+Open data
-Basic information
Entry | Database: PDB / ID: 4l9m | ||||||
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Title | Autoinhibited state of the Ras-specific exchange factor RasGRP1 | ||||||
Components | RAS guanyl-releasing protein 1 | ||||||
Keywords | SIGNALING PROTEIN / Ras nucleotide exchange factor | ||||||
Function / homology | Function and homology information positive regulation of natural killer cell differentiation / diacylglycerol binding / positive regulation of T cell differentiation in thymus / regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / secretory granule localization / Effects of PIP2 hydrolysis / vesicle transport along microtubule / positive regulation of natural killer cell mediated cytotoxicity / phosphatidylcholine binding / natural killer cell activation ...positive regulation of natural killer cell differentiation / diacylglycerol binding / positive regulation of T cell differentiation in thymus / regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / secretory granule localization / Effects of PIP2 hydrolysis / vesicle transport along microtubule / positive regulation of natural killer cell mediated cytotoxicity / phosphatidylcholine binding / natural killer cell activation / Rap1 signalling / inflammatory response to antigenic stimulus / positive regulation of Ras protein signal transduction / activation of GTPase activity / positive regulation of granulocyte macrophage colony-stimulating factor production / mast cell degranulation / B cell activation / B cell proliferation / Activation of RAS in B cells / regulation of ERK1 and ERK2 cascade / T cell proliferation / T cell activation / Integrin signaling / positive regulation of MAP kinase activity / positive regulation of GTPase activity / guanyl-nucleotide exchange factor activity / positive regulation of JNK cascade / FCERI mediated NF-kB activation / positive regulation of type II interferon production / positive regulation of tumor necrosis factor production / RAF/MAP kinase cascade / Ras protein signal transduction / positive regulation of ERK1 and ERK2 cascade / cell differentiation / positive regulation of protein phosphorylation / Golgi membrane / lipid binding / calcium ion binding / endoplasmic reticulum membrane / Golgi apparatus / signal transduction / zinc ion binding / identical protein binding / membrane / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å | ||||||
Authors | Iwig, J.S. / Vercoulen, Y. / Das, R. / Barros, T. / Limnander, A. / Che, Y. / Pelton, J.G. / Wemmer, D.E. / Roose, J.P. / Kuriyan, J. | ||||||
Citation | Journal: Elife / Year: 2013 Title: Structural analysis of autoinhibition in the Ras-specific exchange factor RasGRP1. Authors: Iwig, J.S. / Vercoulen, Y. / Das, R. / Barros, T. / Limnander, A. / Che, Y. / Pelton, J.G. / Wemmer, D.E. / Roose, J.P. / Kuriyan, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4l9m.cif.gz | 232.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4l9m.ent.gz | 188 KB | Display | PDB format |
PDBx/mmJSON format | 4l9m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4l9m_validation.pdf.gz | 457.3 KB | Display | wwPDB validaton report |
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Full document | 4l9m_full_validation.pdf.gz | 467.5 KB | Display | |
Data in XML | 4l9m_validation.xml.gz | 21.5 KB | Display | |
Data in CIF | 4l9m_validation.cif.gz | 28.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l9/4l9m ftp://data.pdbj.org/pub/pdb/validation_reports/l9/4l9m | HTTPS FTP |
-Related structure data
Related structure data | 2ma2C 4l9uC 1bkdS 2ijeS S: Starting model for refinement C: citing same article (ref.) |
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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: 64212.590 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: RASGRP1, RASGRP / Production host: Escherichia coli (E. coli) / References: UniProt: O95267 | ||
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#2: Chemical | ChemComp-CIT / | ||
#3: Chemical | ChemComp-GOL / | ||
#4: Chemical | #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: 2.68 Å3/Da / Density % sol: 54.06 % |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.15 M sodium citrate tribasic, 22% PEG 3350, 1 mM MnCl2, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 296K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å | |||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 28, 2011 | |||||||||
Radiation | Monochromator: Double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||
Reflection | Resolution: 3→47.44 Å / Num. all: 15299 / Num. obs: 15253 / % possible obs: 99.7 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 | |||||||||
Reflection shell |
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-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2IJE and 1BKD Resolution: 3→47.435 Å / SU ML: 0.5 / σ(F): 1.92 / Phase error: 26.88 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 1.1 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3→47.435 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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