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- PDB-2vzg: Crystal structure of the C-terminal calponin homology domain of a... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2vzg | ||||||
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Title | Crystal structure of the C-terminal calponin homology domain of alpha- parvin in complex with paxillin LD2 motif | ||||||
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![]() | CELL ADHESION / CALPONIN HOMOLOGY DOMAIN / CELL MEMBRANE / METAL-BINDING / CYTOSKELETON / CELL JUNCTION / ACTIN-BINDING / MEMBRANE / LD2 MOTIF / LIM DOMAIN / PHOSPHOPROTEIN | ||||||
Function / homology | ![]() actin-mediated cell contraction / smooth muscle cell chemotaxis / Regulation of cytoskeletal remodeling and cell spreading by IPP complex components / Localization of the PINCH-ILK-PARVIN complex to focal adhesions / vinculin binding / Cell-extracellular matrix interactions / neuropilin binding / outflow tract septum morphogenesis / signal complex assembly / heterotypic cell-cell adhesion ...actin-mediated cell contraction / smooth muscle cell chemotaxis / Regulation of cytoskeletal remodeling and cell spreading by IPP complex components / Localization of the PINCH-ILK-PARVIN complex to focal adhesions / vinculin binding / Cell-extracellular matrix interactions / neuropilin binding / outflow tract septum morphogenesis / signal complex assembly / heterotypic cell-cell adhesion / sprouting angiogenesis / microtubule associated complex / growth hormone receptor signaling pathway / establishment or maintenance of cell polarity / protein kinase inhibitor activity / cilium assembly / endothelial cell migration / Smooth Muscle Contraction / GAB1 signalosome / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / stress fiber / positive regulation of stress fiber assembly / substrate adhesion-dependent cell spreading / transforming growth factor beta receptor signaling pathway / beta-catenin binding / VEGFA-VEGFR2 Pathway / Z disc / cellular response to reactive oxygen species / cell-cell junction / cell migration / actin cytoskeleton / lamellipodium / actin binding / cell cortex / regulation of cell shape / actin cytoskeleton organization / protein phosphatase binding / protein stabilization / cell adhesion / cadherin binding / focal adhesion / signal transduction / nucleus / metal ion binding / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Lorenz, S. / Vakonakis, I. / Lowe, E.D. / Campbell, I.D. / Noble, M.E.M. / Hoellerer, M.K. | ||||||
![]() | ![]() Title: Structural analysis of the interactions between paxillin LD motifs and alpha-parvin. Authors: Lorenz, S. / Vakonakis, I. / Lowe, E.D. / Campbell, I.D. / Noble, M.E. / Hoellerer, M.K. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 50.6 KB | Display | ![]() |
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PDB format | ![]() | 36 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 460.7 KB | Display | ![]() |
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Full document | ![]() | 462.6 KB | Display | |
Data in XML | ![]() | 9.2 KB | Display | |
Data in CIF | ![]() | 11.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2vzcSC ![]() 2vzdC ![]() 2vziC C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
-Protein/peptide / Protein , 2 types, 2 molecules AB
#1: Protein/peptide | Mass: 2287.571 Da / Num. of mol.: 1 / Fragment: PAXILLIN LD1 MOTIF, RESIDUES 141-160 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Protein | Mass: 15155.380 Da / Num. of mol.: 1 Fragment: C-TERMINAL CALPONIN HOMOLOGY DOMAIN, RESIDUES 242-372 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
-Non-polymers , 4 types, 72 molecules ![](data/chem/img/PG4.gif)
![](data/chem/img/PGE.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/PGE.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-PG4 / | ||
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#4: Chemical | ChemComp-PGE / | ||
#5: Chemical | ChemComp-EDO / #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 43 % / Description: NONE |
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Crystal grow | Temperature: 286 K / Method: vapor diffusion, sitting drop / pH: 4.5 / Details: 40% (W/V) PEG200, 0.1 M CITRATE PH 4.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD / Date: Aug 2, 2007 / Details: MIRRORS |
Radiation | Monochromator: DCM / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.968 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→27.71 Å / Num. obs: 13920 / % possible obs: 99.6 % / Observed criterion σ(I): 2 / Redundancy: 3.4 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 13.2 |
Reflection shell | Resolution: 1.8→1.9 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 3.2 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2VZC Resolution: 1.8→58.22 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.937 / SU B: 6.158 / SU ML: 0.097 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.153 / ESU R Free: 0.136 / 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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.44 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→58.22 Å
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Refine LS restraints |
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