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- EMDB-22009: Structure of human TRPA1 in complex with agonist GNE551 -

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Basic information

Entry
Database: EMDB / ID: EMD-22009
TitleStructure of human TRPA1 in complex with agonist GNE551
Map data
SampleTRPA1 bound by agonist GNE551
  • Transient receptor potential cation channel subfamily A member 1
  • ligand
Function / homology
Function and homology information


temperature-gated cation channel activity / thermoception / detection of chemical stimulus involved in sensory perception of pain / stereocilium bundle / channel activity / calcium-release channel activity / response to pain / response to organic substance / detection of mechanical stimulus involved in sensory perception of pain / ion transport ...temperature-gated cation channel activity / thermoception / detection of chemical stimulus involved in sensory perception of pain / stereocilium bundle / channel activity / calcium-release channel activity / response to pain / response to organic substance / detection of mechanical stimulus involved in sensory perception of pain / ion transport / calcium ion transmembrane transport / sensory perception of pain / response to cold / response to organic cyclic compound / response to hydrogen peroxide / protein homotetramerization / cell surface receptor signaling pathway / response to drug / integral component of plasma membrane / identical protein binding / plasma membrane
Ankyrin repeat-containing domain / Ankyrin repeat / Ion transport domain / Ankyrin repeat-containing domain superfamily
Transient receptor potential cation channel subfamily A member 1
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3 Å
AuthorsRohou A / Rouge L / Chen H
CitationJournal: Neuron / Year: 2020
Title: A Non-covalent Ligand Reveals Biased Agonism of the TRPA1 Ion Channel.
Authors: Chang Liu / Rebecca Reese / Simon Vu / Lionel Rougé / Shannon D Shields / Satoko Kakiuchi-Kiyota / Huifen Chen / Kevin Johnson / Yu Patrick Shi / Tania Chernov-Rogan / Demi Maria Zabala ...Authors: Chang Liu / Rebecca Reese / Simon Vu / Lionel Rougé / Shannon D Shields / Satoko Kakiuchi-Kiyota / Huifen Chen / Kevin Johnson / Yu Patrick Shi / Tania Chernov-Rogan / Demi Maria Zabala Greiner / Pawan Bir Kohli / David Hackos / Bobby Brillantes / Christine Tam / Tianbo Li / Jianyong Wang / Brian Safina / Steve Magnuson / Matthew Volgraf / Jian Payandeh / Jie Zheng / Alexis Rohou / Jun Chen /
Abstract: The TRPA1 ion channel is activated by electrophilic compounds through the covalent modification of intracellular cysteine residues. How non-covalent agonists activate the channel and whether covalent ...The TRPA1 ion channel is activated by electrophilic compounds through the covalent modification of intracellular cysteine residues. How non-covalent agonists activate the channel and whether covalent and non-covalent agonists elicit the same physiological responses are not understood. Here, we report the discovery of a non-covalent agonist, GNE551, and determine a cryo-EM structure of the TRPA1-GNE551 complex, revealing a distinct binding pocket and ligand-interaction mechanism. Unlike the covalent agonist allyl isothiocyanate, which elicits channel desensitization, tachyphylaxis, and transient pain, GNE551 activates TRPA1 into a distinct conducting state without desensitization and induces persistent pain. Furthermore, GNE551-evoked pain is relatively insensitive to antagonist treatment. Thus, we demonstrate the biased agonism of TRPA1, a finding that has important implications for the discovery of effective drugs tailored to different disease etiologies.
Validation ReportPDB-ID: 6x2j

SummaryFull reportAbout validation report
History
DepositionMay 20, 2020-
Header (metadata) releaseNov 18, 2020-
Map releaseNov 18, 2020-
UpdateDec 2, 2020-
Current statusDec 2, 2020Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.2
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.2
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6x2j
  • Surface level: 0.2
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_22009.map.gz / Format: CCP4 / Size: 129.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1 Å/pix.
x 324 pix.
= 324. Å
1 Å/pix.
x 324 pix.
= 324. Å
1 Å/pix.
x 324 pix.
= 324. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1 Å
Density
Contour LevelBy AUTHOR: 0.2 / Movie #1: 0.2
Minimum - Maximum-1.8475306 - 2.8368795
Average (Standard dev.)0.0000199712 (±0.048187066)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions324324324
Spacing324324324
CellA=B=C: 324.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z111
M x/y/z324324324
origin x/y/z0.0000.0000.000
length x/y/z324.000324.000324.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ256256256
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS324324324
D min/max/mean-1.8482.8370.000

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Supplemental data

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Sample components

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Entire TRPA1 bound by agonist GNE551

EntireName: TRPA1 bound by agonist GNE551 / Number of components: 3

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Component #1: protein, TRPA1 bound by agonist GNE551

ProteinName: TRPA1 bound by agonist GNE551 / Recombinant expression: No
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Spodoptera frugiperda (fall armyworm)

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Component #2: protein, Transient receptor potential cation channel subfamily A ...

ProteinName: Transient receptor potential cation channel subfamily A member 1
Number of Copies: 4 / Recombinant expression: No
MassTheoretical: 72.622125 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Spodoptera frugiperda (fall armyworm)

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Component #3: ligand, 5-amino-1-[(4-bromo-2-fluorophenyl)methyl]-N-(2,5-dimetho...

LigandName: 5-amino-1-[(4-bromo-2-fluorophenyl)methyl]-N-(2,5-dimethoxyphenyl)-1H-1,2,3-triazole-4-carboxamide
Number of Copies: 4 / Recombinant expression: No
MassTheoretical: 0.450262 kDa

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionSpecimen conc.: 0.33 mg/mL / pH: 8.2
Support filmSolarus plasma cleaner
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 277 K / Humidity: 100 %
Details: Triple blot. Put blot in vitroblot Apply 3.5ul to grid, wait 30sec, blot manually Apply 3.5ul to grid, wait 30sec, blot manually, apply final 3.5ul, final blot by vitrobot (3.5s).

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 41.8 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 165000 X (nominal) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Energy filter: GIF Bioquantum
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: GATAN K2 QUANTUM (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 11063 / Sampling size: 5 µm

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C4 (4 fold cyclic) / Number of projections: 58837
3D reconstructionAlgorithm: FOURIER SPACE / Software: cisTEM / Resolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF
Details: Data at spatial frequencies higher than 1/4.0 A-1 were not used during any part of the refinement. The final map was density-modified using Phenix.
FSC plot (resolution estimation)

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Atomic model buiding

Modeling #1Refinement space: REAL
Input PDB model: 6PQQ
Output model

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