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- PDB-6rmv: The crystal structure of a TRP channel peptide bound to a G prote... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6rmv | |||||||||
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Title | The crystal structure of a TRP channel peptide bound to a G protein beta gamma heterodimer | |||||||||
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![]() | PROTEIN BINDING / G protein / TRP Channel / Inhibitor | |||||||||
Function / homology | ![]() new growing cell tip / retinal rod cell development / Activation of the phototransduction cascade / Sensory perception of sweet, bitter, and umami (glutamate) taste / Olfactory Signaling Pathway / G beta:gamma signalling through PLC beta / Presynaptic function of Kainate receptors / Prostacyclin signalling through prostacyclin receptor / G alpha (z) signalling events / Glucagon-type ligand receptors ...new growing cell tip / retinal rod cell development / Activation of the phototransduction cascade / Sensory perception of sweet, bitter, and umami (glutamate) taste / Olfactory Signaling Pathway / G beta:gamma signalling through PLC beta / Presynaptic function of Kainate receptors / Prostacyclin signalling through prostacyclin receptor / G alpha (z) signalling events / Glucagon-type ligand receptors / G beta:gamma signalling through PI3Kgamma / G beta:gamma signalling through CDC42 / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / G beta:gamma signalling through BTK / Adrenaline,noradrenaline inhibits insulin secretion / ADP signalling through P2Y purinoceptor 12 / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / Thromboxane signalling through TP receptor / Thrombin signalling through proteinase activated receptors (PARs) / Activation of G protein gated Potassium channels / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits / G-protein activation / Ca2+ pathway / G alpha (s) signalling events / G alpha (q) signalling events / Extra-nuclear estrogen signaling / G alpha (12/13) signalling events / Vasopressin regulates renal water homeostasis via Aquaporins / G alpha (i) signalling events / GPER1 signaling / cellular response to light stimulus / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / ADP signalling through P2Y purinoceptor 1 / TRP channels / G protein-coupled glutamate receptor signaling pathway / phototransduction, visible light / alkylglycerophosphoethanolamine phosphodiesterase activity / calcium ion transport into cytosol / photoreceptor outer segment membrane / spectrin binding / monoatomic cation transmembrane transport / monoatomic cation transport / photoreceptor outer segment / monoatomic cation channel activity / cardiac muscle cell apoptotic process / visual perception / photoreceptor inner segment / protein tetramerization / calcium channel activity / sensory perception of taste / G-protein beta-subunit binding / heterotrimeric G-protein complex / signaling receptor complex adaptor activity / GTPase binding / myelin sheath / retina development in camera-type eye / phospholipase C-activating G protein-coupled receptor signaling pathway / positive regulation of cytosolic calcium ion concentration / cell body / fibroblast proliferation / cellular response to hypoxia / cell population proliferation / membrane => GO:0016020 / G protein-coupled receptor signaling pathway / GTPase activity / dendrite / protein-containing complex binding / signal transduction / membrane / plasma membrane / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() ![]() | |||||||||
![]() | Gruss, F. / Oberwinkler, J. / Ulens, C. | |||||||||
Funding support | 2items
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![]() | ![]() Title: The structural basis for an on-off switch controlling G beta gamma-mediated inhibition of TRPM3 channels. Authors: Behrendt, M. / Gruss, F. / Enzeroth, R. / Dembla, S. / Zhao, S. / Crassous, P.A. / Mohr, F. / Nys, M. / Louros, N. / Gallardo, R. / Zorzini, V. / Wagner, D. / Economou, A. / Rousseau, F. / ...Authors: Behrendt, M. / Gruss, F. / Enzeroth, R. / Dembla, S. / Zhao, S. / Crassous, P.A. / Mohr, F. / Nys, M. / Louros, N. / Gallardo, R. / Zorzini, V. / Wagner, D. / Economou, A. / Rousseau, F. / Schymkowitz, J. / Philipp, S.E. / Rohacs, T. / Ulens, C. / Oberwinkler, J. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 97.1 KB | Display | ![]() |
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PDB format | ![]() | 71.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 455.6 KB | Display | ![]() |
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Full document | ![]() | 456.7 KB | Display | |
Data in XML | ![]() | 17.1 KB | Display | |
Data in CIF | ![]() | 23.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1xhmS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 37416.930 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Protein | Mass: 8046.260 Da / Num. of mol.: 1 / Mutation: C68S Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
#3: Protein/peptide | Mass: 1731.109 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: TRPM3 exon 17 - encoded residues including 2 N-terminal and 3 C-terminal flanking residues Source: (synth.) ![]() ![]() |
#4: Chemical | ChemComp-GOL / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.22 Å3/Da / Density % sol: 44.58 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.1 M HEPES sodium pH 7.5, 15% (w/v) polyethylene glycol 4,000, 7.5% (v/v) isopropanol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 23, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9754 Å / Relative weight: 1 |
Reflection | Resolution: 1.94→42.52 Å / Num. obs: 31659 / % possible obs: 99.3 % / Redundancy: 6.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.073 / Rpim(I) all: 0.046 / Rrim(I) all: 0.087 / Net I/σ(I): 13.2 |
Reflection shell | Resolution: 1.94→2.01 Å / Redundancy: 6.7 % / Rmerge(I) obs: 1.28 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 3044 / CC1/2: 0.528 / Rpim(I) all: 0.795 / Rrim(I) all: 1.51 / % possible all: 98.3 |
-Phasing
Phasing | Method: ![]() | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1XHM Resolution: 1.94→42.52 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.952 / SU B: 4.597 / SU ML: 0.124 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.165 / ESU R Free: 0.147 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 105.39 Å2 / Biso mean: 45.023 Å2 / Biso min: 25.1 Å2
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Refinement step | Cycle: final / Resolution: 1.94→42.52 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.94→1.99 Å / Rfactor Rfree error: 0
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