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- EMDB-21688: Structure of human TRPA1 in complex with inhibitor GDC-0334 -

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Basic information

Entry
Database: EMDB / ID: EMD-21688
TitleStructure of human TRPA1 in complex with inhibitor GDC-0334
Map dataMain map, used for making figures. Sharpened, FOM-filtered, unmasked.
Sample
  • Complex: TRPA1 bound by inhibitor GDC-0334
    • Protein or peptide: Transient receptor potential cation channel subfamily A member 1
  • Ligand: (4R,5S)-4-fluoro-1-[(4-fluorophenyl)sulfonyl]-5-methyl-N-({5-(trifluoromethyl)-2-[2-(trifluoromethyl)pyrimidin-5-yl]pyridin-4-yl}methyl)-L-prolinamide
KeywordsTRPA1 / channel / inhibitor / antagonist / MEMBRANE PROTEIN / MEMBRANE PROTEIN-Inhibitor 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: 3.6 Å
AuthorsRohou A / Rouge L / Arthur CP
CitationJournal: J Exp Med / Year: 2021
Title: A TRPA1 inhibitor suppresses neurogenic inflammation and airway contraction for asthma treatment.
Authors: Alessia Balestrini / Victory Joseph / Michelle Dourado / Rebecca M Reese / Shannon D Shields / Lionel Rougé / Daniel D Bravo / Tania Chernov-Rogan / Cary D Austin / Huifen Chen / Lan Wang / ...Authors: Alessia Balestrini / Victory Joseph / Michelle Dourado / Rebecca M Reese / Shannon D Shields / Lionel Rougé / Daniel D Bravo / Tania Chernov-Rogan / Cary D Austin / Huifen Chen / Lan Wang / Elisia Villemure / Daniel G M Shore / Vishal A Verma / Baihua Hu / Yong Chen / Laurie Leong / Chris Bjornson / Kathy Hötzel / Alvin Gogineni / Wyne P Lee / Eric Suto / Xiumin Wu / John Liu / Juan Zhang / Vineela Gandham / Jianyong Wang / Jian Payandeh / Claudio Ciferri / Alberto Estevez / Christopher P Arthur / Jens Kortmann / Ryan L Wong / Jose E Heredia / Jonas Doerr / Min Jung / Jason A Vander Heiden / Merone Roose-Girma / Lucinda Tam / Kai H Barck / Richard A D Carano / Han Ting Ding / Bobby Brillantes / Christine Tam / Xiaoying Yang / Simon S Gao / Justin Q Ly / Liling Liu / Liuxi Chen / Bianca M Liederer / Joseph H Lin / Steven Magnuson / Jun Chen / David H Hackos / Justin Elstrott / Alexis Rohou / Brian S Safina / Matthew Volgraf / Rebecca N Bauer / Lorena Riol-Blanco /
Abstract: Despite the development of effective therapies, a substantial proportion of asthmatics continue to have uncontrolled symptoms, airflow limitation, and exacerbations. Transient receptor potential ...Despite the development of effective therapies, a substantial proportion of asthmatics continue to have uncontrolled symptoms, airflow limitation, and exacerbations. Transient receptor potential cation channel member A1 (TRPA1) agonists are elevated in human asthmatic airways, and in rodents, TRPA1 is involved in the induction of airway inflammation and hyperreactivity. Here, the discovery and early clinical development of GDC-0334, a highly potent, selective, and orally bioavailable TRPA1 antagonist, is described. GDC-0334 inhibited TRPA1 function on airway smooth muscle and sensory neurons, decreasing edema, dermal blood flow (DBF), cough, and allergic airway inflammation in several preclinical species. In a healthy volunteer Phase 1 study, treatment with GDC-0334 reduced TRPA1 agonist-induced DBF, pain, and itch, demonstrating GDC-0334 target engagement in humans. These data provide therapeutic rationale for evaluating TRPA1 inhibition as a clinical therapy for asthma.
History
DepositionApr 11, 2020-
Header (metadata) releaseFeb 17, 2021-
Map releaseFeb 17, 2021-
UpdateMay 29, 2024-
Current statusMay 29, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.18
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.18
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6wj5
  • Surface level: 0.18
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_21688.png

Downloads & links

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Map

FileDownload / File: emd_21688.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMain map, used for making figures. Sharpened, FOM-filtered, unmasked.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 300 pix.
= 314.1 Å		1.05 Å/pix.
x 300 pix.
= 314.1 Å		1.05 Å/pix.
x 300 pix.
= 314.1 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.047 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1 / Movie #1: 0.18
Minimum - Maximum-0.558879 - 0.999257
Average (Standard dev.)0.007330487 (±0.03634888)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 314.1 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0471.0471.047
M x/y/z300300300
origin x/y/z0.0000.0000.000
length x/y/z314.100314.100314.100
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS300300300
D min/max/mean-0.5590.9990.007

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Supplemental data

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Sample components

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Entire : TRPA1 bound by inhibitor GDC-0334

EntireName: TRPA1 bound by inhibitor GDC-0334
Components
  • Complex: TRPA1 bound by inhibitor GDC-0334
    • Protein or peptide: Transient receptor potential cation channel subfamily A member 1
  • Ligand: (4R,5S)-4-fluoro-1-[(4-fluorophenyl)sulfonyl]-5-methyl-N-({5-(trifluoromethyl)-2-[2-(trifluoromethyl)pyrimidin-5-yl]pyridin-4-yl}methyl)-L-prolinamide

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Supramolecule #1: TRPA1 bound by inhibitor GDC-0334

SupramoleculeName: TRPA1 bound by inhibitor GDC-0334 / 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: (4R,5S)-4-fluoro-1-[(4-fluorophenyl)sulfonyl]-5-methyl-N-({5-(tri...

MacromoleculeName: (4R,5S)-4-fluoro-1-[(4-fluorophenyl)sulfonyl]-5-methyl-N-({5-(trifluoromethyl)-2-[2-(trifluoromethyl)pyrimidin-5-yl]pyridin-4-yl}methyl)-L-prolinamide
type: ligand / ID: 2 / Number of copies: 4 / Formula: LXY
Molecular weightTheoretical: 609.492 Da
Chemical component information

ChemComp-LXY:
(4R,5S)-4-fluoro-1-[(4-fluorophenyl)sulfonyl]-5-methyl-N-({5-(trifluoromethyl)-2-[2-(trifluoromethyl)pyrimidin-5-yl]pyridin-4-yl}methyl)-L-prolinamide

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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
1.0 mMIns6P
GridModel: C-flat-2/1 / Material: COPPER / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.067 kPa
Details: Grid was gold-coated. Glow discharge using GloQube, negative polarity.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV / Details: 2 x 4s blot time.

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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 / Average exposure time: 10.0 sec. / Average electron dose: 47.5 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: 130000
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: 4114800
Details: 15,630 movies were selected because of the quality of their CTF fits. 4,114,800 coordinates were selected, leading to 466,632 particles which clustered into high-quality 2D class averages
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: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cisTEM
Details: Data at spatial frequencies higher than 1/4.8 A-1 were not used during any part of the refinement.
Number images used: 58836
Initial angle assignmentType: RANDOM ASSIGNMENT / Software - Name: cisTEM
Final angle assignmentType: OTHER / Software - Name: cisTEM
Final 3D classificationNumber classes: 5 / Software - Name: cisTEM
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

3j9p


Chain - Source name: PDB / Chain - Initial model type: experimental model
DetailsCCG MOE was used for refinement after Phenix real-space refinement.
RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-6wj5:
Structure of human TRPA1 in complex with inhibitor GDC-0334

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