+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-5334 | |||||||||
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Title | TRPA1 channel structure at 16A resolution | |||||||||
Map data | This is a TRPA1 channel map at 16A. | |||||||||
Sample |
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Biological species | Mus musculus (house mouse) | |||||||||
Method | single particle reconstruction / negative staining / Resolution: 16.0 Å | |||||||||
Authors | Cvetkov TL / Huynh KW / Cohen MR / Moiseenkova-Bell VY | |||||||||
Citation | Journal: J Biol Chem / Year: 2011 Title: Molecular architecture and subunit organization of TRPA1 ion channel revealed by electron microscopy. Authors: Teresa L Cvetkov / Kevin W Huynh / Matthew R Cohen / Vera Y Moiseenkova-Bell / Abstract: Transient receptor potential ankyrin 1 (TRPA1) is a non-selective ion channel, which is expressed in nociceptor sensory neurons and transduces chemical, inflammatory, and neuropathic pain signals. ...Transient receptor potential ankyrin 1 (TRPA1) is a non-selective ion channel, which is expressed in nociceptor sensory neurons and transduces chemical, inflammatory, and neuropathic pain signals. Numerous non-reactive compounds and electrophilic compounds, such as endogenous inflammatory mediators and exogenous pungent chemicals, can activate TRPA1. Here we report a 16-Å resolution structure of purified, functional, amphipol-stabilized TRPA1 analyzed by single-particle EM. Molecular models of the N and C termini of the channel were generated using the I-TASSER protein structure prediction server and docked into the EM density to provide insight into the TRPA1 subunit organization. This structural analysis suggests a location for critical N-terminal cysteine residues involved in electrophilic activation at the interface between neighboring subunits. Our results indicate that covalent modifications within this pocket may alter interactions between subunits and promote conformational changes that lead to channel activation. | |||||||||
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_5334.map.gz | 2.3 MB | EMDB map data format | |
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Header (meta data) | emd-5334-v30.xml emd-5334.xml | 9.5 KB 9.5 KB | Display Display | EMDB header |
Images | emd_5334_1.png | 133.7 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-5334 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-5334 | HTTPS FTP |
-Validation report
Summary document | emd_5334_validation.pdf.gz | 78.5 KB | Display | EMDB validaton report |
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Full document | emd_5334_full_validation.pdf.gz | 77.6 KB | Display | |
Data in XML | emd_5334_validation.xml.gz | 494 B | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-5334 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-5334 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_5334.map.gz / Format: CCP4 / Size: 15.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | This is a TRPA1 channel map at 16A. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 3.4 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : TRPA1 channel
Entire | Name: TRPA1 channel |
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Components |
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-Supramolecule #1000: TRPA1 channel
Supramolecule | Name: TRPA1 channel / type: sample / ID: 1000 / Details: The sample was monodisperse. / Oligomeric state: Tetramer / Number unique components: 1 |
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Molecular weight | Experimental: 536 KDa / Theoretical: 525 KDa / Method: Gel filtration |
-Macromolecule #1: transient receptor potential cation channel subfamily A member 1
Macromolecule | Name: transient receptor potential cation channel subfamily A member 1 type: protein_or_peptide / ID: 1 / Name.synonym: TRPA1 / Number of copies: 1 / Oligomeric state: Tetramer / Recombinant expression: Yes |
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Source (natural) | Organism: Mus musculus (house mouse) / synonym: house mouse / Location in cell: Plasma Membrane |
Molecular weight | Experimental: 536 KDa / Theoretical: 525 KDa |
Recombinant expression | Organism: Saccharomyces cerevisiae (brewer's yeast) / Recombinant plasmid: YeP |
-Experimental details
-Structure determination
Method | negative staining |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.1 mg/mL |
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Buffer | pH: 8 Details: 20 mM HEPES, pH 8.0, 150 mM NaCl, 10% glycerol, 1.0 mM DTT |
Staining | Type: NEGATIVE Details: TRPA1 was adsorbed on carbon-film coated copper grids, washed with 3 droplets of pure water and subsequently stained with 1% uranyl acetate. |
Grid | Details: 400 mesh copper grids with carbon |
Vitrification | Cryogen name: NONE / Instrument: OTHER |
-Electron microscopy
Microscope | FEI TECNAI F20 |
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Alignment procedure | Legacy - Astigmatism: objective lens astigmatism was corrected at 200,000 times magnification |
Date | May 12, 2011 |
Image recording | Category: CCD / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Average electron dose: 20 e/Å2 |
Tilt angle min | 0 |
Tilt angle max | 0 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 55000 |
Sample stage | Specimen holder: Eucentric / Specimen holder model: OTHER |
Experimental equipment | Model: Tecnai F20 / Image courtesy: FEI Company |
-Image processing
CTF correction | Details: each image |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 16.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: EMAN2 / Number images used: 8505 |
Final two d classification | Number classes: 218 |