+Open data
-Basic information
Entry | Database: PDB / ID: 3x1y | ||||||
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Title | Ras-related protein Rap1B(L9V) with GppNHp | ||||||
Components | Ras-related protein Rap-1b | ||||||
Keywords | SIGNALING PROTEIN / SIGNAL TRANSDUCTION | ||||||
Function / homology | Function and homology information GRB2:SOS provides linkage to MAPK signaling for Integrins / MET activates RAP1 and RAC1 / Integrin signaling / p130Cas linkage to MAPK signaling for integrins / Rap1 signalling / cellular response to gonadotropin-releasing hormone / Rap protein signal transduction / modification of postsynaptic structure / MAP2K and MAPK activation / regulation of cell junction assembly ...GRB2:SOS provides linkage to MAPK signaling for Integrins / MET activates RAP1 and RAC1 / Integrin signaling / p130Cas linkage to MAPK signaling for integrins / Rap1 signalling / cellular response to gonadotropin-releasing hormone / Rap protein signal transduction / modification of postsynaptic structure / MAP2K and MAPK activation / regulation of cell junction assembly / negative regulation of calcium ion-dependent exocytosis / positive regulation of integrin activation / negative regulation of synaptic vesicle exocytosis / calcium-ion regulated exocytosis / response to carbohydrate / establishment of endothelial barrier / regulation of establishment of cell polarity / Neutrophil degranulation / small GTPase-mediated signal transduction / cellular response to organic cyclic compound / cellular response to cAMP / lipid droplet / small monomeric GTPase / G protein activity / establishment of localization in cell / GDP binding / cell-cell junction / cellular response to xenobiotic stimulus / cell population proliferation / positive regulation of ERK1 and ERK2 cascade / GTPase activity / glutamatergic synapse / protein-containing complex binding / GTP binding / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.168 Å | ||||||
Authors | Noguchi, H. / Ikegami, T. / Park, S.Y. / Tame, J.R.H. / Unzai, S. | ||||||
Citation | Journal: Biochem.Biophys.Res.Commun. / Year: 2015 Title: The structure and conformational switching of Rap1B Authors: Noguchi, H. / Ikegami, T. / Nagadoi, A. / Kamatari, Y.O. / Park, S.Y. / Tame, J.R. / Unzai, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3x1y.cif.gz | 92 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3x1y.ent.gz | 68.9 KB | Display | PDB format |
PDBx/mmJSON format | 3x1y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x1/3x1y ftp://data.pdbj.org/pub/pdb/validation_reports/x1/3x1y | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 18979.457 Da / Num. of mol.: 1 / Fragment: RAS-RELATED PROTEIN RAP1B, UNP residues 1-167 / Mutation: L9V Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Rap1b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q62636 |
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-Non-polymers , 5 types, 197 molecules
#2: Chemical | ChemComp-GNP / |
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#3: Chemical | ChemComp-MG / |
#4: Chemical | ChemComp-GOL / |
#5: Chemical | ChemComp-CD / |
#6: 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: 1.83 Å3/Da / Density % sol: 32.94 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.1M HEPES pH 7.5, 12%(w/v) PEG3350, 5mM Cadmium chloride, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 7, 2014 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.168→35.42 Å / Num. all: 413294 / Num. obs: 413294 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.8 % / Rmerge(I) obs: 0.047 / Net I/σ(I): 23.3 |
Reflection shell | Resolution: 1.17→1.19 Å / Redundancy: 7 % / Rmerge(I) obs: 0.167 / Mean I/σ(I) obs: 8.9 / % possible all: 93.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.168→35.416 Å / SU ML: 0.11 / σ(F): 1.34 / Phase error: 19.06 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.168→35.416 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 17
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