[English] 日本語
Yorodumi
- PDB-6oo5: Cryo-EM structure of the C2-symmetric TRPV2/RTx complex in amphip... -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: PDB / ID: 6oo5
TitleCryo-EM structure of the C2-symmetric TRPV2/RTx complex in amphipol resolved to 4.2 A
ComponentsTRPV2
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: 4.2 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

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-20146
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)357,4068
Polymers354,8914
Non-polymers2,5154
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551
Buried area17840 Å2
ΔGint-211 kcal/mol
Surface area117090 Å2

-
Components

#1: Protein/peptide
TRPV2 /


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

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
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

IDConc.NameFormula
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

-
Processing

SoftwareName: PHENIX / Version: 1.15_3459: / Classification: refinement
EM software
IDNameVersionCategoryDetails
4RELION3CTF correctionGctf was used to perform CTF correction.
7Coot0.8.2model fittingModel was built into the density in Coot.
9PHENIX1.15model refinementPhenix real space refine was performed.
10RELION3initial Euler assignment
12RELION3classificationClassification was performed in RELION 3.0.
13RELION33D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 90862 / 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

Refinement-ID: ELECTRON MICROSCOPY

TypeDev idealNumber
f_bond_d0.00718004
f_angle_d0.94624726
f_dihedral_angle_d11.72710276
f_chiral_restr0.052930
f_plane_restr0.0073072

+
About Yorodumi

-
News

-
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force. (see PDBe EMDB page)
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.: Q: What is "EMD"? / ID/Accession-code notation in Yorodumi/EM Navigator

External links: EMDB at PDBe / Contact to PDBj

-
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary. This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated. See below links for details.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software). Now, EM Navigator and Yorodumi are based on the updated data.

External links: wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

+
Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.: Omokage search

+
Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi

+
Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi

Read more

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.

Related info.: EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more