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Yorodumi- PDB-2v8c: Mouse Profilin IIa in complex with the proline-rich domain of VASP -
+Open data
-Basic information
Entry | Database: PDB / ID: 2v8c | ||||||
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Title | Mouse Profilin IIa in complex with the proline-rich domain of VASP | ||||||
Components |
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Keywords | PROTEIN BINDING / ALTERNATIVE SPLICING / PROTEIN-BINDING / CYTOPLASM / ACETYLATION / CYTOSKELETON / ACTIN-BINDING | ||||||
Function / homology | Function and homology information Cell-extracellular matrix interactions / Signaling by ROBO receptors / negative regulation of ruffle assembly / modification of postsynaptic actin cytoskeleton / negative regulation of epithelial cell migration / RHO GTPases Activate Formins / profilin binding / positive regulation of actin filament bundle assembly / negative regulation of actin filament polymerization / regulation of actin filament polymerization ...Cell-extracellular matrix interactions / Signaling by ROBO receptors / negative regulation of ruffle assembly / modification of postsynaptic actin cytoskeleton / negative regulation of epithelial cell migration / RHO GTPases Activate Formins / profilin binding / positive regulation of actin filament bundle assembly / negative regulation of actin filament polymerization / regulation of actin filament polymerization / actin polymerization or depolymerization / filopodium membrane / regulation of synaptic vesicle exocytosis / positive regulation of actin filament polymerization / lamellipodium membrane / actin monomer binding / bicellular tight junction / positive regulation of stress fiber assembly / phosphatidylinositol-4,5-bisphosphate binding / presynaptic modulation of chemical synaptic transmission / filopodium / neural tube closure / axon guidance / Schaffer collateral - CA1 synapse / modulation of chemical synaptic transmission / SH3 domain binding / presynapse / positive regulation of peptidyl-serine phosphorylation / lamellipodium / actin binding / actin cytoskeleton organization / postsynapse / protein homotetramerization / cytoskeleton / protein stabilization / focal adhesion / glutamatergic synapse / ATP hydrolysis activity / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | MUS MUSCULUS (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.98 Å | ||||||
Authors | Kursula, P. / Downer, J. / Witke, W. / Wilmanns, M. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2008 Title: High-Resolution Structural Analysis of Mammalian Profilin 2A Complex Formation with Two Physiological Ligands: The Formin Homology 1 Domain of Mdia1 and the Proline-Rich Domain of Vasp. Authors: Kursula, P. / Kursula, I. / Massimi, M. / Song, Y.H. / Downer, J. / Stanley, W.A. / Witke, W. / Wilmanns, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2v8c.cif.gz | 45.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2v8c.ent.gz | 31.4 KB | Display | PDB format |
PDBx/mmJSON format | 2v8c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v8/2v8c ftp://data.pdbj.org/pub/pdb/validation_reports/v8/2v8c | HTTPS FTP |
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-Related structure data
Related structure data | 2v8fC 1d1jS C: citing same article (ref.) 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
-Protein / Protein/peptide , 2 types, 2 molecules AC
#1: Protein | Mass: 15048.216 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) MUS MUSCULUS (house mouse) / Plasmid: PMW172 / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q3V171, UniProt: Q9JJV2*PLUS |
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#2: Protein/peptide | Mass: 1816.102 Da / Num. of mol.: 1 / Fragment: PROLINE-RICH PEPTIDE, UNP RESIDUES 165-184 / Source method: obtained synthetically / Source: (synth.) MUS MUSCULUS (house mouse) / References: UniProt: P70460 |
-Non-polymers , 5 types, 126 molecules
#3: Chemical | #4: Chemical | #5: Chemical | ChemComp-NA / | #6: Chemical | ChemComp-GOL / | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 1.97 Å3/Da / Density % sol: 36.9 % / Description: NONE |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 1.0408 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jun 18, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0408 Å / Relative weight: 1 |
Reflection | Resolution: 1.98→20 Å / Num. obs: 10355 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 6.8 % / Biso Wilson estimate: 26 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 16.5 |
Reflection shell | Resolution: 1.98→2.02 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 5 / % possible all: 99.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1D1J Resolution: 1.98→20 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.951 / SU B: 3.149 / SU ML: 0.088 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.152 / ESU R Free: 0.132 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.88 Å2
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Refinement step | Cycle: LAST / Resolution: 1.98→20 Å
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