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- EMDB-22490: Structure of human TRPA1 in complex with antagonist compound 21 -

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Basic information

Entry
Database: EMDB / ID: EMD-22490
TitleStructure of human TRPA1 in complex with antagonist compound 21
Map dataOutput from density modification in Phenix
Sample
  • Complex: TRPA1 bound by antagonist compound 21
    • Protein or peptide: Transient receptor potential cation channel subfamily A member 1
  • Ligand: 1-({3-[(3R,5R)-5-(4-fluorophenyl)oxolan-3-yl]-1,2,4-oxadiazol-5-yl}methyl)-7-methyl-1,7-dihydro-6H-purin-6-one
KeywordsTRPA1 / channel / agonist / MEMBRANE PROTEIN / MEMBRANE PROTEIN-Antagonist 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 / 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 ...temperature-gated cation channel activity / stereocilium bundle / detection of chemical stimulus involved in sensory perception of pain / thermoception / TRP channels / 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 / cellular response to hydrogen peroxide / intracellular calcium ion homeostasis / channel activity / 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: 3.05 Å
AuthorsRohou A / Rouge L / Chen H
CitationJournal: J Med Chem / Year: 2021
Title: Tetrahydrofuran-Based Transient Receptor Potential Ankyrin 1 (TRPA1) Antagonists: Ligand-Based Discovery, Activity in a Rodent Asthma Model, and Mechanism-of-Action via Cryogenic Electron Microscopy.
Authors: Jack A Terrett / Huifen Chen / Daniel G Shore / Elisia Villemure / Robin Larouche-Gauthier / Martin Déry / Francis Beaumier / Léa Constantineau-Forget / Chantal Grand-Maître / Luce ...Authors: Jack A Terrett / Huifen Chen / Daniel G Shore / Elisia Villemure / Robin Larouche-Gauthier / Martin Déry / Francis Beaumier / Léa Constantineau-Forget / Chantal Grand-Maître / Luce Lépissier / Stéphane Ciblat / Claudio Sturino / Yong Chen / Baihua Hu / Aijun Lu / Yunli Wang / Andrew P Cridland / Stuart I Ward / David H Hackos / Rebecca M Reese / Shannon D Shields / Jun Chen / Alessia Balestrini / Lorena Riol-Blanco / Wyne P Lee / John Liu / Eric Suto / Xiumin Wu / Juan Zhang / Justin Q Ly / Hank La / Kevin Johnson / Matt Baumgardner / Kang-Jye Chou / Alexis Rohou / Lionel Rougé / Brian S Safina / Steven Magnuson / Matthew Volgraf /
Abstract: Transient receptor potential ankyrin 1 (TRPA1) is a nonselective calcium-permeable ion channel highly expressed in the primary sensory neurons functioning as a polymodal sensor for exogenous and ...Transient receptor potential ankyrin 1 (TRPA1) is a nonselective calcium-permeable ion channel highly expressed in the primary sensory neurons functioning as a polymodal sensor for exogenous and endogenous stimuli and has generated widespread interest as a target for inhibition due to its implication in neuropathic pain and respiratory disease. Herein, we describe the optimization of a series of potent, selective, and orally bioavailable TRPA1 small molecule antagonists, leading to the discovery of a novel tetrahydrofuran-based linker. Given the balance of physicochemical properties and strong target engagement in a rat AITC-induced pain assay, compound was progressed into a guinea pig ovalbumin asthma model where it exhibited significant dose-dependent reduction of inflammatory response. Furthermore, the structure of the TRPA1 channel bound to compound was determined via cryogenic electron microscopy to a resolution of 3 Å, revealing the binding site and mechanism of action for this class of antagonists.
History
DepositionAug 20, 2020-
Header (metadata) releaseMar 31, 2021-
Map releaseMar 31, 2021-
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: 0.46
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.46
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7jup
  • Surface level: 0.46
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_22490.png

Downloads & links

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Map

FileDownload / File: emd_22490.map.gz / Format: CCP4 / Size: 4.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationOutput from density modification in Phenix
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
1.26 Å/pix.
x 99 pix.
= 124.938 Å		1.26 Å/pix.
x 99 pix.
= 124.938 Å		1.26 Å/pix.
x 114 pix.
= 143.868 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 1.262 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.46 / Movie #1: 0.46
Minimum - Maximum-1.6093935 - 2.9291418
Average (Standard dev.)-0.000000000001662 (±0.2242722)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin15015
Dimensions9911499
Spacing9999114
CellA: 124.937996 Å / B: 124.937996 Å / C: 143.868 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.2621.2621.262
M x/y/z9999114
origin x/y/z0.0000.0000.000
length x/y/z124.938124.938143.868
α/β/γ90.00090.00090.000
start NX/NY/NZ15150
NX/NY/NZ9999114
MAP C/R/S321
start NC/NR/NS01515
NC/NR/NS1149999
D min/max/mean-1.6092.929-0.000

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Supplemental data

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Half map: Half-map 1

Fileemd_22490_half_map_1.map
AnnotationHalf-map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map 2

Fileemd_22490_half_map_2.map
Annotationhalf map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : TRPA1 bound by antagonist compound 21

EntireName: TRPA1 bound by antagonist compound 21
Components
  • Complex: TRPA1 bound by antagonist compound 21
    • Protein or peptide: Transient receptor potential cation channel subfamily A member 1
  • Ligand: 1-({3-[(3R,5R)-5-(4-fluorophenyl)oxolan-3-yl]-1,2,4-oxadiazol-5-yl}methyl)-7-methyl-1,7-dihydro-6H-purin-6-one

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Supramolecule #1: TRPA1 bound by antagonist compound 21

SupramoleculeName: TRPA1 bound by antagonist compound 21 / 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: 1-({3-[(3R,5R)-5-(4-fluorophenyl)oxolan-3-yl]-1,2,4-oxadiazol-5-y...

MacromoleculeName: 1-({3-[(3R,5R)-5-(4-fluorophenyl)oxolan-3-yl]-1,2,4-oxadiazol-5-yl}methyl)-7-methyl-1,7-dihydro-6H-purin-6-one
type: ligand / ID: 2 / Number of copies: 4 / Formula: VKM
Molecular weightTheoretical: 396.375 Da
Chemical component information

ChemComp-VKM:
1-({3-[(3R,5R)-5-(4-fluorophenyl)oxolan-3-yl]-1,2,4-oxadiazol-5-yl}methyl)-7-methyl-1,7-dihydro-6H-purin-6-one

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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 mMNaClNaCl
0.5 mMTCEP
GridModel: UltrAuFoil R2/2 / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY / Support film - 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
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
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: 8915 / Average exposure time: 1.6 sec. / Average electron dose: 41.8 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal magnification: 165000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 395169
Startup modelType of model: NONE
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C4 (4 fold cyclic) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.05 Å / Resolution method: FSC 0.143 CUT-OFF / Software:
Namedetails
cisTEM
PHENIXdensity modification
/ Details: No data beyond 4.4 A were used during refinement. / Number images used: 101265
Initial angle assignmentType: RANDOM ASSIGNMENT / Software - Name: cisTEM
Final angle assignmentType: OTHER / Software - Name: cisTEM
Final 3D classificationNumber classes: 1 / Software - Name: cisTEM / Software - details: 3D reconstruction

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Atomic model buiding 1

Initial modelPDB ID:

6x2j


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-7jup:
Structure of human TRPA1 in complex with antagonist compound 21

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