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- PDB-5hi9: Structure of the full-length TRPV2 channel by cryo-electron microscopy -

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Basic information

Entry
Database: PDB / ID: 5hi9
TitleStructure of the full-length TRPV2 channel by cryo-electron microscopy
ComponentsTransient Receptor Potential Cation Channel Subfamily V Member 2
KeywordsTRANSPORT PROTEIN / TRPV2 ion channel
Function / homology
Function and homology information


growth cone membrane / TRP channels / response to temperature stimulus / positive regulation of calcium ion import / monoatomic cation transmembrane transport / endomembrane system / positive regulation of axon extension / axonal growth cone / monoatomic cation channel activity / calcium channel activity ...growth cone membrane / TRP channels / response to temperature stimulus / positive regulation of calcium ion import / monoatomic cation transmembrane transport / endomembrane system / positive regulation of axon extension / axonal growth cone / monoatomic cation channel activity / calcium channel activity / melanosome / lamellipodium / cell body / positive regulation of cold-induced thermogenesis / axon / negative regulation of cell population proliferation / cell surface / identical protein binding / plasma membrane
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 speciesRattus norvegicus (Norway rat)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.4 Å
AuthorsHuynh, K.W. / Cohen, M.R. / Jiansen, J. / Samanta, A. / Lodowski, D.T. / Zhou, Z.H. / Moiseenkova-Bell, V.Y.
Funding support United States, 1items
OrganizationGrant numberCountry
American Heart AssociationNCRP Scientist Development Grant 11SDG5280029 United States
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
DepositionJan 11, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 30, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 13, 2016Group: Database references
Revision 1.2May 11, 2016Group: Other
Revision 1.3Oct 4, 2017Group: Author supporting evidence / Data collection / Category: em_image_scans / em_software / pdbx_audit_support
Item: _em_software.name / _pdbx_audit_support.funding_organization
Revision 1.4Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

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Assembly

Deposited unit
A: 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
D: Transient Receptor Potential Cation Channel Subfamily V Member 2


Theoretical massNumber of molelcules
Total (without water)350,6714
Polymers350,6714
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area16870 Å2
ΔGint-151 kcal/mol
Surface area122370 Å2

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Components

#1: Protein
Transient Receptor Potential Cation Channel Subfamily V Member 2 / TrpV2 / Osm-9-like TRP channel 2 / OTRPC2 / Stretch-activated channel 2B / Vanilloid receptor-like ...TrpV2 / Osm-9-like TRP channel 2 / OTRPC2 / Stretch-activated channel 2B / Vanilloid receptor-like protein 1 / VRL-1


Mass: 87667.789 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Details (production host): YepM Plasmid / Production host: Saccharomycetales (fungus) / Strain (production host): BJ5457 / References: UniProt: Q9WUD2

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Transient Receptor Potential cation Channel Subfamily V Member 2
Type: COMPLEX / Details: Recombinant Purified Protein / Entity ID: all / Source: MULTIPLE SOURCES
Molecular weightValue: 0.340 MDa / Experimental value: YES
Buffer solutionpH: 8
SpecimenConc.: 2.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: This sample was monodisperse
Specimen supportGrid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R2/1
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Humidity: 15 % / Chamber temperature: 298 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 31000 X
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 21 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 988 / Details: Gatan K2 Summit in super-resolution counting mode.

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Processing

SoftwareName: PHENIX / Version: dev_2247: / Classification: refinement
EM software
IDNameVersionCategoryDetails
3RELION1.3image acquisitionAuto-Picking
4RELION1.4image acquisition2D, 3D Classification and Refinement
9Coot0.8model fitting
24PHENIX1.10.1model refinement
CTF correctionType: NONE
SymmetryPoint symmetry: C4 (4 fold cyclic)
3D reconstructionResolution: 4.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 42550 / Symmetry type: POINT
RefinementHighest resolution: 4.4 Å
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00720124
ELECTRON MICROSCOPYf_angle_d1.05427288
ELECTRON MICROSCOPYf_dihedral_angle_d14.42116456
ELECTRON MICROSCOPYf_chiral_restr0.0493064
ELECTRON MICROSCOPYf_plane_restr0.0063380

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