[English] 日本語
Yorodumi- PDB-2o9v: The second SH3 domain from Ponsin in complex with the paxillin pr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2o9v | ||||||
---|---|---|---|---|---|---|---|
Title | The second SH3 domain from Ponsin in complex with the paxillin proline rich region | ||||||
Components |
| ||||||
Keywords | SIGNALING PROTEIN/CELL ADHESION / SH3 DOMAIN / PONSIN / Paxillin / proline-rich-region / SIGNALING PROTEIN-CELL ADHESION COMPLEX | ||||||
Function / homology | Function and homology information Localization of the PINCH-ILK-PARVIN complex to focal adhesions / Regulation of cytoskeletal remodeling and cell spreading by IPP complex components / cell-substrate junction / zonula adherens / vinculin binding / flotillin complex / neuropilin binding / focal adhesion assembly / signal complex assembly / microtubule associated complex ...Localization of the PINCH-ILK-PARVIN complex to focal adhesions / Regulation of cytoskeletal remodeling and cell spreading by IPP complex components / cell-substrate junction / zonula adherens / vinculin binding / flotillin complex / neuropilin binding / focal adhesion assembly / signal complex assembly / microtubule associated complex / growth hormone receptor signaling pathway / stress fiber assembly / cell-substrate adhesion / endothelial cell migration / Smooth Muscle Contraction / positive regulation of glycogen biosynthetic process / GAB1 signalosome / positive regulation of lipid biosynthetic process / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / stress fiber / positive regulation of insulin receptor signaling pathway / positive regulation of stress fiber assembly / cytoskeletal protein binding / substrate adhesion-dependent cell spreading / cell-matrix adhesion / transforming growth factor beta receptor signaling pathway / positive regulation of protein localization to plasma membrane / adherens junction / positive regulation of glucose import / insulin receptor binding / beta-catenin binding / cellular response to reactive oxygen species / nuclear matrix / VEGFA-VEGFR2 Pathway / cellular response to insulin stimulus / cell-cell junction / cell migration / signaling receptor complex adaptor activity / lamellipodium / insulin receptor signaling pathway / actin binding / cell cortex / protein phosphatase binding / cell adhesion / membrane raft / focal adhesion / centrosome / signal transduction / metal ion binding / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.63 Å | ||||||
Authors | Pinotsis, N. / Wilmanns, M. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2007 Title: Paxillin and ponsin interact in nascent costameres of muscle cells Authors: Gehmlich, K. / Pinotsis, N. / Hayess, K. / van der Ven, P.F. / Milting, H. / El Banayosy, A. / Wilmanns, M. / Ehler, E. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2o9v.cif.gz | 47 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2o9v.ent.gz | 33.3 KB | Display | PDB format |
PDBx/mmJSON format | 2o9v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o9/2o9v ftp://data.pdbj.org/pub/pdb/validation_reports/o9/2o9v | HTTPS FTP |
---|
-Related structure data
Related structure data | 2o9sC 2o2wS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 7698.707 Da / Num. of mol.: 1 / Fragment: SRC HOMOLOGY 3 (SH3) DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SORBS1 / Plasmid: PET151 / Production host: Escherichia coli (E. coli) / References: UniProt: A0AED4, UniProt: Q9BX66*PLUS |
---|---|
#2: Protein/peptide | Mass: 983.158 Da / Num. of mol.: 1 / Fragment: Proline rich region / Source method: obtained synthetically Details: The peptide was chemically synthesized. The sequence of the peptide is naturally found in Homo sapiens (human) References: UniProt: P49023 |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 1.74 Å3/Da / Density % sol: 29.11 % |
---|---|
Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.2M Sodium Acetate, 0.1M Sodium Cacodylate, 30% (w/v) PEG 8000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.8156 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Jun 1, 2006 |
Radiation | Monochromator: Ge Single Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8156 Å / Relative weight: 1 |
Reflection | Resolution: 1.63→25 Å / Num. all: 8022 / Num. obs: 7747 / % possible obs: 96.6 % / Redundancy: 5 % / Biso Wilson estimate: 17.1 Å2 / Rmerge(I) obs: 0.059 / Net I/σ(I): 24 |
Reflection shell | Resolution: 1.63→1.66 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.221 / Mean I/σ(I) obs: 4.2 / Num. unique all: 380 / % possible all: 80.5 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2O2W Resolution: 1.63→18.81 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.964 / SU B: 3.481 / SU ML: 0.058 / Cross valid method: THROUGHOUT / ESU R: 0.181 / ESU R Free: 0.092 / Stereochemistry target values: MAXIMUM LIKELIHOOD
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.46 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.63→18.81 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.63→1.672 Å / Total num. of bins used: 20
|