[English] 日本語
Yorodumi- PDB-4rug: Cyrstal structure of SLIT-ROBO Rho GTPase-activating protein 2 fr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4rug | ||||||
---|---|---|---|---|---|---|---|
Title | Cyrstal structure of SLIT-ROBO Rho GTPase-activating protein 2 fragment | ||||||
Components | SLIT-ROBO Rho GTPase-activating protein 2 | ||||||
Keywords | PROTEIN BINDING / srGAP2 / SH3 / Ligand binding / Robo1 / Nuclear / Plasma Membrane | ||||||
Function / homology | Function and homology information lamellipodium assembly involved in ameboidal cell migration / extension of a leading process involved in cell motility in cerebral cortex radial glia guided migration / excitatory synapse assembly / negative regulation of neuron migration / Inactivation of CDC42 and RAC1 / inhibitory synapse assembly / dendritic spine development / actin filament severing / filopodium assembly / RHOF GTPase cycle ...lamellipodium assembly involved in ameboidal cell migration / extension of a leading process involved in cell motility in cerebral cortex radial glia guided migration / excitatory synapse assembly / negative regulation of neuron migration / Inactivation of CDC42 and RAC1 / inhibitory synapse assembly / dendritic spine development / actin filament severing / filopodium assembly / RHOF GTPase cycle / regulation of small GTPase mediated signal transduction / dendritic spine head / RHOQ GTPase cycle / CDC42 GTPase cycle / RHOU GTPase cycle / RAC3 GTPase cycle / phagocytic vesicle / RAC1 GTPase cycle / GTPase activator activity / substrate adhesion-dependent cell spreading / negative regulation of cell migration / neuron projection morphogenesis / RHO GTPases Activate Formins / small GTPase binding / positive regulation of GTPase activity / lamellipodium / postsynaptic membrane / postsynaptic density / signal transduction / protein homodimerization activity / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.73 Å | ||||||
Authors | Opatowsky, Y. / Guez-Hadad, J. | ||||||
Citation | Journal: Structure / Year: 2015 Title: The Neuronal Migration Factor srGAP2 Achieves Specificity in Ligand Binding through a Two-Component Molecular Mechanism. Authors: Guez-Haddad, J. / Sporny, M. / Sasson, Y. / Gevorkyan-Airapetov, L. / Lahav-Mankovski, N. / Margulies, D. / Radzimanowski, J. / Opatowsky, Y. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4rug.cif.gz | 80.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4rug.ent.gz | 61.6 KB | Display | PDB format |
PDBx/mmJSON format | 4rug.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ru/4rug ftp://data.pdbj.org/pub/pdb/validation_reports/ru/4rug | HTTPS FTP |
---|
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||||||||
2 |
| ||||||||||||||||||
Unit cell |
| ||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: PRO / End label comp-ID: PRO / Refine code: 0 / Auth seq-ID: 728 - 808 / Label seq-ID: 5 - 85
|
-Components
#1: Protein | Mass: 10271.398 Da / Num. of mol.: 2 / Fragment: UNP residues 729-815 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SRGAP2, ARHGAP34, FNBP2, KIAA0456, SRGAP2A / Production host: Escherichia coli (E. coli) / References: UniProt: O75044 #2: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.18 Å3/Da / Density % sol: 43.68 % |
---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion / pH: 6.25 Details: 2.35M Ammonium Sulphate; 0.1M MES, pH 6.25, VAPOR DIFFUSION, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.976 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Apr 17, 2013 |
Radiation | Monochromator: Si(311) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976 Å / Relative weight: 1 |
Reflection | Resolution: 1.73→57.81 Å / Num. all: 18910 / Num. obs: 18107 / % possible obs: 95 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.5 % / Rmerge(I) obs: 0.118 / Net I/σ(I): 9.09 |
Reflection shell | Resolution: 1.73→1.84 Å / % possible all: 0.89 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.73→57.81 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.94 / SU B: 6.346 / SU ML: 0.097 / Cross valid method: THROUGHOUT / ESU R: 0.119 / ESU R Free: 0.115 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.1 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.942 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.73→57.81 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints NCS | Ens-ID: 1 / Number: 4349 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.1 Å / Weight position: 0.05
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.731→1.776 Å / Total num. of bins used: 20
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|