-release channel activity / detection of maltose stimulus / maltose binding / maltose transport / maltodextrin transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / carbohydrate transmembrane transporter activity / carbohydrate transport / transporter activity / calcium channel activity / sensory perception of pain / calcium ion transmembrane transport / ion transport / detection of mechanical stimulus involved in sensory perception of pain / response to organic substance / ATP-binding cassette (ABC) transporter complex / cell chemotaxis / response to cold / response to organic cyclic compound / response to hydrogen peroxide / outer membrane-bounded periplasmic space / protein homotetramerization / cell surface receptor signaling pathway / periplasmic space / 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/maltodextrin-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
|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: Transient receptor potential cation channel subfamily A member 1|
|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 |
Data #1: TRP ion channel dataset [picked particles - single frame - processed])
|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|
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