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Open data
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Basic information
Entry | Database: PDB / ID: 5an8 | ||||||
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Title | Cryo-electron microscopy structure of rabbit TRPV2 ion channel | ||||||
![]() | TRPV2 | ||||||
![]() | TRANSPORT PROTEIN / TRP CHANNEL | ||||||
Function / homology | ![]() growth cone membrane / response to temperature stimulus / positive regulation of calcium ion import / calcium ion import across plasma membrane / positive regulation of axon extension / axonal growth cone / calcium channel activity / positive regulation of cold-induced thermogenesis / cell body / cell surface / identical protein binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.8 Å | ||||||
![]() | Zubcevic, L. / Herzik, M.A.J. / Chung, B.C. / Lander, G.C. / Lee, S.Y. | ||||||
![]() | ![]() 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. | ||||||
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Structure visualization
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Structure viewer | Molecule: ![]() ![]() |
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PDBx/mmCIF format | ![]() | 415.3 KB | Display | ![]() |
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PDB format | ![]() | 333.4 KB | Display | ![]() |
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-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6455MC M: map data used to model this data C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Components
#1: Protein | Mass: 69906.391 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: RABBIT TRPV2 / Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: RABBIT TRPV2 / Type: COMPLEX |
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Buffer solution | Name: 20MM PBS / pH: 7.6 / Details: 20MM PBS |
Specimen | Conc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Details: HOLEY CARBON |
Vitrification | Instrument: 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 |
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Microscopy | Model: FEI TITAN KRIOS / Date: May 12, 2015 Details: DATA ACQUIRED USING LEGINON, COLLECTED IN K2 SUPER RESOLUTION MODE |
Electron gun | Electron source: ![]() |
Electron lens | Mode: 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 holder | Temperature: 78 K |
Image recording | Electron dose: 57 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
Image scans | Num. digital images: 747 |
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Processing
Symmetry | Point symmetry: C4 (4 fold cyclic) | ||||||||||||
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3D reconstruction | Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 43879 / Refinement type: HALF-MAPS REFINED INDEPENDENTLY / Symmetry type: POINT | ||||||||||||
Refinement | Highest resolution: 3.8 Å | ||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 3.8 Å
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