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- PDB-7aa5: Human TRPV4 structure in presence of 4a-PDD -

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Entry
Database: PDB / ID: 7aa5
TitleHuman TRPV4 structure in presence of 4a-PDD
ComponentsTransient receptor potential cation channel subfamily V member 4,Green fluorescent protein
KeywordsMEMBRANE 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 / regulation of response to osmotic stress / osmosensor activity / vasopressin secretion / calcium ion import into cytosol / negative regulation of brown fat cell differentiation / positive regulation of microtubule depolymerization / positive regulation of striated muscle contraction / positive regulation of macrophage inflammatory protein 1 alpha production ...stretch-activated, monoatomic cation-selective, calcium channel activity / blood vessel endothelial cell delamination / regulation of response to osmotic stress / osmosensor activity / vasopressin secretion / calcium ion import into cytosol / negative regulation of brown fat cell differentiation / positive regulation of microtubule depolymerization / positive regulation of striated muscle contraction / positive regulation of macrophage inflammatory protein 1 alpha production / hyperosmotic salinity response / 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 salinity response / cellular hypotonic response / cortical microtubule organization / multicellular organismal-level water homeostasis / positive regulation of vascular permeability / osmosensory signaling pathway / cell-cell junction assembly / positive regulation of monocyte chemotactic protein-1 production / calcium ion import / cell volume homeostasis / cellular response to osmotic stress / regulation of aerobic respiration / TRP channels / cortical actin cytoskeleton / diet induced thermogenesis / positive regulation of macrophage chemotaxis / microtubule polymerization / calcium ion import across plasma membrane / response to mechanical stimulus / alpha-tubulin binding / beta-tubulin binding / monoatomic cation channel activity / cytoplasmic microtubule / SH2 domain binding / protein kinase C binding / actin filament organization / bioluminescence / generation of precursor metabolites and energy / positive regulation of JNK cascade / adherens junction / filopodium / response to insulin / calcium ion transmembrane transport / positive regulation of interleukin-6 production / calcium channel activity / ruffle membrane / intracellular calcium ion homeostasis / positive regulation of inflammatory response / actin filament binding / calcium ion transport / glucose homeostasis / lamellipodium / negative regulation of neuron projection development / cellular response to heat / positive regulation of cytosolic calcium ion concentration / actin binding / growth cone / actin cytoskeleton organization / High laminar flow shear stress activates signaling by PIEZO1 and PECAM1:CDH5:KDR in endothelial cells / microtubule binding / calmodulin binding / response to hypoxia / positive regulation of ERK1 and ERK2 cascade / cilium / apical plasma membrane / focal adhesion / lipid binding / protein kinase binding / cell surface / endoplasmic reticulum / negative regulation of transcription by RNA polymerase II / ATP binding / metal ion binding / identical protein binding / membrane / 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 / Ankyrin repeat / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / 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 / Ankyrin repeat / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / 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 speciesHomo sapiens (human)
Aequorea victoria (jellyfish)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.18 Å
AuthorsBotte, 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.
CitationJournal: 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
DepositionSep 3, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 18, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond / em_admin / Item: _em_admin.last_update

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Structure visualization

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Assembly

Deposited unit
A: Transient receptor potential cation channel subfamily V member 4,Green fluorescent protein
B: Transient receptor potential cation channel subfamily V member 4,Green fluorescent protein
C: Transient receptor potential cation channel subfamily V member 4,Green fluorescent protein
D: Transient receptor potential cation channel subfamily V member 4,Green fluorescent protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)425,0075
Polymers424,9674
Non-polymers401
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area15950 Å2
ΔGint-149 kcal/mol
Surface area118900 Å2
MethodPISA

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Components

#1: Protein
Transient receptor potential cation channel subfamily V member 4,Green fluorescent protein / TrpV4 / Osm-9-like TRP channel 4 / OTRPC4 / Transient receptor potential protein 12 / TRP12 / ...TrpV4 / Osm-9-like TRP channel 4 / OTRPC4 / Transient receptor potential protein 12 / TRP12 / Vanilloid receptor-like channel 2 / Vanilloid receptor-like protein 2 / VRL-2 / Vanilloid receptor-related osmotically-activated channel / VR-OAC


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 / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Human TRPV4 in complex with 4a-PDD / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Homo sapiens (human)9606
31Aequorea victoria (jellyfish)6100
Source (recombinant)Organism: Baculovirus expression vector pFastBac1-HM
Buffer solutionpH: 8
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 90 % / Chamber temperature: 283 K / Details: blot for 3 seconds before plunging

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 50 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 4.18 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 51215 / Symmetry type: POINT

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