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Yorodumi- PDB-6rmv: The crystal structure of a TRP channel peptide bound to a G prote... -
+Open data
-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 | |||||||||
Components |
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Keywords | PROTEIN BINDING / G protein / TRP Channel / Inhibitor | |||||||||
Function / homology | Function and homology information 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 / G protein-coupled glutamate receptor signaling pathway / ADP signalling through P2Y purinoceptor 1 / TRP channels / 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 / calcium ion transmembrane transport / protein tetramerization / calcium channel activity / sensory perception of taste / G-protein beta-subunit binding / heterotrimeric G-protein complex / signaling receptor complex adaptor activity / retina development in camera-type eye / GTPase binding / myelin sheath / cell body / phospholipase C-activating G protein-coupled receptor signaling pathway / positive regulation of cytosolic calcium ion concentration / 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 | Mus musculus (house mouse) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.94 Å | |||||||||
Authors | Gruss, F. / Oberwinkler, J. / Ulens, C. | |||||||||
Funding support | 2items
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Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2020 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6rmv.cif.gz | 97.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6rmv.ent.gz | 71.9 KB | Display | PDB format |
PDBx/mmJSON format | 6rmv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rm/6rmv ftp://data.pdbj.org/pub/pdb/validation_reports/rm/6rmv | HTTPS FTP |
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-Related structure data
Related structure data | 1xhmS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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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.) Mus musculus (house mouse) / Gene: Gnb1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P62874 |
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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.) Mus musculus (house mouse) / Gene: Gng2 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P63213 |
#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.) Mus musculus (house mouse) / References: UniProt: Q5F4S7, UniProt: Q2TV84*PLUS |
#4: Chemical | ChemComp-GOL / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.9754 Å |
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: molecular replacement | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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