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- PDB-6oo4: Cryo-EM structure of the C2-symmetric TRPV2/RTx complex in amphip... -

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Database: PDB / ID: 6oo4
TitleCryo-EM structure of the C2-symmetric TRPV2/RTx complex in amphipol resolved to 3.3 A
KeywordsMETAL TRANSPORT / ion channel / calcium channel / TRP channel / metal transport
Function / homology
Function and homology information

growth cone membrane / positive regulation of calcium ion import / positive regulation of axon extension / calcium channel activity / axonal growth cone / cell body / positive regulation of cold-induced thermogenesis / response to heat / cell surface / integral component of membrane / identical protein binding
Ankyrin repeat / Ankyrin repeat-containing domain / 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 / Transient receptor potential cation channel subfamily V / Ion transport domain / Transient receptor potential channel, vanilloid 1-4
Transient receptor potential cation channel subfamily V member 2
Biological speciesOryctolagus cuniculus (rabbit)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsZubcevic, L. / Hsu, A.L. / Borgnia, M.J. / Lee, S.-Y.
Funding supportUnited States , 2件
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Neurological Disorders and StrokeR35NS097241United States
National Institutes of Health/National Institute of Environmental Health SciencesZIC ES103326United States
CitationJournal: Elife / Year: 2019
Title: Symmetry transitions during gating of the TRPV2 ion channel in lipid membranes.
Authors: Lejla Zubcevic / Allen L Hsu / Mario J Borgnia / Seok-Yong Lee /
Abstract: The Transient Receptor Potential Vanilloid 2 (TRPV2) channel is a member of the temperature-sensing thermoTRPV family. Recent advances in cryo-electronmicroscopy (cryo-EM) and X-ray crystallography ...The Transient Receptor Potential Vanilloid 2 (TRPV2) channel is a member of the temperature-sensing thermoTRPV family. Recent advances in cryo-electronmicroscopy (cryo-EM) and X-ray crystallography have provided many important insights into the gating mechanisms of thermoTRPV channels. Interestingly, crystallographic studies of ligand-dependent TRPV2 gating have shown that the TRPV2 channel adopts two-fold symmetric arrangements during the gating cycle. However, it was unclear if crystal packing forces played a role in stabilizing the two-fold symmetric arrangement of the channel. Here, we employ cryo-EM to elucidate the structure of full-length rabbit TRPV2 in complex with the agonist resiniferatoxin (RTx) in nanodiscs and amphipol. We show that RTx induces two-fold symmetric conformations of TRPV2 in both environments. However, the two-fold symmetry is more pronounced in the native-like lipid environment of the nanodiscs. Our data offers insights into a gating pathway in TRPV2 involving symmetry transitions.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Apr 22, 2019 / Release: May 29, 2019
RevisionDateData content typeProviderType
1.0May 29, 2019Structure modelrepositoryInitial release

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Deposited unit
hetero molecules

Theoretical massNumber of molelcules
Total (without water)357,4068

TypeNameSymmetry operationNumber
identity operation1_5551
Buried area21320 Å2
ΔGint-226 kcal/mol
Surface area108390 Å2


#1: Protein/peptide

Mass: 88722.680 Da / Num. of mol.: 4 / Mutation: F470S, L505M, L508T, Q528E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Gene: TRPV2 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: G1SNM3
#2: Chemical
ChemComp-6EU / resiniferatoxin / RTX

Mass: 628.708 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C37H40O9 / Resiniferatoxin

Experimental details


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

Sample preparation

ComponentName: TRPV2 / Type: COMPLEX
Details: TRPV2 in complex with RTx reconstituted into amphipol A8-35
Entity ID: 1 / Source: RECOMBINANT
Molecular weightValue: 0.300 MDa / Experimental value: NO
Source (natural)Organism: Oryctolagus cuniculus (rabbit)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm) / Cell: Sf9
Buffer solutionpH: 8
Buffer component

Buffer-ID: 1

1150 mMsodium chlorideNaClSodium chloride
250 mMTris
32 uMresiniferatoxin
SpecimenConc.: 2 mg/ml
Details: TRPV2 in complex with RTx reconstituted into amphipol A8-35, monodisperse
Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil, UltrAuFoil, R1.2/1.3
VitrificationInstrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 90 % / Chamber temperature: 296 K / Details: Blotted 3 seconds before plunging

Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: OTHER / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: OTHER
Specimen holderCryogen: NITROGEN
Image recordingElectron dose: 42 e/Å2 / Film or detector model: FEI FALCON III (4k x 4k) / Num. of real images: 1293


SoftwareName: PHENIX / Version: 1.15_3459: / Classification: refinement
EM software
4RELION3CTF correctionGctf was used to perform CTF correction.
7Coot0.8.2model fittingModel was built into the density in Coot.
9PHENIX1.15model refinementPhenix real space refinement was performed.
10RELION3initial Euler assignment
12RELION3classificationClassification was performed in RELION 3.0.
13RELION33D reconstruction
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 109623 / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Atomic model buildingPDB-ID: 5AN8
Pdb chain-ID: A
Refine LS restraints


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