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

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Basic information

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 / homologyBacterial extracellular solute-binding protein / Ankyrin repeat-containing domain superfamily / Ankyrin repeat / Ion transport domain / Bacterial extracellular solute-binding protein / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Ankyrin repeat-containing domain / Transient receptor potential cation channel subfamily A member 1 / Ion transport protein ...Bacterial extracellular solute-binding protein / Ankyrin repeat-containing domain superfamily / Ankyrin repeat / Ion transport domain / Bacterial extracellular solute-binding protein / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Ankyrin repeat-containing domain / Transient receptor potential cation channel subfamily A member 1 / Ion transport protein / Ankyrin repeats (3 copies) / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding proteins, family 1 signature. / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / TRP channels / Ankyrin repeat / thermoception / temperature-gated cation channel activity / detection of chemical stimulus involved in sensory perception of pain / stereocilium bundle / channel activity / detection of mechanical stimulus involved in sensory perception of pain / response to pain / calcium-release channel activity / detection of maltose stimulus / maltose binding / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / maltose transport / maltodextrin transport / carbohydrate transmembrane transporter activity / calcium channel activity / carbohydrate transport / calcium ion transmembrane transport / sensory perception of pain / transporter activity / ATP-binding cassette (ABC) transporter complex / cell chemotaxis / ion transport / response to cold / response to organic substance / response to organic cyclic compound / response to hydrogen peroxide / protein homotetramerization / outer membrane-bounded periplasmic space / cell surface receptor signaling pathway / periplasmic space / cellular response to DNA damage stimulus / integral component of plasma membrane / identical protein binding / plasma membrane / Transient receptor potential cation channel subfamily A member 1 / Maltose/maltodextrin-binding periplasmic protein
Function and homology information
Specimen sourceEscherichia coli (E. coli)
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 4.24 Å resolution
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
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Feb 14, 2015 / Release: Apr 8, 2015
RevisionDateData content typeGroupCategoryItemProviderType
1.0Apr 8, 2015Structure modelrepositoryInitial release
1.1Apr 22, 2015Structure modelDatabase references
1.2Apr 29, 2015Structure modelDatabase references
1.3Jul 18, 2018Structure modelData collectionem_software_em_software.image_processing_id / _em_software.name

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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
Polyers690,3024
Non-polymers00
Water0
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein/peptide
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 / Transient Receptor Potential Ankyrin 1 ion channel


Mass: 172575.562 Da / Num. of mol.: 4 / Fragment: SEE REMARK 999 / 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 / 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 / Details: 20 mM HEPES, 150 mM NaCl, 1 mM DTT, 1 mM IP6 / pH: 8
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
MicroscopyMicroscope model: 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 FIELDBright-field microscopy / Nominal magnification: 31000 / Calibrated magnification: 31000 / Nominal defocus max: 2800 nm / Nominal defocus min: 1500 nm / Cs: 2 mm
Specimen holderTemperature: 120 kelvins
Image recordingElectron dose: 21 e/Å2
Details: Gatan K2 Summit in super-resolution counting mode. Motion correction as described in Li et al. (2013) Nature Methods.
Film or detector model: GATAN K2 (4k x 4k)
Image scansNumber digital images: 1160
RadiationDiffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m 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
3D reconstructionMethod: Maximum likelihood / Resolution: 4.24 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 43585 / Nominal pixel size: 1.2156 / Actual pixel size: 1.2156 / Symmetry type: POINT
Number of atoms included #LASTProtein: 16952 / Nucleic acid: 0 / Ligand: 0 / Solvent: 0 / Total: 16952

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