+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-6269 | |||||||||
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Title | Human TRPA1 ion channel with antagonist HC030031 | |||||||||
Map data | Reconstruction of hTRPA1 treated with HC03031: summed half-maps, unfiltered and unsharpened. Two associated maps are low-pass filtered and negative-B-factor sharpened. | |||||||||
Sample |
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Keywords | TRPA1 / TRP / ion / ion channel | |||||||||
Function / homology | Function and homology information temperature-gated cation channel activity / stereocilium bundle / detection of chemical stimulus involved in sensory perception of pain / thermoception / TRP channels / channel activity / : / response to pain / intracellularly gated calcium channel activity / : ...temperature-gated cation channel activity / stereocilium bundle / detection of chemical stimulus involved in sensory perception of pain / thermoception / TRP channels / channel activity / : / response to pain / intracellularly gated calcium channel activity / : / detection of mechanical stimulus involved in sensory perception of pain / monoatomic ion transport / sensory perception of pain / response to cold / calcium ion transmembrane transport / calcium channel activity / response to organic cyclic compound / intracellular calcium ion homeostasis / cellular response to hydrogen peroxide / protein homotetramerization / cell surface receptor signaling pathway / response to xenobiotic stimulus / identical protein binding / plasma membrane Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.67 Å | |||||||||
Authors | Paulsen CE / Armache J-P / 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. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_6269.map.gz | 76.4 MB | EMDB map data format | |
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Header (meta data) | emd-6269-v30.xml emd-6269.xml | 10 KB 10 KB | Display Display | EMDB header |
Images | emd_6269.png | 4.6 MB | ||
Others | emd_6269_additional_1.map.gz emd_6269_additional_2.map.gz | 2.9 MB 3 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-6269 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-6269 | HTTPS FTP |
-Validation report
Summary document | emd_6269_validation.pdf.gz | 78.8 KB | Display | EMDB validaton report |
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Full document | emd_6269_full_validation.pdf.gz | 77.6 KB | Display | |
Data in XML | emd_6269_validation.xml.gz | 495 B | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-6269 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-6269 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_6269.map.gz / Format: CCP4 / Size: 100.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Reconstruction of hTRPA1 treated with HC03031: summed half-maps, unfiltered and unsharpened. Two associated maps are low-pass filtered and negative-B-factor sharpened. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.2156 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Supplemental map: emd 6269 additional 1.map
File | emd_6269_additional_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Supplemental map: emd 6269 additional 2.map
File | emd_6269_additional_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Recombinant human TRPA1 treated with HC03031
Entire | Name: Recombinant human TRPA1 treated with HC03031 |
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Components |
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-Supramolecule #1000: Recombinant human TRPA1 treated with HC03031
Supramolecule | Name: Recombinant human TRPA1 treated with HC03031 / type: sample / ID: 1000 / Details: The sample was monodisperse. / Oligomeric state: tetramer / Number unique components: 1 |
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Molecular weight | Theoretical: 688 KDa |
-Macromolecule #1: TRPA1
Macromolecule | Name: TRPA1 / type: protein_or_peptide / ID: 1 Name.synonym: Transient receptor potential cation channel, member A1 Number of copies: 4 / Oligomeric state: tetramer / Recombinant expression: Yes |
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Source (natural) | Organism: Homo sapiens (human) / synonym: human |
Molecular weight | Experimental: 172 KDa / Theoretical: 172 KDa |
Recombinant expression | Organism: Homo sapiens (human) / Recombinant cell: HEK293 GnTi- |
Sequence | UniProtKB: Transient receptor potential cation channel subfamily A member 1 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.5 mg/mL |
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Buffer | pH: 8 / Details: 20 mM HEPES, 150 mM NaCl, 1 mM DTT, 1 mM IP6 |
Grid | Details: 400 mesh holey carbon |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 120 K / Instrument: FEI VITROBOT MARK I / Method: Blot for 7 seconds before plunging. |
-Electron microscopy
Microscope | FEI POLARA 300 |
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Details | Gatan K2 Summit in super-resolution counting mode. Motion correction as described in Li et al. (2013) Nature Methods. |
Date | Sep 8, 2014 |
Image recording | Category: CCD / Film or detector model: GATAN K2 (4k x 4k) / Number real images: 810 / Average electron dose: 21 e/Å2 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. |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated magnification: 31000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 2.8 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 31000 |
Sample stage | Specimen holder model: OTHER |
Experimental equipment | Model: Tecnai Polara / Image courtesy: FEI Company |
-Image processing
Details | The particles were selected using an automatic selection program and manually screened. Defocus was calculated using CTFFIND3. Data were processed and refined using RELION 1.3. |
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CTF correction | Details: Each particle |
Final reconstruction | Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 4.67 Å / Resolution method: OTHER / Software - Name: RELION / Number images used: 21930 |