+Open data
-Basic information
Entry | Database: PDB / ID: 7aa5 | ||||||
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Title | Human TRPV4 structure in presence of 4a-PDD | ||||||
Components | Transient receptor potential cation channel subfamily V member 4,Green fluorescent protein | ||||||
Keywords | MEMBRANE PROTEIN / Ion channel. open-conformation / agonist / 4a-PDD | ||||||
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 / 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 / osmosensory signaling pathway / positive regulation of vascular permeability / cell volume homeostasis / cellular response to osmotic stress / positive regulation of monocyte chemotactic protein-1 production / calcium ion import / cell-cell junction assembly / TRP channels / cortical actin cytoskeleton / regulation of aerobic respiration / positive regulation of macrophage chemotaxis / diet induced thermogenesis / cytoplasmic microtubule / beta-tubulin binding / microtubule polymerization / alpha-tubulin binding / monoatomic cation channel activity / response to mechanical stimulus / SH2 domain binding / bioluminescence / actin filament organization / filopodium / generation of precursor metabolites and energy / adherens junction / calcium ion transmembrane transport / protein kinase C binding / positive regulation of JNK cascade / response to insulin / calcium channel activity / cilium / positive regulation of interleukin-6 production / ruffle membrane / intracellular calcium ion homeostasis / positive regulation of inflammatory response / calcium ion transport / actin filament binding / negative regulation of neuron projection development / lamellipodium / glucose homeostasis / actin binding / cellular response to heat / positive regulation of cytosolic calcium ion concentration / actin cytoskeleton organization / growth cone / microtubule binding / positive regulation of ERK1 and ERK2 cascade / response to hypoxia / 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 / identical protein binding / membrane / metal ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Aequorea victoria (jellyfish) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.18 Å | ||||||
Authors | Botte, M. / Ulrich, A.K.G. / Adaixo, R. / Gnutt, D. / Brockmann, A. / Bucher, D. / Chami, M. / Bocquet, M. / Ebbinghaus-Kintscher, U. / Puetter, V. ...Botte, M. / Ulrich, A.K.G. / Adaixo, R. / Gnutt, D. / Brockmann, A. / Bucher, D. / Chami, M. / Bocquet, M. / Ebbinghaus-Kintscher, U. / Puetter, V. / Becker, A. / Egner, U. / Stahlberg, H. / Hennig, M. / Holton, S.J. | ||||||
Citation | Journal: To Be Published Title: Cryo-EM structural studies of the agonist complexed human TRPV4 ion-channel reveals novel structural rearrangements resulting in an open-conformation Authors: Botte, M. / Ulrich, A.K.G. / Adaixo, R. / Gnutt, D. / Brockmann, A. / Bucher, D. / Chami, M. / Bocquet, M. / Ebbinghaus-Kintscher, U. / Puetter, V. / Becker, A. / Egner, U. / Stahlberg, H. / ...Authors: Botte, M. / Ulrich, A.K.G. / Adaixo, R. / Gnutt, D. / Brockmann, A. / Bucher, D. / Chami, M. / Bocquet, M. / Ebbinghaus-Kintscher, U. / Puetter, V. / Becker, A. / Egner, U. / Stahlberg, H. / Hennig, M. / Holton, S.J. | ||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 7aa5.cif.gz | 462.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7aa5.ent.gz | 361.2 KB | Display | PDB format |
PDBx/mmJSON format | 7aa5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7aa5_validation.pdf.gz | 934.9 KB | Display | wwPDB validaton report |
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Full document | 7aa5_full_validation.pdf.gz | 1002.3 KB | Display | |
Data in XML | 7aa5_validation.xml.gz | 76.8 KB | Display | |
Data in CIF | 7aa5_validation.cif.gz | 111.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/aa/7aa5 ftp://data.pdbj.org/pub/pdb/validation_reports/aa/7aa5 | HTTPS FTP |
-Related structure data
Related structure data | 11690MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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-Components
#1: Protein | Mass: 106241.820 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Aequorea victoria (jellyfish) Gene: TRPV4, VRL2, VROAC, GFP / Production host: Baculovirus expression vector pFastBac1-HM / References: UniProt: Q9HBA0, UniProt: P42212 #2: Chemical | ChemComp-CA / | Has ligand of interest | N | |
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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: Human TRPV4 in complex with 4a-PDD / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT | ||||||||||||
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Molecular weight | Experimental value: NO | ||||||||||||
Source (natural) |
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Source (recombinant) | Organism: Baculovirus expression vector pFastBac1-HM | ||||||||||||
Buffer solution | pH: 8 | ||||||||||||
Specimen | Conc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||
Specimen support | Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3 | ||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 90 % / Chamber temperature: 283 K / Details: blot for 3 seconds before plunging |
-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 FIELD |
Image recording | Electron dose: 50 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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3D reconstruction | Resolution: 4.18 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 51215 / Symmetry type: POINT |