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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 dataDensity-modified map
Sample
  • Complex: TRPA1 bound by agonist GNE551
    • Protein or peptide: Transient receptor potential cation channel subfamily A member 1
  • Ligand: 5-amino-1-[(4-bromo-2-fluorophenyl)methyl]-N-(2,5-dimethoxyphenyl)-1H-1,2,3-triazole-4-carboxamide
KeywordsTRPA1 / channel / agonist / MEMBRANE PROTEIN / MEMBRANE PROTEIN-Agonist complex
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 / cellular response to organic substance / intracellularly gated calcium channel activity / detection of mechanical stimulus involved in sensory perception of pain ...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 / cellular response to organic substance / 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 / response to organic substance / calcium ion transmembrane transport / calcium channel activity / intracellular calcium ion homeostasis / response to organic cyclic compound / cellular response to hydrogen peroxide / protein homotetramerization / cell surface receptor signaling pathway / response to xenobiotic stimulus / identical protein binding / plasma membrane
Similarity search - Function
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
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsRohou A / Rouge L / Chen H
CitationJournal: Neuron / Year: 2021
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.
History
DepositionMay 20, 2020-
Header (metadata) releaseNov 18, 2020-
Map releaseNov 18, 2020-
UpdateMar 6, 2024-
Current statusMar 6, 2024Processing 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

emd_22009.png

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)
AnnotationDensity-modified map
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.)0.00001997122 (±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
Components
  • Complex: TRPA1 bound by agonist GNE551
    • Protein or peptide: Transient receptor potential cation channel subfamily A member 1
  • Ligand: 5-amino-1-[(4-bromo-2-fluorophenyl)methyl]-N-(2,5-dimethoxyphenyl)-1H-1,2,3-triazole-4-carboxamide

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Supramolecule #1: TRPA1 bound by agonist GNE551

SupramoleculeName: TRPA1 bound by agonist GNE551 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Transient receptor potential cation channel subfamily A member 1

MacromoleculeName: Transient receptor potential cation channel subfamily A member 1
type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 72.622125 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: SPLHFAASYG RINTCQRLLQ DISDTRLLNE GDLHGMTPLH LAAKNGHDKV VQLLLKKGAL FLSDHNGWTA LHHASMGGYT QTMKVILDT NLKCTDRLDE DGNTALHFAA REGHAKAVAL LLSHNADIVL NKQQASFLHL ALHNKRKEVV LTIIRSKRWD E CLKIFSHN ...String:
SPLHFAASYG RINTCQRLLQ DISDTRLLNE GDLHGMTPLH LAAKNGHDKV VQLLLKKGAL FLSDHNGWTA LHHASMGGYT QTMKVILDT NLKCTDRLDE DGNTALHFAA REGHAKAVAL LLSHNADIVL NKQQASFLHL ALHNKRKEVV LTIIRSKRWD E CLKIFSHN SPGNKCPITE MIEYLPECMK VLLDFCMLHS TEDKSCRDYY IEYNFKYLQC PLEFTKKTPT QDVIYEPLTA LN AMVQNNR IELLNHPVCK EYLLMKWLAY GFRAHMMNLG SYCLGLIPMT ILVVNIKPGM AFNSTGIINE TSDHSEILDT TNS YLIKTC MILVFLSSIF GYCKEAGQIF QQKRNYFMDI SNVLEWIIYT TGIIFVLPLF VEIPAHLQWQ CGAIAVYFYW MNFL LYLQR FENCGIFIVM LEVILKTLLR STVVFIFLLL AFGLSFYILL NLQDPFSSPL LSIIQTFSMM LGDINYRESF LEPYL RNEL AHPVLSFAQL VSFTIFVPIV LMNLLIGLAV GDIADVQKHA SLKRIAMQVE LHTSLEKKLP LWFLRKVDQK STIVYP NKP RSGGMLFHIF CFLFCTGEIR QEIPNADKSL EMEILKQKYR LKDLTFLLEK QHELIKLIIQ KMEIISET

UniProtKB: Transient receptor potential cation channel subfamily A member 1

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Macromolecule #2: 5-amino-1-[(4-bromo-2-fluorophenyl)methyl]-N-(2,5-dimethoxyphenyl...

MacromoleculeName: 5-amino-1-[(4-bromo-2-fluorophenyl)methyl]-N-(2,5-dimethoxyphenyl)-1H-1,2,3-triazole-4-carboxamide
type: ligand / ID: 2 / Number of copies: 4 / Formula: ULJ
Molecular weightTheoretical: 450.262 Da
Chemical component information

ChemComp-ULJ:
5-amino-1-[(4-bromo-2-fluorophenyl)methyl]-N-(2,5-dimethoxyphenyl)-1H-1,2,3-triazole-4-carboxamide

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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

Concentration0.33 mg/mL
BufferpH: 8.2
Component:
ConcentrationNameFormula
25.0 mMTris
150.0 mMNaClSodium chlorideNaClSodium chloride
0.5 mMTCEP
GridModel: Quantifoil R0.6/1 / Material: GOLD / Mesh: 300 / Support film - #0 - Film type ID: 1 / Support film - #0 - Material: CARBON / Support film - #0 - topology: HOLEY / Support film - #1 - Film type ID: 2 / Support film - #1 - Material: GOLD / Support film - #1 - topology: HOLEY / Support film - #1 - Film thickness: 25 / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: OTHER / Pretreatment - Pressure: 0.1 kPa / Details: Solarus plasma cleaner
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV
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

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal magnification: 165000
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: COUNTING / Digitization - Frames/image: 1-40 / Number grids imaged: 1 / Number real images: 11063 / Average exposure time: 1.6 sec. / Average electron dose: 41.8 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 505112
Startup modelType of model: NONE
Initial angle assignmentType: RANDOM ASSIGNMENT / Software - Name: cisTEM
Final 3D classificationNumber classes: 5
Software:
Namedetails
cisTEM3D reconstruction
PHENIXDensity modification
Final angle assignmentType: OTHER / Software - Name: cisTEM
Final reconstructionApplied symmetry - Point group: C4 (4 fold cyclic) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cisTEM
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.
Number images used: 58837
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

6pqq


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-6x2j:
Structure of human TRPA1 in complex with agonist GNE551

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