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- EMDB-7118: Open state structure of the full-length TRPV2 cation channel with... -

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Basic information

Entry
Database: EMDB / ID: 7118
TitleOpen state structure of the full-length TRPV2 cation channel with a resolved pore turret domain
Map dataWT rat TRPV2 ion channel in an open state and with a resolved pore turret domain.
SampleTRPV2
  • Transient receptor potential cation channel subfamily V member 2
Function / homologyAnkyrin repeat / Transient receptor potential cation channel subfamily V / Ankyrin repeat region circular profile. / Ankyrin repeat profile. / Ankyrin repeats (3 copies) / Ion transport protein / Ankyrin repeat-containing domain superfamily / Transient receptor potential channel, vanilloid 2 / Ion transport domain / Transient receptor potential channel, vanilloid 1-4 ...Ankyrin repeat / Transient receptor potential cation channel subfamily V / Ankyrin repeat region circular profile. / Ankyrin repeat profile. / Ankyrin repeats (3 copies) / Ion transport protein / Ankyrin repeat-containing domain superfamily / Transient receptor potential channel, vanilloid 2 / Ion transport domain / Transient receptor potential channel, vanilloid 1-4 / Ankyrin repeat-containing domain / endomembrane system / calcium channel activity / positive regulation of cold-induced thermogenesis / melanosome / lamellipodium / ion channel activity / response to heat / negative regulation of cell population proliferation / integral component of plasma membrane / identical protein binding / plasma membrane / cytoplasm / Transient receptor potential cation channel subfamily V member 2
Function and homology information
SourceRattus norvegicus (Norway rat)
Methodsingle particle reconstruction / cryo EM / 4 Å resolution
AuthorsDosey TL / Wang Z
CitationJournal: Nat. Struct. Mol. Biol. / Year: 2019
Title: Structures of TRPV2 in distinct conformations provide insight into role of the pore turret.
Authors: Timothy L Dosey / Zhao Wang / Guizhen Fan / Zhixian Zhang / Irina I Serysheva / Wah Chiu / Theodore G Wensel
Validation ReportPDB-ID: 6bo4

SummaryFull reportAbout validation report
DateDeposition: Nov 18, 2017 / Header (metadata) release: Jan 24, 2018 / Map release: Dec 5, 2018 / Last update: Dec 5, 2018

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0219
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.0219
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-6bo4
  • Surface level: 0.0219
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_7118.map.gz (map file in CCP4 format, 16385 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
160 pix
1.25 Å/pix.
= 200. Å
160 pix
1.25 Å/pix.
= 200. Å
160 pix
1.25 Å/pix.
= 200. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.25 Å
Density
Contour Level:0.0219 (by author), 0.0219 (movie #1):
Minimum - Maximum-0.032625854 - 0.08778848
Average (Standard dev.)0.0020586336 (0.006388918)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions160160160
Origin0.00.00.0
Limit159.0159.0159.0
Spacing160160160
CellA=B=C: 200.0 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.251.251.25
M x/y/z160160160
origin x/y/z0.0000.0000.000
length x/y/z200.000200.000200.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ450450450
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS160160160
D min/max/mean-0.0330.0880.002

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Supplemental data

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Sample components

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Entire TRPV2

EntireName: TRPV2 / Number of components: 2

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Component #1: protein, TRPV2

ProteinName: TRPV2 / Recombinant expression: No
MassTheoretical: 320 kDa
SourceSpecies: Rattus norvegicus (Norway rat)
Source (engineered)Expression System: Saccharomyces cerevisiae (baker's yeast) / Vector: pYEPM / Strain: BJ5457

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Component #2: protein, Transient receptor potential cation channel subfamily V ...

ProteinName: Transient receptor potential cation channel subfamily V member 2
Number of Copies: 4 / Recombinant expression: No
MassTheoretical: 79.999422 kDa
SourceSpecies: Rattus norvegicus (Norway rat)
Source (engineered)Expression System: Saccharomyces cerevisiae (baker's yeast)

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionSpecimen conc.: .5 mg/ml / pH: 8
Support filmunspecified
VitrificationCryogen name: ETHANE / Temperature: 298 K / Humidity: 98 %

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Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
ImagingMicroscope: FEI POLARA 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 63 e/Å2 / Illumination mode: SPOT SCAN
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C4 (4 fold cyclic) / Number of projections: 11789
3D reconstructionSoftware: RELION / Resolution: 4 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Output model

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