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- EMDB-6267: Human TRPA1 ion channel with agonist AITC -

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Basic information

Entry
Database: EMDB / ID: 6267
TitleHuman TRPA1 ion channel with agonist AITC
Map dataReconstruction of hTRPA1 treated with AITC comprising summed half-maps, unfiltered and unsharpened. Two associated maps are low-pass-filtered and negative-B-factor-sharpened.
SampleRecombinant human TRPA1 treated with AITC:
TRPA1
KeywordsTRPA1 / TRP / ion channel
Function / homologyTransient receptor potential cation channel subfamily A member 1 / Ankyrin repeat-containing domain / TRP channels / Ankyrin repeat region circular profile. / Ankyrin repeat profile. / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Ankyrin repeat / Ankyrin repeats (3 copies) / Ion transport protein ...Transient receptor potential cation channel subfamily A member 1 / Ankyrin repeat-containing domain / TRP channels / Ankyrin repeat region circular profile. / Ankyrin repeat profile. / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Ankyrin repeat / Ankyrin repeats (3 copies) / Ion transport protein / Ankyrin repeat-containing domain superfamily / Ion transport domain / Bacterial extracellular solute-binding protein / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / 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 / carbohydrate transport / calcium channel activity / sensory perception of pain / calcium ion transmembrane transport / 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 / periplasmic space / cell surface receptor signaling pathway / 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
SourceHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / 4.24 Å resolution
AuthorsPaulsen CE / Armache JP / 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 ReportPDB-ID: 3j9p

SummaryFull reportAbout validation report
DateDeposition: Feb 14, 2015 / Header (metadata) release: Apr 8, 2015 / Map release: Apr 8, 2015 / Last update: Oct 7, 2015

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 8
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 8
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-3j9p
  • Surface level: 8
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_6267.map.gz (map file in CCP4 format, 105470 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
300 pix
1.22 Å/pix.
= 364.68 Å
300 pix
1.22 Å/pix.
= 364.68 Å
300 pix
1.22 Å/pix.
= 364.68 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.2156 Å
Density
Contour Level:8 (by author), 8 (movie #1):
Minimum - Maximum-12.64960575 - 20.72408104
Average (Standard dev.)0E-8 (0.99999994)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions300300300
Origin-150-150-150
Limit149149149
Spacing300300300
CellA=B=C: 364.68 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.21561.21561.2156
M x/y/z300300300
origin x/y/z0.0000.0000.000
length x/y/z364.680364.680364.680
α/β/γ90.00090.00090.000
start NX/NY/NZ-800-4
NX/NY/NZ1611358
MAP C/R/S123
start NC/NR/NS-150-150-150
NC/NR/NS300300300
D min/max/mean-12.65020.7240.000

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Supplemental data

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Sample components

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Entire Recombinant human TRPA1 treated with AITC

EntireName: Recombinant human TRPA1 treated with AITC / Details: The sample was monodisperse. / Number of components: 1 / Oligomeric State: tetramer
MassTheoretical: 688 kDa

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Component #1: protein, TRPA1

ProteinName: TRPA1
a.k.a: Transient receptor potential cation channel, member A1
Oligomeric Details: tetramer / Recombinant expression: Yes / Number of Copies: 4
MassTheoretical: 172 kDa / Experimental: 172 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human) / Cell of expression system: HEK293 GnTi-
External referencesUniProt: Transient receptor potential cation channel subfamily A member 1

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionSpecimen conc.: 0.5 mg/ml
Buffer solution: 20 mM HEPES, 150 mM NaCl, 1 mM DTT, 1 mM IP6
pH: 8
Support film400 mesh holey carbon
VitrificationInstrument: FEI VITROBOT MARK I / Cryogen name: ETHANE / Temperature: 120 K / Humidity: 100 % / Method: Blot for 7 seconds before plunging.

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Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
ImagingMicroscope: 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 / Electron dose: 21 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 31000 X (nominal), 31000 X (calibrated) / Cs: 2 mm / Imaging mode: BRIGHT FIELD / Defocus: 1500 - 2800 nm
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 1160
Details: Every image is the average of 30 frames recorded using the K2 Summit. The final reconstruction was calculated from images motion-corrected and weighted using the method described in Scheres, 2014.
URL of raw data: http://dx.doi.org/10.6019/EMPIAR-10024
Raw dataEMPIAR-10024 (Title: Human TRPA1 ion channel with agonist AITC / Data size: 453.0
Data #1: TRP ion channel dataset [picked particles - single frame - processed])

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C4 (4 fold cyclic) / Number of projections: 43585
Details: Particles were selected using an automatic selection program and manually screened. Defocus was calculated using CTFFIND3 and data were processed and refined using RELION 1.3.
3D reconstructionAlgorithm: Maximum likelihood / Software: RELION / CTF correction: Each particle / Resolution: 4.24 Å / Resolution method: FSC 0.143, gold-standard

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Atomic model buiding

Output model

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