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- EMDB-33774: 2-APB bound state of mTRPV2 -

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Basic information

Entry
Database: EMDB / ID: EMD-33774
Title2-APB bound state of mTRPV2
Map data
Sample
  • Complex: complex of mTRPV2 and 2-APB
    • Protein or peptide: Transient receptor potential cation channel subfamily V member 2
  • Ligand: 2-aminoethyl diphenylborinate
Function / homology
Function and homology information


growth cone membrane / TRP channels / response to temperature stimulus / positive regulation of calcium ion import / endomembrane system / positive regulation of axon extension / axonal growth cone / monoatomic cation channel activity / calcium channel activity / melanosome ...growth cone membrane / TRP channels / response to temperature stimulus / positive regulation of calcium ion import / 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 speciesMus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.83 Å
AuthorsSu N
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32122040 China
CitationJournal: Nat Chem Biol / Year: 2023
Title: Structural mechanisms of TRPV2 modulation by endogenous and exogenous ligands.
Authors: Nannan Su / Wenxuan Zhen / Heng Zhang / Lingyi Xu / Yitian Jin / Xiaoying Chen / Cheng Zhao / Qinrui Wang / Xinyan Wang / Shaowei Li / Han Wen / Wei Yang / Jiangtao Guo / Fan Yang /
Abstract: The transient receptor potential vanilloid 2 (TRPV2) ion channel is a polymodal receptor widely involved in many physiological and pathological processes. Despite many TRPV2 modulators being ...The transient receptor potential vanilloid 2 (TRPV2) ion channel is a polymodal receptor widely involved in many physiological and pathological processes. Despite many TRPV2 modulators being identified, whether and how TRPV2 is regulated by endogenous lipids remains elusive. Here, we report an endogenous cholesterol molecule inside the vanilloid binding pocket (VBP) of TRPV2, with a 'head down, tail up' configuration, resolved at 3.2 Å using cryo-EM. Cholesterol binding antagonizes ligand activation of TRPV2, which is removed from VBP by methyl-β-cyclodextrin (MβCD) as resolved at 2.9 Å. We also observed that estradiol (E2) potentiated TRPV2 activation by 2-aminoethoxydiphenyl borate (2-APB), a classic tool compound for TRP channels. Our cryo-EM structures (resolved at 2.8-3.3 Å) further suggest how E2 disturbed cholesterol binding and how 2-APB bound within the VBP with E2 or without both E2 and endogenous cholesterol, respectively. Therefore, our study has established the structural basis for ligand recognition of the inhibitory endogenous cholesterol and excitatory exogenous 2-APB in TRPV2.
History
DepositionJul 6, 2022-
Header (metadata) releaseAug 17, 2022-
Map releaseAug 17, 2022-
UpdateMar 1, 2023-
Current statusMar 1, 2023Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_33774.png

Downloads & links

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Map

FileDownload / File: emd_33774.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.93 Å
Density
Contour LevelBy AUTHOR: 0.016
Minimum - Maximum-0.05759238 - 0.122524716
Average (Standard dev.)0.00012875916 (±0.004579162)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 223.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_33774_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_33774_half_map_1.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Half map: #1

Fileemd_33774_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : complex of mTRPV2 and 2-APB

EntireName: complex of mTRPV2 and 2-APB
Components
  • Complex: complex of mTRPV2 and 2-APB
    • Protein or peptide: Transient receptor potential cation channel subfamily V member 2
  • Ligand: 2-aminoethyl diphenylborinate

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Supramolecule #1: complex of mTRPV2 and 2-APB

SupramoleculeName: complex of mTRPV2 and 2-APB / type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Mus musculus (house mouse)

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Macromolecule #1: Transient receptor potential cation channel subfamily V member 2

MacromoleculeName: Transient receptor potential cation channel subfamily V member 2
type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 86.058195 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MTSASNPPAF RLETSDGDEE GSAEVNKGKN EPPPMESPFQ GEDRNFSPQI KVNLNYRKGL GPSQQDPNRF DRDRLFSVVS RGVPEELTG LLEYLRRTSK YLTDSAYTEG STGKTCLMKA VLNLQDGVNA CILPLLQIDR DSGNPQPLVN AQCTDEFYRG H SALHIAIE ...String:
MTSASNPPAF RLETSDGDEE GSAEVNKGKN EPPPMESPFQ GEDRNFSPQI KVNLNYRKGL GPSQQDPNRF DRDRLFSVVS RGVPEELTG LLEYLRRTSK YLTDSAYTEG STGKTCLMKA VLNLQDGVNA CILPLLQIDR DSGNPQPLVN AQCTDEFYRG H SALHIAIE KRSLWCVKLL VENGANVHIR ACGRFFQKHQ GTCFYFGELP LSLAACTKQW DVVTYLLENP HQPASLEATD SL GNTVLHA LVMIADNSPE NSALVIHMYD SLLQMGARLC PTVQLEDICN HQGLTPLKLA AKEGKIEIFR HILQREFSGL YQP LSRKFT EWCYGPVRVS LYDLSSVDSW EKNSVLEIIA FHCKSPHRHR MVVLEPLNKL LQEKWDRLIP RFFFNFACYL VYMI IFTIV AYHQPSLEQP AIPSSKATFG DSMLLLGHIL ILLGGIYLLL GQLWYFWRRR LFIWISFMDS YFEILFLVQA LLTVL SQVL RFVETEWYLP LLVSSLVLGW LNLLYYTRGF QHTGIYSVMI QKVILRDLLR FLLVYLVFLF GFAVALVSLS REARSP KAP EDSNTTVTEK PTLGQEEEPV PYGGILDASL ELFKFTIGMG ELAFQEQLRF RGVVLLLLLA YVLLTYVLLL NMLIALM SE TVNSVATDSW SIWKLQKAIS VLEMENGYWW CRRKRHRAGR LLKVGTKGDG IPDERWCFRV EEVNWAAWEK TLPTLSED P SGAGITGYKK NPTSKPGKNS ASEEDHLPLQ VLQSH

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Macromolecule #2: 2-aminoethyl diphenylborinate

MacromoleculeName: 2-aminoethyl diphenylborinate / type: ligand / ID: 2 / Number of copies: 4 / Formula: FZ4
Molecular weightTheoretical: 225.094 Da
Chemical component information

ChemComp-FZ4:
2-aminoethyl diphenylborinate / 2-Aminoethoxydiphenyl borate

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration5 mg/mL
BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 1.5 µm / Nominal defocus min: 1.0 µm
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average exposure time: 6.0 sec. / Average electron dose: 52.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.83 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 121357

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