[English] 日本語
![](img/lk-miru.gif)
- EMDB-41219: Wildtype rabbit TRPV5 into nanodiscs in the presence of PI(4,5)P2... -
+
Open data
-
Basic information
Entry | ![]() | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Wildtype rabbit TRPV5 into nanodiscs in the presence of PI(4,5)P2 and econazole | |||||||||
![]() | TRPV5 PIP2 ECN | |||||||||
![]() |
| |||||||||
![]() | TRPV5 / TRP channel / PI(4 / 5)P2 / econazole / MEMBRANE PROTEIN | |||||||||
Function / homology | ![]() regulation of urine volume / calcium ion import across plasma membrane / calcium ion homeostasis / calcium ion transmembrane transport / calcium channel activity / calcium ion transport / protein homotetramerization / calmodulin binding / apical plasma membrane / identical protein binding ...regulation of urine volume / calcium ion import across plasma membrane / calcium ion homeostasis / calcium ion transmembrane transport / calcium channel activity / calcium ion transport / protein homotetramerization / calmodulin binding / apical plasma membrane / identical protein binding / metal ion binding / plasma membrane Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.86 Å | |||||||||
![]() | De Jesus-Perez JJ / Fluck EC / Moiseenkova-Bell VY | |||||||||
Funding support | ![]()
| |||||||||
![]() | ![]() Title: Structural mechanism of TRPV5 inhibition by econazole. Authors: José J De Jesús-Pérez / Matthew Gabrielle / Sumiyya Raheem / Edwin C Fluck / Tibor Rohacs / Vera Y Moiseenkova-Bell / ![]() Abstract: The calcium-selective TRPV5 channel activated by phosphatidylinositol 4,5-bisphosphate [PI(4,5)P] is involved in calcium homeostasis. Recently, cryoelectron microscopy (cryo-EM) provided molecular ...The calcium-selective TRPV5 channel activated by phosphatidylinositol 4,5-bisphosphate [PI(4,5)P] is involved in calcium homeostasis. Recently, cryoelectron microscopy (cryo-EM) provided molecular details of TRPV5 modulation by exogenous and endogenous molecules. However, the details of TRPV5 inhibition by the antifungal agent econazole (ECN) remain elusive due to the low resolution of the currently available structure. In this study, we employ cryo-EM to comprehensively examine how the ECN inhibits TRPV5. By combining our structural findings with site-directed mutagenesis, calcium measurements, electrophysiology, and molecular dynamics simulations, we determined that residues F472 and L475 on the S4 helix, along with residue W495 on the S5 helix, collectively constitute the ECN-binding site. Additionally, the structure of TRPV5 in the presence of ECN and PI(4,5)P, which does not show the bound activator, reveals a potential inhibition mechanism in which ECN competes with PI(4,5)P, preventing the latter from binding, and ultimately pore closure. | |||||||||
History |
|
-
Structure visualization
Supplemental images |
---|
-
Downloads & links
-EMDB archive
Map data | ![]() | 85.9 MB | ![]() | |
---|---|---|---|---|
Header (meta data) | ![]() ![]() | 16.8 KB 16.8 KB | Display Display | ![]() |
Images | ![]() | 142.7 KB | ||
Filedesc metadata | ![]() | 6 KB | ||
Others | ![]() ![]() | 84.3 MB 84.3 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8tf4MC ![]() 8tf2C ![]() 8tf3C M: atomic model generated by this map C: citing same article ( |
---|---|
Similar structure data | Similarity search - Function & homology ![]() |
-
Links
EMDB pages | ![]() ![]() |
---|---|
Related items in Molecule of the Month |
-
Map
File | ![]() | ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | TRPV5 PIP2 ECN | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.83 Å | ||||||||||||||||||||
Density |
| ||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
|
-Supplemental data
-Half map: TRPV5 PIP2 ECN half1
File | emd_41219_half_map_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | TRPV5 PIP2 ECN half1 | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: TRPV5 PIP2 ECN half2
File | emd_41219_half_map_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | TRPV5 PIP2 ECN half2 | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-
Sample components
-Entire : Tetramer of wildtype rabbit TRPV5 into nanodiscs in the presence ...
Entire | Name: Tetramer of wildtype rabbit TRPV5 into nanodiscs in the presence of PI(4,5)P2 and econazole |
---|---|
Components |
|
-Supramolecule #1: Tetramer of wildtype rabbit TRPV5 into nanodiscs in the presence ...
Supramolecule | Name: Tetramer of wildtype rabbit TRPV5 into nanodiscs in the presence of PI(4,5)P2 and econazole type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
---|---|
Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 335.14 KDa |
-Macromolecule #1: Transient receptor potential cation channel subfamily V member 5
Macromolecule | Name: Transient receptor potential cation channel subfamily V member 5 type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 83.784586 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MGACPPKAKG PWAQLQKLLI SWPVGEQDWE QYRDRVNMLQ QERIRDSPLL QAAKENDLRL LKILLLNQSC DFQQRGAVGE TALHVAALY DNLEAATLLM EAAPELAKEP ALCEPFVGQT ALHIAVMNQN LNLVRALLAR GASVSARATG AAFRRSPHNL I YYGEHPLS ...String: MGACPPKAKG PWAQLQKLLI SWPVGEQDWE QYRDRVNMLQ QERIRDSPLL QAAKENDLRL LKILLLNQSC DFQQRGAVGE TALHVAALY DNLEAATLLM EAAPELAKEP ALCEPFVGQT ALHIAVMNQN LNLVRALLAR GASVSARATG AAFRRSPHNL I YYGEHPLS FAACVGSEEI VRLLIEHGAD IRAQDSLGNT VLHILILQPN KTFACQMYNL LLSYDEHSDH LQSLELVPNH QG LTPFKLA GVEGNTVMFQ HLMQKRKHVQ WTCGPLTSTL YDLTEIDSWG EELSFLELVV SSKKREARQI LEQTPVKELV SFK WKKYGR PYFCVLASLY ILYMICFTTC CIYRPLKLRD DNRTDPRDIT ILQQKLLQEA YVTHQDNIRL VGELVTVTGA VIIL LLEIP DIFRVGASRY FGQTILGGPF HVIIITYASL VLLTMVMRLT NMNGEVVPLS FALVLGWCSV MYFARGFQML GPFTI MIQK MIFGDLMRFC WLMAVVILGF ASAFHITFQT EDPNNLGEFS DYPTALFSTF ELFLTIIDGP ANYSVDLPFM YCITYA AFA IIATLLMLNL FIAMMGDTHW RVAQERDELW RAQVVATTVM LERKMPRFLW PRSGICGYEY GLGDRWFLRV ENHHDQN PL RVLRYVEAFK CSDKEDGQEQ LSEKRPSTVE SGMLSRASVA FQTPSLSRTT SQSSNSHRGW EILRRNTLGH LNLGLDLG E GDGEEVYHFT ETSQVAPA UniProtKB: Transient receptor potential cation channel subfamily V member 5 |
-Macromolecule #2: ERGOSTEROL
Macromolecule | Name: ERGOSTEROL / type: ligand / ID: 2 / Number of copies: 8 / Formula: ERG |
---|---|
Molecular weight | Theoretical: 396.648 Da |
Chemical component information | ![]() ChemComp-ERG: |
-Macromolecule #3: 1-PALMITOYL-2-LINOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE
Macromolecule | Name: 1-PALMITOYL-2-LINOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / type: ligand / ID: 3 / Number of copies: 8 / Formula: CPL |
---|---|
Molecular weight | Theoretical: 758.06 Da |
Chemical component information | ![]() ChemComp-CPL: |
-Macromolecule #4: 1-[(2S)-2-[(4-CHLOROBENZYL)OXY]-2-(2,4-DICHLOROPHENYL)ETHYL]-1H-I...
Macromolecule | Name: 1-[(2S)-2-[(4-CHLOROBENZYL)OXY]-2-(2,4-DICHLOROPHENYL)ETHYL]-1H-IMIDAZOLE type: ligand / ID: 4 / Number of copies: 4 / Formula: ECN |
---|---|
Molecular weight | Theoretical: 381.684 Da |
Chemical component information | ![]() ChemComp-ECN: |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
![]() | single particle reconstruction |
Aggregation state | particle |
-
Sample preparation
Buffer | pH: 8 |
---|---|
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % |
-
Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Number real images: 11346 / Average electron dose: 41.6 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 105000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
+
Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: FLEXIBLE FIT |
---|---|
Output model | ![]() PDB-8tf4: |