- EMDB-11690: Human TRPV4 structure in presence of 4a-PDD -
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Open data
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Basic information
Entry
Database: EMDB / ID: EMD-11690
Title
Human TRPV4 structure in presence of 4a-PDD
Map data
Sample
Complex: Human TRPV4 in complex with 4a-PDD
Protein or peptide: Transient receptor potential cation channel subfamily V member 4,Green fluorescent protein
Ligand: CALCIUM ION
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 / cortical microtubule organization / regulation of response to osmotic stress / 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 / cellular hypotonic salinity response / multicellular organismal-level water homeostasis / positive regulation of vascular permeability / cellular response to osmotic stress / calcium ion import / osmosensory signaling pathway / 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 / cytoplasmic microtubule / alpha-tubulin binding / calcium ion import across plasma membrane / monoatomic cation channel activity / response to mechanical stimulus / SH2 domain binding / bioluminescence / filopodium / generation of precursor metabolites and energy / calcium ion transmembrane transport / protein kinase C binding / actin filament organization / adherens junction / positive regulation of JNK cascade / calcium channel activity / response to insulin / cilium / ruffle membrane / intracellular calcium ion homeostasis / positive regulation of inflammatory response / positive regulation of interleukin-6 production / calcium ion transport / actin filament binding / lamellipodium / negative regulation of neuron projection development / glucose homeostasis / actin binding / cellular response to heat / growth cone / positive regulation of cytosolic calcium ion concentration / actin cytoskeleton organization / microtubule binding / positive regulation of ERK1 and ERK2 cascade / calmodulin binding / response to hypoxia / apical plasma membrane / focal adhesion / lipid binding / protein kinase binding / cell surface / negative regulation of transcription by RNA polymerase II / endoplasmic reticulum / ATP binding / membrane / identical protein binding / metal ion binding / plasma membrane Similarity search - Function
Transient receptor potential cation channel subfamily V member 4 / Transient receptor potential cation channel subfamily V member 1-4 / Transient receptor potential cation channel subfamily V / Green fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / Ankyrin repeat / Ankyrin repeat profile. / Ankyrin repeat region circular profile. ...Transient receptor potential cation channel subfamily V member 4 / Transient receptor potential cation channel subfamily V member 1-4 / Transient receptor potential cation channel subfamily V / Green fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / Ankyrin repeat / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Ion transport domain / Ion transport protein Similarity search - Domain/homology
Green fluorescent protein / Transient receptor potential cation channel subfamily V member 4 Similarity search - Component
Biological species
Homo sapiens (human) / Aequorea victoria (jellyfish)
Method
single particle reconstruction / cryo EM / Resolution: 4.18 Å
Macromolecule #1: Transient receptor potential cation channel subfamily V member 4,...
Macromolecule
Name: Transient receptor potential cation channel subfamily V member 4,Green fluorescent protein type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Name: CALCIUM ION / type: ligand / ID: 2 / Number of copies: 1 / Formula: CA
Molecular weight
Theoretical: 40.078 Da
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Experimental details
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Structure determination
Method
cryo EM
Processing
single particle reconstruction
Aggregation state
particle
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Sample preparation
Concentration
1 mg/mL
Buffer
pH: 8
Grid
Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.0533 kPa
Vitrification
Cryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 283 K / Instrument: FEI VITROBOT MARK IV / Details: blot for 3 seconds before plunging.
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Electron microscopy
Microscope
FEI TITAN KRIOS
Image recording
Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 50.0 e/Å2
Electron beam
Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron optics
Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
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Image processing
Final reconstruction
Resolution.type: BY AUTHOR / Resolution: 4.18 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 51215
Initial angle assignment
Type: RANDOM ASSIGNMENT
Final angle assignment
Type: MAXIMUM LIKELIHOOD
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