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- EMDB-9119: Structure of human TRPV3 in the presence of 2-APB in C4 symmetry -

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Basic information

Entry
Database: EMDB / ID: EMD-9119
TitleStructure of human TRPV3 in the presence of 2-APB in C4 symmetry
Map dataSingle-particle cryo-EM reconstruction of human TRPV3 purified in the presence of 2-APB (state 1)
Sample
  • Complex: Human TRPV3 in the presence of 2-APB
    • Protein or peptide: Transient receptor potential cation channel subfamily V member 3
Keywordsmembrane protein / ion channel / TRP channel / calcium transport / TRANSPORT PROTEIN
Function / homology
Function and homology information


negative regulation of hair cycle / TRP channels / response to temperature stimulus / positive regulation of calcium ion import / calcium ion transmembrane transport / calcium channel activity / lysosome / receptor complex / identical protein binding / plasma membrane / cytoplasm
Similarity search - Function
Transient receptor potential cation channel subfamily V member 1-4 / Transient receptor potential cation channel subfamily V / Ankyrin repeat / 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 3
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsZubcevic L / Herzik MA
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)R35NS097241 United States
National Institutes of Health/National Institute of Biomedical Imaging and Bioengineering (NIH/NIBIB)DP2EB020402 United States
National Institutes of Health/National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIH/NIAMS)R21AR072910 United States
CitationJournal: Nat Commun / Year: 2018
Title: Conformational ensemble of the human TRPV3 ion channel.
Authors: Lejla Zubcevic / Mark A Herzik / Mengyu Wu / William F Borschel / Marscha Hirschi / Albert S Song / Gabriel C Lander / Seok-Yong Lee /
Abstract: Transient receptor potential vanilloid channel 3 (TRPV3), a member of the thermosensitive TRP (thermoTRPV) channels, is activated by warm temperatures and serves as a key regulator of normal skin ...Transient receptor potential vanilloid channel 3 (TRPV3), a member of the thermosensitive TRP (thermoTRPV) channels, is activated by warm temperatures and serves as a key regulator of normal skin physiology through the release of pro-inflammatory messengers. Mutations in trpv3 have been identified as the cause of the congenital skin disorder, Olmsted syndrome. Unlike other members of the thermoTRPV channel family, TRPV3 sensitizes upon repeated stimulation, yet a lack of structural information about the channel precludes a molecular-level understanding of TRPV3 sensitization and gating. Here, we present the cryo-electron microscopy structures of apo and sensitized human TRPV3, as well as several structures of TRPV3 in the presence of the common thermoTRPV agonist 2-aminoethoxydiphenyl borate (2-APB). Our results show α-to-π-helix transitions in the S6 during sensitization, and suggest a critical role for the S4-S5 linker π-helix during ligand-dependent gating.
History
DepositionSep 18, 2018-
Header (metadata) releaseOct 3, 2018-
Map releaseOct 3, 2018-
UpdateMar 13, 2024-
Current statusMar 13, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.07
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.07
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6mhv
  • Surface level: 0.07
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_9119.png

Downloads & links

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Map

FileDownload / File: emd_9119.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSingle-particle cryo-EM reconstruction of human TRPV3 purified in the presence of 2-APB (state 1)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.15 Å/pix.
x 288 pix.
= 331.2 Å		1.15 Å/pix.
x 288 pix.
= 331.2 Å		1.15 Å/pix.
x 288 pix.
= 331.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.15 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.07 / Movie #1: 0.07
Minimum - Maximum-0.2962902 - 0.5267865
Average (Standard dev.)0.00069370965 (±0.011121423)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions288288288
Spacing288288288
CellA=B=C: 331.19998 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.151.151.15
M x/y/z288288288
origin x/y/z0.0000.0000.000
length x/y/z331.200331.200331.200
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS288288288
D min/max/mean-0.2960.5270.001

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Supplemental data

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Half map: Even half map

Fileemd_9119_half_map_1.map
AnnotationEven half map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Odd half map

Fileemd_9119_half_map_2.map
AnnotationOdd half map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Human TRPV3 in the presence of 2-APB

EntireName: Human TRPV3 in the presence of 2-APB
Components
  • Complex: Human TRPV3 in the presence of 2-APB
    • Protein or peptide: Transient receptor potential cation channel subfamily V member 3

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Supramolecule #1: Human TRPV3 in the presence of 2-APB

SupramoleculeName: Human TRPV3 in the presence of 2-APB / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Transient receptor potential cation channel subfamily V member 3

MacromoleculeName: Transient receptor potential cation channel subfamily V member 3
type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 94.860219 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MEKAHPKEMV PLMGKRVAAP SGNPAILPEK RPAEITPTKK SAHFFLEIEG FEPNPTVAKT SPPVFSKPMD SNIRQCISGN CDDMDSPQS PQDDVTETPS NPNSPSAQLA KEEQRRKKRR LKKRIFAAVS EGCVEELVEL LVELQELCRR RHDEDVPDFL M HKLTASDT ...String:
MEKAHPKEMV PLMGKRVAAP SGNPAILPEK RPAEITPTKK SAHFFLEIEG FEPNPTVAKT SPPVFSKPMD SNIRQCISGN CDDMDSPQS PQDDVTETPS NPNSPSAQLA KEEQRRKKRR LKKRIFAAVS EGCVEELVEL LVELQELCRR RHDEDVPDFL M HKLTASDT GKTCLMKALL NINPNTKEIV RILLAFAEEN DILGRFINAE YTEEAYEGQT ALNIAIERRQ GDIAALLIAA GA DVNAHAK GAFFNPKYQH EGFYFGETPL ALAACTNQPE IVQLLMEHEQ TDITSRDSRG NNILHALVTV AEDFKTQNDF VKR MYDMIL LRSGNWELET TRNNDGLTPL QLAAKMGKAE ILKYILSREI KEKRLRSLSR KFTDWAYGPV SSSLYDLTNV DTTT DNSVL EITVYNTNID NRHEMLTLEP LHTLLHMKWK KFAKHMFFLS FCFYFFYNIT LTLVSYYRPR EEEAIPHPLA LTHKM GWLQ LLGRMFVLIW AMCISVKEGI AIFLLRPSDL QSILSDAWFH FVFFIQAVLV ILSVFLYLFA YKEYLACLVL AMALGW ANM LYYTRGFQSM GMYSVMIQKV ILHDVLKFLF VYIVFLLGFG VALASLIEKC PKDNKDCSSY GSFSDAVLEL FKLTIGL GD LNIQQNSKYP ILFLFLLITY VILTFVLLLN MLIALMGETV ENVSKESERI WRLQRARTIL EFEKMLPEWL RSRFRMGE L CKVAEDDFRL CLRINEVKWT EWKTHVSFLN EDPGPVRRTD FNKIQDSSRN NSKTTLNAFE EVEEFPETSV VDAGLEVLF QGPAAAVDYK DDDDKAHHHH HHHHHH

UniProtKB: Transient receptor potential cation channel subfamily V member 3

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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

Concentration0.5 mg/mL
BufferpH: 8 / Details: Buffer contained 1 mM 2-APB
GridModel: Quantifoil, UltrAuFoil, R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 7 sec. / Pretreatment - Atmosphere: OTHER / Details: Gatan Solarus
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 277 K / Instrument: HOMEMADE PLUNGER
Details: Specimen was manually blotted for 4 seconds immediately prior to plunge-freezing in liquid ethane cooled by liquid nitrogen..

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
TemperatureMin: 93.0 K / Max: 93.0 K
DetailsAlignment performed as described in Herzik, Wu, Lander, Nat Methods 2017 (PMID: 28991891)
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 3710 pixel / Digitization - Dimensions - Height: 3838 pixel / Digitization - Frames/image: 1-60 / Number grids imaged: 1 / Number real images: 1908 / Average exposure time: 15.0 sec. / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 36000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 897643
Startup modelType of model: EMDB MAP
EMDB ID:

9115


Details: The apo TRPV3 volume (EMDB-9115) was low-pass filtered to 30 angstroms and used as an initial model
Final reconstructionApplied symmetry - Point group: C4 (4 fold cyclic) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.1) / Number images used: 141832
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 2.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 2.1)
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Overall B value: 145
Output model

PDB-6mhv:
Structure of human TRPV3 in the presence of 2-APB in C4 symmetry

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