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- PDB-2rex: Crystal structure of the effector domain of PLXNB1 bound with Rnd... -
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Basic information
Entry | Database: PDB / ID: 2rex | ||||||
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Title | Crystal structure of the effector domain of PLXNB1 bound with Rnd1 GTPase | ||||||
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![]() | SIGNALING PROTEIN/LIPOPROTEIN / complex / Structural Genomics Consortium / SGC / gtpase / gnp / Plexin / effector domain / Glycoprotein / Membrane / Phosphorylation / Receptor / Secreted / Transmembrane / Cytoskeleton / GTP-binding / Lipoprotein / Methylation / Nucleotide-binding / Prenylation / SIGNALING PROTEIN-LIPOPROTEIN COMPLEX | ||||||
Function / homology | ![]() semaphorin receptor binding / negative regulation of osteoblast proliferation / semaphorin receptor complex / inhibitory synapse assembly / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / semaphorin receptor activity / negative regulation of cell adhesion / RHOD GTPase cycle / Sema4D induced cell migration and growth-cone collapse / GTPase activating protein binding ...semaphorin receptor binding / negative regulation of osteoblast proliferation / semaphorin receptor complex / inhibitory synapse assembly / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / semaphorin receptor activity / negative regulation of cell adhesion / RHOD GTPase cycle / Sema4D induced cell migration and growth-cone collapse / GTPase activating protein binding / ossification involved in bone maturation / RND1 GTPase cycle / Sema4D mediated inhibition of cell attachment and migration / positive regulation of Rho protein signal transduction / neuron remodeling / positive regulation of axonogenesis / small GTPase-mediated signal transduction / regulation of cytoskeleton organization / semaphorin-plexin signaling pathway / regulation of cell migration / GTPase activator activity / neuron projection morphogenesis / positive regulation of GTPase activity / actin filament organization / regulation of actin cytoskeleton organization / adherens junction / transmembrane signaling receptor activity / G alpha (12/13) signalling events / actin cytoskeleton / cell migration / regulation of cell shape / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / intracellular signal transduction / intracellular membrane-bounded organelle / signaling receptor binding / GTPase activity / GTP binding / protein kinase binding / signal transduction / extracellular region / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Tong, Y. / Tempel, W. / Shen, L. / Arrowsmith, C.H. / Edwards, A.M. / Sundstrom, M. / Weigelt, J. / Bochkarev, A. / Park, H. / Structural Genomics Consortium (SGC) | ||||||
![]() | ![]() Title: Crystal structure of the effector domain of PLXNB1 bound with Rnd1 GTPase. Authors: Tong, Y. / Tempel, W. / Shen, L. / Arrowsmith, C.H. / Edwards, A.M. / Sundstrom, M. / Weigelt, J. / Bochkarev, A. / Park, H. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 129.7 KB | Display | ![]() |
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PDB format | ![]() | 96.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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3 | ![]()
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4 | ![]()
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Unit cell |
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Details | The authors state that the relationships between chains A and B and between chains C and D of the asymmetric unit reflect the biologically relevant interface between the plexin effector domain and RND1 gtpase. |
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Components
-Protein , 2 types, 4 molecules ACBD
#1: Protein | Mass: 13297.139 Da / Num. of mol.: 2 / Fragment: Residues 1743-1862 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein | Mass: 21946.164 Da / Num. of mol.: 2 / Fragment: Residues 5-200 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 5 types, 111 molecules ![](data/chem/img/UNX.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/GNP.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/GNP.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-UNX / #4: Chemical | #5: Chemical | #6: Chemical | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.05 Å3/Da / Density % sol: 59.65 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 20% PEG 3350, 0.2M Calcium chloride, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Jun 24, 2007 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9179 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.3→30 Å / Num. obs: 36932 / % possible obs: 97.3 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.06 / Χ2: 1.503 / Net I/σ(I): 9.1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entries 2CLS,2R2O Resolution: 2.3→20 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.915 / WRfactor Rfree: 0.245 / WRfactor Rwork: 0.214 / SU B: 11.089 / SU ML: 0.136 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.251 / ESU R Free: 0.204 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. Atomic B factors are residuals of TLS refinement. Programs coot, molprobity have also been used in refinement.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.565 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→20 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: 20
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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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