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- EMDB-6618: Structure of the full-length TRPV2 channel by cryoEM -

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Basic information

Entry
Database: EMDB / ID: EMD-6618
TitleStructure of the full-length TRPV2 channel by cryoEM
Map dataStructure of full-Length TRPV2 after signal subtraction 3D classification
Sample
  • Sample: Recombinant rat full-length TRPV2
  • Protein or peptide: Transient Receptor Potential Cation Channel, Subfamily V, Member 2
KeywordsTRPV2 / ion channel
Function / homology
Function and homology information


transport / growth cone membrane / TRP channels / response to temperature stimulus / positive regulation of calcium ion import / endomembrane system / positive regulation of axon extension / axonal growth cone / monoatomic cation channel activity / calcium channel activity ...transport / growth cone membrane / TRP channels / response to temperature stimulus / positive regulation of calcium ion import / endomembrane system / positive regulation of axon extension / axonal growth cone / monoatomic cation channel activity / calcium channel activity / melanosome / lamellipodium / positive regulation of cold-induced thermogenesis / cell body / negative regulation of cell population proliferation / axon / cell surface / identical protein binding / plasma membrane
Similarity search - Function
Transient receptor potential cation channel subfamily V member 2 / Transient receptor potential cation channel subfamily V member 1-4 / 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: 4.7 Å
AuthorsHuynh KW / Cohen MR / Jiang J / Samanta A / Lodowski DT / Zhou ZH / Moiseenkova-Bell VY
CitationJournal: Nat Commun / Year: 2016
Title: Structure of the full-length TRPV2 channel by cryo-EM.
Authors: Kevin W Huynh / Matthew R Cohen / Jiansen Jiang / Amrita Samanta / David T Lodowski / Z Hong Zhou / Vera Y Moiseenkova-Bell /
Abstract: Transient receptor potential (TRP) proteins form a superfamily Ca(2+)-permeable cation channels regulated by a range of chemical and physical stimuli. Structural analysis of a 'minimal' TRP vanilloid ...Transient receptor potential (TRP) proteins form a superfamily Ca(2+)-permeable cation channels regulated by a range of chemical and physical stimuli. Structural analysis of a 'minimal' TRP vanilloid subtype 1 (TRPV1) elucidated a mechanism of channel activation by agonists through changes in its outer pore region. Though homologous to TRPV1, other TRPV channels (TRPV2-6) are insensitive to TRPV1 activators including heat and vanilloids. To further understand the structural basis of TRPV channel function, we determined the structure of full-length TRPV2 at ∼5 Å resolution by cryo-electron microscopy. Like TRPV1, TRPV2 contains two constrictions, one each in the pore-forming upper and lower gates. The agonist-free full-length TRPV2 has wider upper and lower gates compared with closed and agonist-activated TRPV1. We propose these newly revealed TRPV2 structural features contribute to diversity of TRPV channels.
History
DepositionMar 9, 2016-
Header (metadata) releaseMar 23, 2016-
Map releaseMar 30, 2016-
UpdateApr 13, 2016-
Current statusApr 13, 2016Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.02
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.02
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-5hi9
  • Surface level: 0.02
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_6618.png

Downloads & links

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Map

FileDownload / File: emd_6618.map.gz / Format: CCP4 / Size: 26.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationStructure of full-Length TRPV2 after signal subtraction 3D classification
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.29 Å/pix.
x 192 pix.
= 247.68 Å		1.29 Å/pix.
x 192 pix.
= 247.68 Å		1.29 Å/pix.
x 192 pix.
= 247.68 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.29 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.02 / Movie #1: 0.02
Minimum - Maximum-0.03318456 - 0.08514521
Average (Standard dev.)0.00035344 (±0.00475416)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions192192192
Spacing192192192
CellA=B=C: 247.68 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.291.291.29
M x/y/z192192192
origin x/y/z0.0000.0000.000
length x/y/z247.680247.680247.680
α/β/γ90.00090.00090.000
start NX/NY/NZ-8211244
NX/NY/NZ115138149
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS192192192
D min/max/mean-0.0330.0850.000

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Supplemental data

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Sample components

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Entire : Recombinant rat full-length TRPV2

EntireName: Recombinant rat full-length TRPV2
Components
  • Sample: Recombinant rat full-length TRPV2
  • Protein or peptide: Transient Receptor Potential Cation Channel, Subfamily V, Member 2

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Supramolecule #1000: Recombinant rat full-length TRPV2

SupramoleculeName: Recombinant rat full-length TRPV2 / type: sample / ID: 1000 / Details: The sample was monodisperse / Oligomeric state: tetramer / Number unique components: 1
Molecular weightExperimental: 600 KDa / Theoretical: 340 KDa / Method: gel filtration

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Macromolecule #1: Transient Receptor Potential Cation Channel, Subfamily V, Member 2

MacromoleculeName: Transient Receptor Potential Cation Channel, Subfamily V, Member 2
type: protein_or_peptide / ID: 1 / Name.synonym: TRPV2 / Number of copies: 4 / Oligomeric state: tetramer / Recombinant expression: Yes
Source (natural)Organism: Rattus norvegicus (Norway rat) / synonym: rat / Location in cell: intracellular and plasma membrane
Molecular weightExperimental: 600 KDa / Theoretical: 340 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast) / Recombinant strain: BJ5457 / Recombinant plasmid: YepM
SequenceUniProtKB: Transient receptor potential cation channel subfamily V member 2
GO: transport
InterPro: Transient receptor potential cation channel subfamily V member 2

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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: 0.064 mM DMNG, 150 mM NaCl, 20 mM HEPES, 1.0 mM DTT
GridDetails: Quantifoil R2/1 400 mesh copper grid
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 120 K / Instrument: HOMEMADE PLUNGER / Method: Blotted twice.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Alignment procedureLegacy - Astigmatism: Objective lens astigmatism was corrected at 100,000 times magnification.
DateJan 12, 2014
Image recordingCategory: CCD / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Number real images: 988
Details: Every image is the average of 14 frames recorded by the direct electron detector.
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 31000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

DetailsRelion 1.3, Relion 1.4 Signal Subtraction 3D Classification
CTF correctionDetails: Each particle
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.7 Å / Resolution method: OTHER / Software - Name: Relion / Number images used: 29765
FSC plot (resolution estimation)

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