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- PDB-5an8: Cryo-electron microscopy structure of rabbit TRPV2 ion channel -

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Basic information

Entry
Database: PDB / ID: 5an8
TitleCryo-electron microscopy structure of rabbit TRPV2 ion channel
ComponentsTRPV2
KeywordsTRANSPORT PROTEIN / TRP CHANNEL
Function / homology
Function and homology information


growth cone membrane / response to temperature stimulus / positive regulation of calcium ion import / calcium ion import across plasma membrane / axonal growth cone / positive regulation of axon extension / calcium channel activity / positive regulation of cold-induced thermogenesis / cell body / cell surface / identical protein binding
Similarity search - Function
Ankyrin repeat-containing domain / 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 / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat ...Ankyrin repeat-containing domain / 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 / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Ion transport domain / Ion transport protein / Alpha Horseshoe / Mainly Alpha
Similarity search - Domain/homology
Transient receptor potential cation channel subfamily V member 2
Similarity search - Component
Biological speciesORYCTOLAGUS CUNICULUS (rabbit)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsZubcevic, L. / Herzik, M.A.J. / Chung, B.C. / Lander, G.C. / Lee, S.Y.
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, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 23, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 20, 2016Group: Database references / Other / Structure summary
Revision 1.2Jan 27, 2016Group: Database references
Revision 1.3Mar 2, 2016Group: Database references
Revision 1.4Apr 3, 2019Group: Data collection / Source and taxonomy / Category: entity_src_gen / Item: _entity_src_gen.pdbx_host_org_cell_line
Revision 1.5Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

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Assembly

Deposited unit
A: TRPV2
B: TRPV2
C: TRPV2
D: TRPV2


Theoretical massNumber of molelcules
Total (without water)279,6264
Polymers279,6264
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA

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Components

#1: Protein
TRPV2


Mass: 69906.391 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: RABBIT TRPV2 / Source: (gene. exp.) ORYCTOLAGUS CUNICULUS (rabbit) / Plasmid: PFASTBAC / Cell line (production host): Sf9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: G1SNM3
Has protein modificationY

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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: RABBIT TRPV2 / Type: COMPLEX
Buffer solutionName: 20MM PBS / pH: 7.6 / Details: 20MM PBS
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: HOLEY CARBON
VitrificationInstrument: GATAN CRYOPLUNGE 3 / Cryogen name: ETHANE / Details: PLUNGE FROZEN IN LIQUID ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS / Date: May 12, 2015
Details: DATA ACQUIRED USING LEGINON, COLLECTED IN K2 SUPER RESOLUTION MODE
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 22500 X / Calibrated magnification: 38168 X / Nominal defocus max: 3000 nm / Nominal defocus min: 1200 nm / Cs: 2.7 mm
Specimen holderTemperature: 78 K
Image recordingElectron dose: 57 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)
Image scansNum. digital images: 747

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Processing

SymmetryPoint symmetry: C4 (4 fold cyclic)
3D reconstructionResolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 43879 / Refinement type: HALF-MAPS REFINED INDEPENDENTLY / Symmetry type: POINT
RefinementHighest resolution: 3.8 Å
Refinement stepCycle: LAST / Highest resolution: 3.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15832 0 0 0 15832

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