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- EMDB-6455: TRPV2 ion channel from rabbit -

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Basic information

Entry
Database: EMDB / ID: EMD-6455
TitleTRPV2 ion channel from rabbit
Map dataTRPV2, sharpened with a B factor of -76 using RELION postprocess
Sample
  • Sample: Rabbit TRPV2
  • Protein or peptide: TRPV2
KeywordsTRP channel / ion transport
Function / homology
Function and homology information


growth cone membrane / response to temperature stimulus / positive regulation of calcium ion import / positive regulation of axon extension / axonal growth cone / calcium channel activity / cell body / positive regulation of cold-induced thermogenesis / cell surface / identical protein binding
Similarity search - Function
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 speciesOryctolagus cuniculus (rabbit)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsHerzik MA / Zubcevic L / Chung BC / Lander GC / Lee SY
CitationJournal: Nat Struct Mol Biol / Year: 2016
Title: Cryo-electron microscopy structure of the TRPV2 ion channel.
Authors: Lejla Zubcevic / Mark A Herzik / Ben C Chung / Zhirui Liu / Gabriel C Lander / Seok-Yong Lee /
Abstract: Transient receptor potential vanilloid (TRPV) cation channels are polymodal sensors involved in a variety of physiological processes. TRPV2, a member of the TRPV family, is regulated by temperature, ...Transient receptor potential vanilloid (TRPV) cation channels are polymodal sensors involved in a variety of physiological processes. TRPV2, a member of the TRPV family, is regulated by temperature, by ligands, such as probenecid and cannabinoids, and by lipids. TRPV2 has been implicated in many biological functions, including somatosensation, osmosensation and innate immunity. Here we present the atomic model of rabbit TRPV2 in its putative desensitized state, as determined by cryo-EM at a nominal resolution of ∼4 Å. In the TRPV2 structure, the transmembrane segment 6 (S6), which is involved in gate opening, adopts a conformation different from the one observed in TRPV1. Structural comparisons of TRPV1 and TRPV2 indicate that a rotation of the ankyrin-repeat domain is coupled to pore opening via the TRP domain, and this pore opening can be modulated by rearrangements in the secondary structure of S6.
History
DepositionSep 4, 2015-
Header (metadata) releaseOct 14, 2015-
Map releaseJan 20, 2016-
UpdateFeb 17, 2016-
Current statusFeb 17, 2016Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.032
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.032
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-5an8
  • Surface level: 0.032
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

400_6455.gif

Downloads & links

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Map

FileDownload / File: emd_6455.map.gz / Format: CCP4 / Size: 15.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationTRPV2, sharpened with a B factor of -76 using RELION postprocess
Voxel sizeX=Y=Z: 1.31 Å
Density
Contour LevelBy AUTHOR: 0.032 / Movie #1: 0.032
Minimum - Maximum-0.05208801 - 0.09613334
Average (Standard dev.)-0.0001422 (±0.00714275)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-16-16-16
Dimensions160160160
Spacing160160160
CellA=B=C: 209.59999 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.311.311.31
M x/y/z160160160
origin x/y/z0.0000.0000.000
length x/y/z209.600209.600209.600
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-16-16-16
NC/NR/NS160160160
D min/max/mean-0.0520.096-0.000

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Supplemental data

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Supplemental map: recls4 run1 half1 class001 unfil.map

Filerecls4_run1_half1_class001_unfil.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Supplemental map: recls4 run1 half2 class001 unfil.map

Filerecls4_run1_half2_class001_unfil.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Supplemental map: unsharpened.map

Fileunsharpened.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Rabbit TRPV2

EntireName: Rabbit TRPV2
Components
  • Sample: Rabbit TRPV2
  • Protein or peptide: TRPV2

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Supramolecule #1000: Rabbit TRPV2

SupramoleculeName: Rabbit TRPV2 / type: sample / ID: 1000 / Oligomeric state: homotetramer / Number unique components: 1

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Macromolecule #1: TRPV2

MacromoleculeName: TRPV2 / type: protein_or_peptide / ID: 1 / Recombinant expression: Yes
Source (natural)Organism: Oryctolagus cuniculus (rabbit) / synonym: Rabbit
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm) / Recombinant cell: SF9 / Recombinant plasmid: pFastBac

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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

Concentration1.0 mg/mL
BufferpH: 7.6 / Details: PBS
GridDetails: 400 mesh C-flat copper grid with carbon support, 1.2 micron holes spaced 1.3 microns
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 120 K / Instrument: GATAN CRYOPLUNGE 3 / Method: Blot for 2.5 seconds before plunging.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 38168 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 22500
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
TemperatureMin: 77 K / Max: 79 K / Average: 78 K
Alignment procedureLegacy - Astigmatism: Objective astigmatism was corrected at 22500 times magnification using Thon rings visualized with a K2 camera.
DetailsData was acquired using Leginon and collected in K2 super-resolution mode.
DateMay 12, 2015
Image recordingCategory: CCD / Film or detector model: GATAN K2 (4k x 4k) / Number real images: 747 / Average electron dose: 57 e/Å2 / Details: 50 frames, 200 ms per frame
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionDetails: whole micrograph
Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: OTHER / Software - Name: Appion, CTFFIND3, FindEM, EMAN, RELION
Details: Per-frame dose weighting was performed using the RELION particle polishing method.
Number images used: 43879
DetailsPre-processing was performed in the Appion pipeline using a template for particle selection, CTFFIND3 for CTF estimation, MSA/MRA for 2D classification, and RELION for 3D classification and refinement.
FSC plot (resolution estimation)

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