[English] 日本語
Yorodumi
- EMDB-22490: Structure of human TRPA1 in complex with antagonist compound 21 -

+
Open data


ID or keywords:

Loading...

-
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 / 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: 3.05 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

-
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
  • Download
  • 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

-
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
Voxel sizeX=Y=Z: 1.262 Å
Density
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

-
Supplemental data

-
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)

-
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)

-
Sample components

-
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

-
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)

-
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

-
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

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.33 mg/mL
BufferpH: 8.2
Component:
ConcentrationNameFormula
25.0 mMTris
150.0 mMNaClSodium chlorideNaClSodium chloride
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).

-
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: 8915 / Average exposure time: 1.6 sec. / Average electron dose: 41.8 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Particle selectionNumber selected: 395169
Startup modelType of model: NONE
Initial angle assignmentType: RANDOM ASSIGNMENT / Software - Name: cisTEM
Final 3D classificationNumber classes: 1 / Software - Name: cisTEM / Software - details: 3D reconstruction
Final angle assignmentType: OTHER / Software - Name: cisTEM
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more