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- PDB-3j9p: Structure of the TRPA1 ion channel determined by electron cryo-mi... -

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Entry
Database: PDB / ID: 3j9p
TitleStructure of the TRPA1 ion channel determined by electron cryo-microscopy
ComponentsMaltose-binding periplasmic protein, Transient receptor potential cation channel subfamily A member 1 chimera
KeywordsTRANSPORT PROTEIN / TRPA1 / TRP / transient / potential / receptor / ion channel / membrane protein
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 / detection of maltose stimulus / maltose transport complex / maltose binding / carbohydrate transport ...temperature-gated cation channel activity / stereocilium bundle / detection of chemical stimulus involved in sensory perception of pain / thermoception / TRP channels / response to pain / detection of maltose stimulus / maltose transport complex / maltose binding / carbohydrate transport / maltose transport / intracellularly gated calcium channel activity / maltodextrin transmembrane transport / carbohydrate transmembrane transporter activity / detection of mechanical stimulus involved in sensory perception of pain / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / monoatomic ion transport / sensory perception of pain / response to cold / ATP-binding cassette (ABC) transporter complex / cell chemotaxis / calcium ion transmembrane transport / calcium channel activity / response to organic cyclic compound / cellular response to hydrogen peroxide / intracellular calcium ion homeostasis / channel activity / outer membrane-bounded periplasmic space / protein homotetramerization / periplasmic space / cell surface receptor signaling pathway / response to xenobiotic stimulus / DNA damage response / identical protein binding / membrane / plasma membrane
Similarity search - Function
: / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / Ankyrin repeat / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. ...: / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / 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 / Maltose/maltodextrin-binding periplasmic protein
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.24 Å
AuthorsPaulsen, C.E. / Armache, J.-P. / Gao, Y. / Cheng, Y. / Julius, D.
CitationJournal: Nature / Year: 2015
Title: Structure of the TRPA1 ion channel suggests regulatory mechanisms.
Authors: Candice E Paulsen / Jean-Paul Armache / Yuan Gao / Yifan Cheng / David Julius /
Abstract: The TRPA1 ion channel (also known as the wasabi receptor) is a detector of noxious chemical agents encountered in our environment or produced endogenously during tissue injury or drug metabolism. ...The TRPA1 ion channel (also known as the wasabi receptor) is a detector of noxious chemical agents encountered in our environment or produced endogenously during tissue injury or drug metabolism. These include a broad class of electrophiles that activate the channel through covalent protein modification. TRPA1 antagonists hold potential for treating neurogenic inflammatory conditions provoked or exacerbated by irritant exposure. Despite compelling reasons to understand TRPA1 function, structural mechanisms underlying channel regulation remain obscure. Here we use single-particle electron cryo- microscopy to determine the structure of full-length human TRPA1 to ∼4 Å resolution in the presence of pharmacophores, including a potent antagonist. Several unexpected features are revealed, including an extensive coiled-coil assembly domain stabilized by polyphosphate co-factors and a highly integrated nexus that converges on an unpredicted transient receptor potential (TRP)-like allosteric domain. These findings provide new insights into the mechanisms of TRPA1 regulation, and establish a blueprint for structure-based design of analgesic and anti-inflammatory agents.
History
DepositionFeb 14, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 8, 2015Provider: repository / Type: Initial release
Revision 1.1Apr 22, 2015Group: Database references
Revision 1.2Apr 29, 2015Group: Database references
Revision 1.3Jul 18, 2018Group: Data collection / Category: em_software / Item: _em_software.image_processing_id / _em_software.name
Revision 1.4Feb 1, 2023Group: Database references / Category: citation_author / database_2 / struct_ref_seq_dif
Item: _citation_author.name / _database_2.pdbx_DOI ..._citation_author.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5May 15, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Assembly

Deposited unit
D: Maltose-binding periplasmic protein, Transient receptor potential cation channel subfamily A member 1 chimera
A: Maltose-binding periplasmic protein, Transient receptor potential cation channel subfamily A member 1 chimera
B: Maltose-binding periplasmic protein, Transient receptor potential cation channel subfamily A member 1 chimera
C: Maltose-binding periplasmic protein, Transient receptor potential cation channel subfamily A member 1 chimera


Theoretical massNumber of molelcules
Total (without water)690,3024
Polymers690,3024
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
Maltose-binding periplasmic protein, Transient receptor potential cation channel subfamily A member 1 chimera / Ankyrin-like with transmembrane domains protein 1 / Transformation-sensitive protein p120 / ...Ankyrin-like with transmembrane domains protein 1 / Transformation-sensitive protein p120 / Transient Receptor Potential Ankyrin 1 ion channel


Mass: 172575.562 Da / Num. of mol.: 4 / Fragment: SEE REMARK 999
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli, Homo sapiens / Gene: malE, ANKTM1, TRPA1 / Cell line (production host): HEK293 GnTi- / Production host: Homo sapiens (human) / References: UniProt: P0AEX9, UniProt: O75762
Sequence detailsPROTEIN IS A CHIMERA COMPRISING RESIDUES 27-392 OF UNP P0AEX9 LINKED TO RESIDUES 2-1119 OF UNP O75762.

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Recombinant human TRPA1 ion channel / Type: COMPLEX
Buffer solutionName: 20 mM HEPES, 150 mM NaCl, 1 mM DTT, 1 mM IP6 / pH: 8 / Details: 20 mM HEPES, 150 mM NaCl, 1 mM DTT, 1 mM IP6
SpecimenConc.: 0.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: 400 mesh holey carbon
VitrificationInstrument: FEI VITROBOT MARK I / Cryogen name: ETHANE / Temp: 120 K / Humidity: 100 %
Details: Blot for 7 seconds before plunging into liquid ethane (FEI VITROBOT MARK I).
Method: Blot for 7 seconds before plunging.

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Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
MicroscopyModel: FEI POLARA 300 / Date: Jul 18, 2014
Details: Gatan K2 Summit in super-resolution counting mode. Motion correction as described in Li et al. (2013) Nature Methods.
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 31000 X / Calibrated magnification: 31000 X / Nominal defocus max: 2800 nm / Nominal defocus min: 1500 nm / Cs: 2 mm
Specimen holderTemperature: 120 K
Image recordingElectron dose: 21 e/Å2 / Film or detector model: GATAN K2 (4k x 4k)
Details: Gatan K2 Summit in super-resolution counting mode. Motion correction as described in Li et al. (2013) Nature Methods.
Image scansNum. digital images: 1160
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

EM softwareName: RELION / Category: 3D reconstruction
CTF correctionDetails: Each particle
SymmetryPoint symmetry: C4 (4 fold cyclic)
3D reconstructionMethod: Maximum likelihood / Resolution: 4.24 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 43585 / Nominal pixel size: 1.2156 Å / Actual pixel size: 1.2156 Å / Symmetry type: POINT
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms16952 0 0 0 16952

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