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Yorodumi- PDB-8t1d: Open-state cryo-EM structure of full-length human TRPV4 in comple... -
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-Basic information
Entry | Database: PDB / ID: 8t1d | |||||||||||||||||||||
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Title | Open-state cryo-EM structure of full-length human TRPV4 in complex with agonist 4a-PDD | |||||||||||||||||||||
Components | Transient receptor potential cation channel subfamily V member 4/Enhanced green fluorescent protein chimera | |||||||||||||||||||||
Keywords | MEMBRANE PROTEIN / transient receptor potential V family member 4 / TRP / channel / TRPV4 / TRP channels / agonist / 4a-PDD / open state / 4alpha-Phorbol 12 / 13-didecanoate | |||||||||||||||||||||
Function / homology | Function and homology information stretch-activated, monoatomic cation-selective, calcium channel activity / blood vessel endothelial cell delamination / osmosensor activity / vasopressin secretion / positive regulation of striated muscle contraction / calcium ion import into cytosol / positive regulation of macrophage inflammatory protein 1 alpha production / negative regulation of brown fat cell differentiation / positive regulation of microtubule depolymerization / hyperosmotic salinity response ...stretch-activated, monoatomic cation-selective, calcium channel activity / blood vessel endothelial cell delamination / osmosensor activity / vasopressin secretion / positive regulation of striated muscle contraction / calcium ion import into cytosol / positive regulation of macrophage inflammatory protein 1 alpha production / negative regulation of brown fat cell differentiation / positive regulation of microtubule depolymerization / hyperosmotic salinity response / cortical microtubule organization / positive regulation of chemokine (C-X-C motif) ligand 1 production / positive regulation of chemokine (C-C motif) ligand 5 production / cartilage development involved in endochondral bone morphogenesis / cellular hypotonic response / regulation of response to osmotic stress / cellular hypotonic salinity response / osmosensory signaling pathway / multicellular organismal-level water homeostasis / positive regulation of vascular permeability / cellular response to osmotic stress / calcium ion import / cell volume homeostasis / positive regulation of monocyte chemotactic protein-1 production / cell-cell junction assembly / TRP channels / regulation of aerobic respiration / cortical actin cytoskeleton / positive regulation of macrophage chemotaxis / beta-tubulin binding / diet induced thermogenesis / microtubule polymerization / alpha-tubulin binding / cytoplasmic microtubule / response to mechanical stimulus / monoatomic cation channel activity / SH2 domain binding / bioluminescence / protein kinase C binding / filopodium / generation of precursor metabolites and energy / actin filament organization / calcium ion transmembrane transport / adherens junction / positive regulation of JNK cascade / response to insulin / calcium channel activity / cilium / ruffle membrane / intracellular calcium ion homeostasis / positive regulation of inflammatory response / positive regulation of interleukin-6 production / calcium ion transport / actin filament binding / glucose homeostasis / negative regulation of neuron projection development / lamellipodium / cellular response to heat / actin binding / growth cone / positive regulation of cytosolic calcium ion concentration / actin cytoskeleton organization / microtubule binding / response to hypoxia / positive regulation of ERK1 and ERK2 cascade / calmodulin binding / apical plasma membrane / focal adhesion / lipid binding / protein kinase binding / negative regulation of transcription by RNA polymerase II / cell surface / endoplasmic reticulum / ATP binding / membrane / identical protein binding / metal ion binding / plasma membrane Similarity search - Function | |||||||||||||||||||||
Biological species | Homo sapiens (human) Human betaherpesvirus 5 | |||||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.35 Å | |||||||||||||||||||||
Authors | Talyzina, I.A. / Nadezhdin, K.D. / Neuberger, A. / Sobolevsky, A.I. | |||||||||||||||||||||
Funding support | United States, Germany, 6items
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Citation | Journal: Nat Commun / Year: 2023 Title: Structure of human TRPV4 in complex with GTPase RhoA. Authors: Kirill D Nadezhdin / Irina A Talyzina / Aravind Parthasarathy / Arthur Neuberger / David X Zhang / Alexander I Sobolevsky / Abstract: Transient receptor potential (TRP) channel TRPV4 is a polymodal cellular sensor that responds to moderate heat, cell swelling, shear stress, and small-molecule ligands. It is involved in ...Transient receptor potential (TRP) channel TRPV4 is a polymodal cellular sensor that responds to moderate heat, cell swelling, shear stress, and small-molecule ligands. It is involved in thermogenesis, regulation of vascular tone, bone homeostasis, renal and pulmonary functions. TRPV4 is implicated in neuromuscular and skeletal disorders, pulmonary edema, and cancers, and represents an important drug target. The cytoskeletal remodeling GTPase RhoA has been shown to suppress TRPV4 activity. Here, we present a structure of the human TRPV4-RhoA complex that shows RhoA interaction with the membrane-facing surface of the TRPV4 ankyrin repeat domains. The contact interface reveals residues that are mutated in neuropathies, providing an insight into the disease pathogenesis. We also identify the binding sites of the TRPV4 agonist 4α-PDD and the inhibitor HC-067047 at the base of the S1-S4 bundle, and show that agonist binding leads to pore opening, while channel inhibition involves a π-to-α transition in the pore-forming helix S6. Our structures elucidate the interaction interface between hTRPV4 and RhoA, as well as residues at this interface that are involved in TRPV4 disease-causing mutations. They shed light on TRPV4 activation and inhibition and provide a template for the design of future therapeutics for treatment of TRPV4-related diseases. | |||||||||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8t1d.cif.gz | 474.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8t1d.ent.gz | 373.8 KB | Display | PDB format |
PDBx/mmJSON format | 8t1d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t1/8t1d ftp://data.pdbj.org/pub/pdb/validation_reports/t1/8t1d | HTTPS FTP |
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-Related structure data
Related structure data | 40960MC 8t1bC 8t1cC 8t1eC 8t1fC C: citing same article (ref.) M: map data used to model this data |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 127717.938 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Human betaherpesvirus 5 Gene: TRPV4, VRL2, VROAC, egfp / Cell line (production host): HEK293S / Production host: Homo sapiens (human) / References: UniProt: Q9HBA0, UniProt: C5MKY7 #2: Chemical | ChemComp-XS9 / ( Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: full-length human TRPV4 in complex with agonist 4a-PDD Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT | ||||||||||||||||||||||||||||||
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Molecular weight | Value: 0.51 MDa / Experimental value: NO | ||||||||||||||||||||||||||||||
Source (natural) | Organism: Homo sapiens (human) | ||||||||||||||||||||||||||||||
Source (recombinant) | Organism: Homo sapiens (human) / Cell: Human embryonic kidney 293 / Plasmid: pEG BacMam | ||||||||||||||||||||||||||||||
Buffer solution | pH: 8 | ||||||||||||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 3.2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: human TRPV4 | ||||||||||||||||||||||||||||||
Specimen support | Grid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: UltrAuFoil R1.2/1.3 | ||||||||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 295 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: TFS KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 1500 nm / Nominal defocus min: 750 nm / Cs: 2.7 mm |
Image recording | Average exposure time: 2.4 sec. / Electron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 15624 |
Image scans | Width: 11520 / Height: 8184 |
-Processing
EM software | Name: PHENIX / Version: 1.11.1_2575: / Category: model refinement | ||||||||||||||||||||||||
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CTF correction | Type: NONE | ||||||||||||||||||||||||
Particle selection | Num. of particles selected: 3935964 | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.35 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 80823 / Symmetry type: POINT | ||||||||||||||||||||||||
Atomic model building | Space: REAL | ||||||||||||||||||||||||
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