[English] 日本語
Yorodumi
- EMDB-7119: TRPV2 ion channel in partially closed state -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: EMDB / ID: 7119
TitleTRPV2 ion channel in partially closed state
Map dataTRPV2 ion channel in a partially closed state and with a deletion in the pore turret domain.
SampleTRPV2 in a partially open state and with a deletion in the pore turret domain (564-589).
  • 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 / 3.6 Å resolution
AuthorsDosey TL / Wang Z
CitationJournal: To Be Published
Title: TRPV2 ion channel gating through allosteric domain coupling revealed by cryo-EM
Authors: Dosey TL / Wang Z / Fan G / Zhang Z / Serysheva I / Chiu W / Wensel TG
Validation ReportPDB-ID: 6bo5

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

-
Structure visualization

Movie
  • Surface view colored by cylindrical radius
  • Surface level: 0.018
  • Imaged by UCSF Chimera
  • Download
  • Surface view with section colored by density value
  • Surface level: 0.018
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-6bo5
  • Surface level: 0.018
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

-
Map

Fileemd_7119.map.gz (map file in CCP4 format, 42593 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
220 pix
1.23 Å/pix.
= 270.6 Å
220 pix
1.23 Å/pix.
= 270.6 Å
220 pix
1.23 Å/pix.
= 270.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.23 Å
Density
Contour Level:0.018 (by author), 0.018 (movie #1):
Minimum - Maximum-0.025153792 - 0.06453739
Average (Standard dev.)0.00018316944 (0.003981216)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions220220220
Origin0.00.00.0
Limit219.0219.0219.0
Spacing220220220
CellA=B=C: 270.6 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.231.231.23
M x/y/z220220220
origin x/y/z0.0000.0000.000
length x/y/z270.600270.600270.600
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ450450450
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS220220220
D min/max/mean-0.0250.0650.000

-
Supplemental data

-
Sample components

-
Entire TRPV2 in a partially open state and with a deletion in the pore t...

EntireName: TRPV2 in a partially open state and with a deletion in the pore turret domain (564-589).
Number of components: 2

-
Component #1: protein, TRPV2 in a partially open state and with a deletion in t...

ProteinName: TRPV2 in a partially open state and with a deletion in the pore turret domain (564-589).
Recombinant expression: No
MassTheoretical: 320 kDa
SourceSpecies: Rattus norvegicus (Norway rat)
Source (engineered)Expression System: Saccharomyces cerevisiae (baker's yeast) / Vector: pYepm

-
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: 79.476828 kDa
SourceSpecies: Rattus norvegicus (Norway rat)
Source (engineered)Expression System: Saccharomyces cerevisiae (baker's yeast)

-
Experimental details

-
Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionSpecimen conc.: .5 mg/ml / pH: 8
Support filmunspecified
VitrificationCryogen name: ETHANE / Temperature: 293 K / Humidity: 98 %

-
Electron microscopy imaging

ImagingMicroscope: JEOL 3200FSC
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)

-
Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C4 (4 fold cyclic) / Number of projections: 50509
3D reconstructionSoftware: RELION / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF

-
Atomic model buiding

Output model

+
About Yorodumi

-
News

-
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary. This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated. See below links for details.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software). Now, EM Navigator and Yorodumi are based on the updated data.

External links: wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.: Omokage search

+
Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi

+
Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi

+
Apr 13, 2016. Omokage search got faster

Omokage search got faster

  • The computation time became ~1/2 compared to the previous version by re-optimization of data accession
  • Enjoy "shape similarity" of biomolecules, more!

Related info.: Omokage search

Read more

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.

Related info.: EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more