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- EMDB-7075: Xenopus Tropicalis TRPV4 -

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Basic information

Entry
Database: EMDB / ID: EMD-7075
TitleXenopus Tropicalis TRPV4
Map dataTransient receptor potential cation channel, subfamily V, member 4
Sample
  • Organelle or cellular component: TRPV4
    • Protein or peptide: Transient receptor potential cation channel, subfamily V, member 4
KeywordsIon Channel / TRP channel / METAL TRANSPORT
Function / homology
Function and homology information


TRP channels / plasma membrane => GO:0005886 / osmosensory signaling pathway / calcium ion import across plasma membrane / monoatomic ion channel activity / actin filament organization / calcium channel activity / cilium
Similarity search - Function
Domain of unknown function DUF3447 / Transient receptor potential cation channel subfamily V member 4 / 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 ...Domain of unknown function DUF3447 / Transient receptor potential cation channel subfamily V member 4 / 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 4
Similarity search - Component
Biological speciesXenopus tropicalis (tropical clawed frog)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsDeng Z / Hite RK
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)R01NS099341-01A1 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)P30 CA008748 United States
American Heart Association17SDG33400229 United States
CitationJournal: Nat Struct Mol Biol / Year: 2018
Title: Cryo-EM and X-ray structures of TRPV4 reveal insight into ion permeation and gating mechanisms.
Authors: Zengqin Deng / Navid Paknejad / Grigory Maksaev / Monica Sala-Rabanal / Colin G Nichols / Richard K Hite / Peng Yuan /
Abstract: The transient receptor potential (TRP) channel TRPV4 participates in multiple biological processes, and numerous TRPV4 mutations underlie several distinct and devastating diseases. Here we present ...The transient receptor potential (TRP) channel TRPV4 participates in multiple biological processes, and numerous TRPV4 mutations underlie several distinct and devastating diseases. Here we present the cryo-EM structure of Xenopus tropicalis TRPV4 at 3.8-Å resolution. The ion-conduction pore contains an intracellular gate formed by the inner helices, but lacks any extracellular gate in the selectivity filter, as observed in other TRPV channels. Anomalous X-ray diffraction analyses identify a single ion-binding site in the selectivity filter, thus explaining TRPV4 nonselectivity. Structural comparisons with other TRP channels and distantly related voltage-gated cation channels reveal an unprecedented, unique packing interface between the voltage-sensor-like domain and the pore domain, suggesting distinct gating mechanisms. Moreover, our structure begins to provide mechanistic insights to the large set of pathogenic mutations, offering potential opportunities for drug development.
History
DepositionOct 18, 2017-
Header (metadata) releaseNov 8, 2017-
Map releaseFeb 28, 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: 3.5
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 3.5
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6bbj
  • Surface level: 3.5
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_7075.png

Downloads & links

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Map

FileDownload / File: emd_7075.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationTransient receptor potential cation channel, subfamily V, member 4
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.09 Å/pix.
x 256 pix.
= 278.528 Å		1.09 Å/pix.
x 256 pix.
= 278.528 Å		1.09 Å/pix.
x 256 pix.
= 278.528 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.088 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 3.5 / Movie #1: 3.5
Minimum - Maximum-6.70362 - 13.688321999999999
Average (Standard dev.)0.036700796 (±0.4561089)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 278.528 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0881.0881.088
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z278.528278.528278.528
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-6.70413.6880.037

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Supplemental data

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Half map: Transient receptor potential cation channel, subfamily V, member 4

Fileemd_7075_half_map_1.map
AnnotationTransient receptor potential cation channel, subfamily V, member 4
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Transient receptor potential cation channel, subfamily V, member 4

Fileemd_7075_half_map_2.map
AnnotationTransient receptor potential cation channel, subfamily V, member 4
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : TRPV4

EntireName: TRPV4
Components
  • Organelle or cellular component: TRPV4
    • Protein or peptide: Transient receptor potential cation channel, subfamily V, member 4

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Supramolecule #1: TRPV4

SupramoleculeName: TRPV4 / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all
Details: Xenopis tropicalis TRPV4 purified in DDM and lipids
Source (natural)Organism: Xenopus tropicalis (tropical clawed frog)
Molecular weightTheoretical: 300 KDa

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Macromolecule #1: Transient receptor potential cation channel, subfamily V, member 4

MacromoleculeName: Transient receptor potential cation channel, subfamily V, member 4
type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Xenopus tropicalis (tropical clawed frog)
Molecular weightTheoretical: 99.087852 KDa
Recombinant expressionOrganism: Pichia (fungus)
SequenceString: MADPSHLLKH NASVDIDDSQ GDDGSNHNDS FPLSSLANLF ENEESSAPNE GVRSPQVPGD NKQNLRIRFQ GPFRKGISNP MDLLESTIY ESSAPKKAPM DSLFGYETYH HHPTENRRKR KKILLEKENL NSQAPSPDPP PVIKMFNRHM LFDIVSRGST A ELEGFLPF ...String:
MADPSHLLKH NASVDIDDSQ GDDGSNHNDS FPLSSLANLF ENEESSAPNE GVRSPQVPGD NKQNLRIRFQ GPFRKGISNP MDLLESTIY ESSAPKKAPM DSLFGYETYH HHPTENRRKR KKILLEKENL NSQAPSPDPP PVIKMFNRHM LFDIVSRGST A ELEGFLPF LLAQKKRLTD EEFREASTGK TCLTKALMNL NGGKNDTIPM LIDIAEKTGN LREFINSPFR DVYYRGQTAL HI AIERRCK HYVELLVEKG ADVHAQARGR FFQPKDEGGY FYFGELPLSL AACTNQPDIV HYLTENAHKK ADIRRQDSRG NTV LHALVA IADNTRENTK FVTKVYDLLV IKCVKLYPDS SLEAIFNNDS MSPLMMAAKL GKIGIFQHII RLEIKDEEAR HLSR KFRDW AYGPVYSSLY DLSMLDTCGE EVSVLEILVY NSKVENRHEM LAVEPINELL RDKWQKFGAV SFYISVVSYL IAMII FTLI AYYRPMDGTP PYPYRTTMDY MRLAGEIVTL LTGVVFFITN IKDLFMKKCP GVNSLFIDGS FQLLYFIYSV LVIITA VLY LVGIESYLAV MVFALVLGWM NALYFTRGLK LTGTYSIMLQ KILFKDLFRF LLVYLLFMIG YASALVSLLN PCTSQES CI ETSSNCTVPE YPSCRDSSTF SKFLLDLFKL TIGMGDLEMI NSAKYPAVFI ILLVTYIILT FVLLLNMLIA LMGETVGQ V SKESKQIWKL QWATTILDIE RSFPVCMRKA FRSGEMVTVG KNLDGTPDRR WCFRVDEVNW SHWNQNLGII NEDPGRNDG YQYYGFSQTV GRLRRDRWSV VVPRVVELNK APQHSDDVVV PLGNIPQVQT YSQRQENAQN WKKDETHI

UniProtKB: Transient receptor potential cation channel, subfamily V, member 4

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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

Concentration4.5 mg/mL
BufferpH: 8
Component:
ConcentrationNameFormula
20.0 mMTris, pH 8.0
150.0 mMsodium chlorideNaCl
5.0 mMDTT
1.0 mMdodecyl maltoside
0.06 mg/ml1-Palmitoyl-2-Oleoyl-sn-Glycero-3-Phosphocholine
0.02 mg/ml-Palmitoyl-2-Oleoyl-sn-Glycero-3-Phosphoethanolamine
0.02 mg/ml1-Palmitoyl-2-Oleoyl-sn-Glycero-3-Phospho-1-rac-glycerol
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 10 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK IV / Details: 2 second blot time.
DetailsTRPV4 in DDM and lipids

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Dimensions - Width: 7420 pixel / Digitization - Dimensions - Height: 7676 pixel / Digitization - Frames/image: 2-20 / Number grids imaged: 1 / Number real images: 1604 / Average exposure time: 4.0 sec. / Average electron dose: 27.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Calibrated defocus max: 2.5 µm / Calibrated defocus min: 0.8 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 22500
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 85253
Startup modelType of model: OTHER / Details: Initial model generated in cryosparc
Final reconstructionNumber classes used: 4 / Applied symmetry - Point group: C4 (4 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: FREALIGN (ver. 9.11)
Details: Refined using Frealign with reference map low-pass filtered to 6 Angstroms
Number images used: 72684
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
Final 3D classificationNumber classes: 5 / Avg.num./class: 17000 / Software - Name: RELION (ver. 2.1)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL / Target criteria: FSC
Output model

PDB-6bbj:
Xenopus Tropicalis TRPV4

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