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- PDB-6bo4: Open state structure of the full-length TRPV2 cation channel with... -

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Basic information

Entry
Database: PDB / ID: 6bo4
TitleOpen state structure of the full-length TRPV2 cation channel with a resolved pore turret domain
ComponentsTransient receptor potential cation channel subfamily V member 2
KeywordsMEMBRANE PROTEIN / channel / TRP / cation / open
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
Specimen sourceRattus norvegicus (Norway rat)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 4 Å resolution
AuthorsDosey, T.L. / 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 Report
SummaryFull reportAbout validation report
DateDeposition: Nov 18, 2017 / Release: Dec 5, 2018

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Assembly

Deposited unit
A: Transient receptor potential cation channel subfamily V member 2
D: Transient receptor potential cation channel subfamily V member 2
B: Transient receptor potential cation channel subfamily V member 2
C: Transient receptor potential cation channel subfamily V member 2


Theoretical massNumber of molelcules
Total (without water)319,9984
Polyers319,9984
Non-polymers00
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein/peptide
Transient receptor potential cation channel subfamily V member 2 / TrpV2 / Osm-9-like TRP channel 2 / OTRPC2 / Stretch-activated channel 2B / Vanilloid receptor-like protein 1 / VRL-1


Mass: 79999.422 Da / Num. of mol.: 4 / Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Trpv2, Sac2b, Vrl1 / Production host: Saccharomyces cerevisiae (baker's yeast) / References: UniProt: Q9WUD2

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / Reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: TRPV2 / Type: COMPLEX / Entity ID: 1 / Source: RECOMBINANT
Molecular weightValue: .320 MDa / Experimental value: NO
Source (natural)Organism: Rattus norvegicus (Norway rat)
Source (recombinant)Organism: Saccharomyces cerevisiae (baker's yeast) / Plasmid: pYEPM / Strain: BJ5457
Buffer solutionpH: 8
SpecimenConc.: .5 / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: unspecified
VitrificationCryogen name: ETHANE / Humidity: 98 % / Chamber temperature: 298

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Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI POLARA 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingAverage exposure time: 10 / Electron dose: 63 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.11.1_2575: / Classification: refinement
EM software
IDNameVersionCategoryDetails
4EMAN2CTF correction
12RELION1.4classificationto manually select particle images
13RELION1.43D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNumber of particles selected: 494689
SymmetryPoint symmetry: C4
3D reconstructionResolution: 4 / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 11789 / Symmetry type: POINT
Refine LS restraints
Refine IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00818872
ELECTRON MICROSCOPYf_angle_d1.30725800
ELECTRON MICROSCOPYf_dihedral_angle_d5.99811016
ELECTRON MICROSCOPYf_chiral_restr0.0613044
ELECTRON MICROSCOPYf_plane_restr0.0083264

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