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- EMDB-6267: Human TRPA1 ion channel with agonist AITC -

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Basic information

Entry
Database: EMDB / ID: EMD-6267
TitleHuman TRPA1 ion channel with agonist AITC
Map dataReconstruction 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
  • Sample: Recombinant human TRPA1 treated with AITC
  • Protein or peptide: TRPA1
KeywordsTRPA1 / TRP / 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 / response to pain / detection of maltose stimulus / maltose transport complex / maltose binding / carbohydrate transport ...temperature-gated cation channel activity / stereocilium bundle / detection of chemical stimulus involved in sensory perception of pain / thermoception / TRP channels / response to pain / detection of maltose stimulus / maltose transport complex / maltose binding / carbohydrate transport / maltose transport / intracellularly gated calcium channel activity / maltodextrin transmembrane transport / carbohydrate transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / detection of mechanical stimulus involved in sensory perception of pain / monoatomic ion transport / sensory perception of pain / response to cold / ATP-binding cassette (ABC) transporter complex / cell chemotaxis / calcium ion transmembrane transport / calcium channel activity / response to organic cyclic compound / cellular response to hydrogen peroxide / intracellular calcium ion homeostasis / channel activity / outer membrane-bounded periplasmic space / protein homotetramerization / periplasmic space / cell surface receptor signaling pathway / response to xenobiotic stimulus / DNA damage response / identical protein binding / membrane / plasma membrane
Similarity search - Function
: / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / Ankyrin repeat / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. ...: / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / Ankyrin repeat / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Ion transport domain / Ion transport protein
Similarity search - Domain/homology
Transient receptor potential cation channel subfamily A member 1 / Maltose/maltodextrin-binding periplasmic protein
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.24 Å
AuthorsPaulsen CE / Armache JP / Gao Y / Cheng Y / Julius D
CitationJournal: 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
DepositionFeb 14, 2015-
Header (metadata) releaseApr 8, 2015-
Map releaseApr 8, 2015-
UpdateOct 7, 2015-
Current statusOct 7, 2015Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 8
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 8
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-3j9p
  • Surface level: 8
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_6267.png

Downloads & links

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Map

FileDownload / File: emd_6267.map.gz / Format: CCP4 / Size: 100.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of hTRPA1 treated with AITC comprising summed half-maps, unfiltered and unsharpened. Two associated maps are low-pass-filtered and negative-B-factor-sharpened.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.22 Å/pix.
x 300 pix.
= 364.68 Å		1.22 Å/pix.
x 300 pix.
= 364.68 Å		1.22 Å/pix.
x 300 pix.
= 364.68 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.2156 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 8.0 / Movie #1: 8
Minimum - Maximum-12.649605749999999 - 20.724081040000002
Average (Standard dev.)0.0 (±0.99999994)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-150-150-150
Dimensions300300300
Spacing300300300
CellA=B=C: 364.68 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.21561.21561.2156
M x/y/z300300300
origin x/y/z0.0000.0000.000
length x/y/z364.680364.680364.680
α/β/γ90.00090.00090.000
start NX/NY/NZ-800-4
NX/NY/NZ1611358
MAP C/R/S123
start NC/NR/NS-150-150-150
NC/NR/NS300300300
D min/max/mean-12.65020.7240.000

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Supplemental data

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Supplemental map: emd 6267 additional 1.map

Fileemd_6267_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Supplemental map: emd 6267 additional 2.map

Fileemd_6267_additional_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Recombinant human TRPA1 treated with AITC

EntireName: Recombinant human TRPA1 treated with AITC
Components
  • Sample: Recombinant human TRPA1 treated with AITC
  • Protein or peptide: TRPA1

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Supramolecule #1000: Recombinant human TRPA1 treated with AITC

SupramoleculeName: Recombinant human TRPA1 treated with AITC / type: sample / ID: 1000 / Details: The sample was monodisperse. / Oligomeric state: tetramer / Number unique components: 1
Molecular weightTheoretical: 688 KDa

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Macromolecule #1: TRPA1

MacromoleculeName: 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
Source (natural)Organism: Homo sapiens (human) / synonym: human
Molecular weightExperimental: 172 KDa / Theoretical: 172 KDa
Recombinant expressionOrganism: Homo sapiens (human) / Recombinant cell: HEK293 GnTi-
SequenceUniProtKB: Transient receptor potential cation channel subfamily A member 1

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.5 mg/mL
BufferpH: 8 / Details: 20 mM HEPES, 150 mM NaCl, 1 mM DTT, 1 mM IP6
GridDetails: 400 mesh holey carbon
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 120 K / Instrument: FEI VITROBOT MARK I / Method: Blot for 7 seconds before plunging.

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Electron microscopy

MicroscopeFEI POLARA 300
DetailsGatan K2 Summit in super-resolution counting mode. Motion correction as described in Li et al. (2013) Nature Methods.
DateJul 18, 2014
Image recordingCategory: CCD / Film or detector model: GATAN K2 (4k x 4k) / Number real images: 1160 / 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 beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated 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 stageSpecimen holder model: OTHER
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

DetailsParticles 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.
CTF correctionDetails: Each particle
Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 4.24 Å / Resolution method: OTHER / Software - Name: RELION / Number images used: 43585

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