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Yorodumi- PDB-7d2k: Crystal structure of rat TRPV6 in complex with (4- phenylcyclohex... -
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-Basic information
Entry | Database: PDB / ID: 7d2k | ||||||
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Title | Crystal structure of rat TRPV6 in complex with (4- phenylcyclohexyl)piperazine inhibitor Br-cis-22a | ||||||
Components | Transient receptor potential cation channel subfamily V member 6 | ||||||
Keywords | TRANSPORT PROTEIN/INHIBITOR / Ion channels / TRP channels / Membrane proteins / TRANSPORT PROTEIN-INHIBITOR complex | ||||||
Function / homology | Function and homology information parathyroid hormone secretion / TRP channels / calcium-activated cation channel activity / calcium ion import / calcium ion import across plasma membrane / calcium ion homeostasis / calcium channel complex / calcium ion transmembrane transport / calcium channel activity / response to calcium ion ...parathyroid hormone secretion / TRP channels / calcium-activated cation channel activity / calcium ion import / calcium ion import across plasma membrane / calcium ion homeostasis / calcium channel complex / calcium ion transmembrane transport / calcium channel activity / response to calcium ion / calcium ion transport / protein homotetramerization / calmodulin binding / apical plasma membrane / identical protein binding / metal ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.698 Å | ||||||
Authors | Singh, A.K. / Neuberger, A. / Nadezhdin, K.D. / Sobolevsky, A.I. | ||||||
Funding support | United States, 1items
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Citation | Journal: Sci Adv / Year: 2020 Title: Inactivation-mimicking block of the epithelial calcium channel TRPV6. Authors: Rajesh Bhardwaj / Sonja Lindinger / Arthur Neuberger / Kirill D Nadezhdin / Appu K Singh / Micael R Cunha / Isabella Derler / Gergely Gyimesi / Jean-Louis Reymond / Matthias A Hediger / ...Authors: Rajesh Bhardwaj / Sonja Lindinger / Arthur Neuberger / Kirill D Nadezhdin / Appu K Singh / Micael R Cunha / Isabella Derler / Gergely Gyimesi / Jean-Louis Reymond / Matthias A Hediger / Christoph Romanin / Alexander I Sobolevsky / Abstract: Epithelial calcium channel TRPV6 plays vital roles in calcium homeostasis, and its dysregulation is implicated in multifactorial diseases, including cancers. Here, we study the molecular mechanism of ...Epithelial calcium channel TRPV6 plays vital roles in calcium homeostasis, and its dysregulation is implicated in multifactorial diseases, including cancers. Here, we study the molecular mechanism of selective nanomolar-affinity TRPV6 inhibition by (4-phenylcyclohexyl)piperazine derivatives (PCHPDs). We use x-ray crystallography and cryo-electron microscopy to solve the inhibitor-bound structures of TRPV6 and identify two types of inhibitor binding sites in the transmembrane region: (i) modulatory sites between the S1-S4 and pore domains normally occupied by lipids and (ii) the main site in the ion channel pore. Our structural data combined with mutagenesis, functional and computational approaches suggest that PCHPDs plug the open pore of TRPV6 and convert the channel into a nonconducting state, mimicking the action of calmodulin, which causes inactivation of TRPV6 channels under physiological conditions. This mechanism of inhibition explains the high selectivity and potency of PCHPDs and opens up unexplored avenues for the design of future-generation biomimetic drugs. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7d2k.cif.gz | 135 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7d2k.ent.gz | 102.5 KB | Display | PDB format |
PDBx/mmJSON format | 7d2k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7d2k_validation.pdf.gz | 886.3 KB | Display | wwPDB validaton report |
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Full document | 7d2k_full_validation.pdf.gz | 867.5 KB | Display | |
Data in XML | 7d2k_validation.xml.gz | 23.6 KB | Display | |
Data in CIF | 7d2k_validation.cif.gz | 31.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d2/7d2k ftp://data.pdbj.org/pub/pdb/validation_reports/d2/7d2k | HTTPS FTP |
-Related structure data
Related structure data | 7k4aC 7k4bC 7k4cC 7k4dC 7k4eC 7k4fC 5wo7S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 77133.492 Da / Num. of mol.: 1 / Fragment: UNP residues 41-709 / Mutation: I62Y, L132N, M96Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Trpv6 / Cell line (production host): HEK293T / Production host: Homo sapiens (human) / References: UniProt: Q9R186 | ||
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#2: Chemical | ChemComp-CA / | ||
#3: Chemical | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.94 Å3/Da / Density % sol: 68.78 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 150 mM nacl, 100 mM TRIS, 22% PEG 350 / PH range: 8.0-8.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.92 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 12, 2019 |
Radiation | Monochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92 Å / Relative weight: 1 |
Reflection | Resolution: 3.6→47.129 Å / Num. obs: 14416 / % possible obs: 99.12 % / Redundancy: 8.13 % / CC1/2: 0.99 / Net I/σ(I): 1.45 |
Reflection shell | Resolution: 3.6→3.9 Å / Num. unique obs: 2587 / CC1/2: 0.61 / % possible all: 96.2 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5WO7 Resolution: 3.698→47.12 Å / SU ML: 0.76 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 48.89 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.698→47.12 Å
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Refine LS restraints |
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LS refinement shell |
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