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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-7075 | ||||||||||||
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Title | Xenopus Tropicalis TRPV4 | ||||||||||||
![]() | Transient receptor potential cation channel, subfamily V, member 4 | ||||||||||||
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![]() | Ion Channel / TRP channel / METAL TRANSPORT | ||||||||||||
Function / homology | ![]() TRP channels / osmosensory signaling pathway / calcium ion import across plasma membrane / plasma membrane => GO:0005886 / actin filament organization / calcium channel activity / cilium / monoatomic ion channel activity Similarity search - Function | ||||||||||||
Biological species | ![]() | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.8 Å | ||||||||||||
![]() | Deng Z / Hite RK | ||||||||||||
Funding support | ![]()
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![]() | ![]() 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 |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 1.6 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 20.2 KB 20.2 KB | Display Display | ![]() |
Images | ![]() | 174.9 KB | ||
Filedesc metadata | ![]() | 6.6 KB | ||
Others | ![]() ![]() | 53.8 MB 53.8 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6bbjMC ![]() 6c8fC ![]() 6c8gC ![]() 6c8hC M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | Transient receptor potential cation channel, subfamily V, member 4 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.088 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Half map: Transient receptor potential cation channel, subfamily V, member 4
File | emd_7075_half_map_1.map | ||||||||||||
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Annotation | Transient receptor potential cation channel, subfamily V, member 4 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Transient receptor potential cation channel, subfamily V, member 4
File | emd_7075_half_map_2.map | ||||||||||||
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Annotation | Transient receptor potential cation channel, subfamily V, member 4 | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
-Entire : TRPV4
Entire | Name: TRPV4 |
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Components |
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-Supramolecule #1: TRPV4
Supramolecule | Name: TRPV4 / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all Details: Xenopis tropicalis TRPV4 purified in DDM and lipids |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 300 KDa |
-Macromolecule #1: Transient receptor potential cation channel, subfamily V, member 4
Macromolecule | Name: Transient receptor potential cation channel, subfamily V, member 4 type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 99.087852 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: 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 |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 4.5 mg/mL | ||||||||||||||||||||||||
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Buffer | pH: 8 Component:
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Grid | Model: 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 | ||||||||||||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK IV / Details: 2 second blot time. | ||||||||||||||||||||||||
Details | TRPV4 in DDM and lipids |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film 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 beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | C2 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 stage | Specimen 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
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: AB INITIO MODEL / Target criteria: FSC |
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Output model | ![]() PDB-6bbj: |