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- EMDB-5688: Structural insight into the thermoTRPV channels assembly -

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Basic information

Entry
Database: EMDB / ID: EMD-5688
TitleStructural insight into the thermoTRPV channels assembly
Map dataTRPV2 structure at 13.6 A
Sample
  • Sample: Rat Transient Receptor Potential Vanilloid 2 (TRPV2)
  • Protein or peptide: Transient Receptor Potential Vanilloid 2
KeywordsTRP channel
Function / homology
Function and homology information


plasma membrane => GO:0005886 / growth cone membrane / TRP channels / response to temperature stimulus / positive regulation of calcium ion import / calcium ion import across plasma membrane / axonal growth cone / positive regulation of axon extension / monoatomic cation channel activity / endomembrane system ...plasma membrane => GO:0005886 / growth cone membrane / TRP channels / response to temperature stimulus / positive regulation of calcium ion import / calcium ion import across plasma membrane / axonal growth cone / positive regulation of axon extension / monoatomic cation channel activity / endomembrane system / calcium channel activity / melanosome / lamellipodium / positive regulation of cold-induced thermogenesis / cell body / axon / negative regulation of cell population proliferation / cell surface / identical protein binding / plasma membrane
Similarity search - Function
Transient receptor potential cation channel subfamily V member 1-4 / Transient receptor potential cation channel subfamily V / Transient receptor potential cation channel subfamily V / 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 V member 2
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
Methodsingle particle reconstruction / cryo EM / Resolution: 13.6 Å
AuthorsHuynh KW / Cohen MR / Chakrapani S / Holdaway HA / Stewart PL / Moiseenkova-Bell VY
CitationJournal: Structure / Year: 2014
Title: Structural insight into the assembly of TRPV channels.
Authors: Kevin W Huynh / Matthew R Cohen / Sudha Chakrapani / Heather A Holdaway / Phoebe L Stewart / Vera Y Moiseenkova-Bell /
Abstract: Transient receptor potential (TRP) proteins are a large family of polymodal nonselective cation channels. The TRP vanilloid (TRPV) subfamily consists of six homologous members with diverse functions. ...Transient receptor potential (TRP) proteins are a large family of polymodal nonselective cation channels. The TRP vanilloid (TRPV) subfamily consists of six homologous members with diverse functions. TRPV1-TRPV4 are nonselective cation channels proposed to play a role in nociception, while TRPV5 and TRPV6 are involved in epithelial Ca²⁺ homeostasis. Here we present the cryo-electron microscopy (cryo-EM) structure of functional, full-length TRPV2 at 13.6 Å resolution. The map reveals that the TRPV2 cytoplasmic domain displays a 4-fold petal-like shape in which high-resolution N-terminal ankyrin repeat domain (ARD) structures can be unambiguously fitted. Fitting of the available ARD structures for other TRPV subfamily members into the TRPV2 EM map suggests that TRPV subfamily members have highly homologous structural topologies. These results allowed us to postulate a structural explanation for the functional diversity among TRPV channels and their differential regulation by proteins and ligands.
History
DepositionJun 6, 2013-
Header (metadata) releaseJul 3, 2013-
Map releaseDec 11, 2013-
UpdateApr 2, 2014-
Current statusApr 2, 2014Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 1
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_5688.png

Downloads & links

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Map

FileDownload / File: emd_5688.map.gz / Format: CCP4 / Size: 15.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationTRPV2 structure at 13.6 A
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.66 Å/pix.
x 160 pix.
= 425.6 Å		2.66 Å/pix.
x 160 pix.
= 425.6 Å		2.66 Å/pix.
x 160 pix.
= 425.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.66 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.0 / Movie #1: 1
Minimum - Maximum-0.83958972 - 2.72564459
Average (Standard dev.)0.04829006 (±0.16496764)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-80-80-80
Dimensions160160160
Spacing160160160
CellA=B=C: 425.6 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.662.662.66
M x/y/z160160160
origin x/y/z0.0000.0000.000
length x/y/z425.600425.600425.600
α/β/γ90.00090.00090.000
start NX/NY/NZ-132-122-147
NX/NY/NZ250274261
MAP C/R/S123
start NC/NR/NS-80-80-80
NC/NR/NS160160160
D min/max/mean-0.8402.7260.048

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Supplemental data

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Sample components

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Entire : Rat Transient Receptor Potential Vanilloid 2 (TRPV2)

EntireName: Rat Transient Receptor Potential Vanilloid 2 (TRPV2)
Components
  • Sample: Rat Transient Receptor Potential Vanilloid 2 (TRPV2)
  • Protein or peptide: Transient Receptor Potential Vanilloid 2

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Supramolecule #1000: Rat Transient Receptor Potential Vanilloid 2 (TRPV2)

SupramoleculeName: Rat Transient Receptor Potential Vanilloid 2 (TRPV2) / type: sample / ID: 1000 / Details: sample was monodisperse / Oligomeric state: tetramer / Number unique components: 1
Molecular weightExperimental: 600 KDa / Theoretical: 360 KDa / Method: Size-exclusion chromatography

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Macromolecule #1: Transient Receptor Potential Vanilloid 2

MacromoleculeName: Transient Receptor Potential Vanilloid 2 / type: protein_or_peptide / ID: 1 / Name.synonym: TRPV2 / Number of copies: 1 / Oligomeric state: tetramer / Recombinant expression: Yes
Source (natural)Organism: Rattus norvegicus (Norway rat) / synonym: rat / Location in cell: plasma membrane
Molecular weightExperimental: 600 KDa / Theoretical: 300 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast) / Recombinant strain: BJ5457 / Recombinant plasmid: YeP
SequenceUniProtKB: Transient receptor potential cation channel subfamily V member 2
GO: plasma membrane => GO:0005886
InterPro: Transient receptor potential cation channel subfamily V

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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

Concentration2.5 mg/mL
BufferpH: 8 / Details: 20 mM HEPES, 150 mM NaCl, 1.0mM DTT, 0.006% DMNG
GridDetails: 400 mesh Quantifoil R2/1 copper grids
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 120 K / Instrument: FEI VITROBOT MARK IV / Method: blot for 1, 2, or 3 sec

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Electron microscopy

MicroscopeFEI TECNAI F20
TemperatureMin: 80 K / Max: 105 K / Average: 100 K
Alignment procedureLegacy - Astigmatism: Objective lens astigmatism was corrected at 200,000 times magnification
DateOct 17, 2012
Image recordingCategory: CCD / Film or detector model: TVIPS TEMCAM-F416 (4k x 4k) / Number real images: 650 / Average electron dose: 10 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 117293 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.12 mm / Nominal defocus max: -3.0 µm / Nominal defocus min: -1.5 µm / Nominal magnification: 62000
Sample stageSpecimen holder: 626 / Specimen holder model: GATAN LIQUID NITROGEN
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

DetailsEMAN2
CTF correctionDetails: each image
Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 13.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: Imagic, FREALIGN / Number images used: 23051

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