+Open data
-Basic information
Entry | Database: PDB / ID: 8j1d | ||||||
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Title | Cryo-EM structure of apo state mTRPV4 | ||||||
Components | Transient receptor potential cation channel subfamily V member 4 | ||||||
Keywords | MEMBRANE PROTEIN / mTRPV4 / STRUCTURAL PROTEIN | ||||||
Function / homology | Function and homology information blood vessel endothelial cell delamination / osmosensor activity / vasopressin secretion / stretch-activated, monoatomic cation-selective, calcium channel activity / 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 ...blood vessel endothelial cell delamination / osmosensor activity / vasopressin secretion / stretch-activated, monoatomic cation-selective, calcium channel activity / 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 / hypotonic 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 / TRP channels / multicellular organismal-level water homeostasis / osmosensory signaling pathway / positive regulation of vascular permeability / cellular response to osmotic stress / calcium ion import / positive regulation of monocyte chemotactic protein-1 production / cell-cell junction assembly / response to osmotic stress / regulation of aerobic respiration / cortical actin cytoskeleton / positive regulation of macrophage chemotaxis / beta-tubulin binding / diet induced thermogenesis / cytoplasmic microtubule / microtubule polymerization / calcium ion import across plasma membrane / alpha-tubulin binding / monoatomic cation channel activity / energy homeostasis / SH2 domain binding / filopodium / actin filament organization / calcium ion transmembrane transport / protein kinase C binding / positive regulation of JNK cascade / adherens junction / calcium channel activity / response to insulin / cilium / ruffle membrane / positive regulation of inflammatory response / intracellular calcium ion homeostasis / positive regulation of interleukin-6 production / actin filament binding / lamellipodium / negative regulation of neuron projection development / glucose homeostasis / actin binding / cellular response to heat / positive regulation of cytosolic calcium ion concentration / growth cone / actin cytoskeleton organization / microtubule binding / positive regulation of ERK1 and ERK2 cascade / calmodulin binding / response to hypoxia / apical plasma membrane / focal adhesion / lipid binding / positive regulation of gene expression / protein kinase binding / negative regulation of transcription by RNA polymerase II / cell surface / ATP binding / identical protein binding / metal ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.59 Å | ||||||
Authors | Zhen, W.X. / Yang, F. | ||||||
Funding support | China, 1items
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Citation | Journal: Cell Discov / Year: 2023 Title: Structural basis of ligand activation and inhibition in a mammalian TRPV4 ion channel. Authors: Wenxuan Zhen / Zhijun Zhao / Shenghai Chang / Xiaoying Chen / Yangzhuoqun Wan / Fan Yang / | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8j1d.cif.gz | 816.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8j1d.ent.gz | 691.6 KB | Display | PDB format |
PDBx/mmJSON format | 8j1d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j1/8j1d ftp://data.pdbj.org/pub/pdb/validation_reports/j1/8j1d | HTTPS FTP |
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-Related structure data
Related structure data | 35919MC 8j1bC 8j1fC 8j1hC 8jkmC M: map data used to model this data C: citing same article (ref.) |
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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: 75666.594 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Trpv4, Trp12, Vrl2, Vroac / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: Q9EPK8 |
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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: apo state of mTRPV4 / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Source (natural) | Organism: Mus musculus (house mouse) |
Source (recombinant) | Organism: Homo sapiens (human) |
Buffer solution | pH: 8 |
Specimen | Conc.: 5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN 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: 1600 nm / Nominal defocus min: 800 nm |
Image recording | Electron dose: 52 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.20.1_4487: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.59 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 201371 / Symmetry type: POINT | ||||||||||||||||||||||||
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