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Yorodumi- PDB-2vzi: Crystal structure of the C-terminal calponin homology domain of a... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2vzi | ||||||
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Title | Crystal structure of the C-terminal calponin homology domain of alpha- parvin in complex with paxillin LD4 motif | ||||||
Components |
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Keywords | CELL ADHESION / CELL MEMBRANE / METAL-BINDING / CALPONIN HOMOLOGY DOMAIN / CYTOSKELETON / CELL JUNCTION / ACTIN-BINDING / MEMBRANE / LD2 MOTIF / LIM DOMAIN / PHOSPHOPROTEIN | ||||||
Function / homology | Function and homology information actin-mediated cell contraction / smooth muscle cell chemotaxis / Localization of the PINCH-ILK-PARVIN complex to focal adhesions / Regulation of cytoskeletal remodeling and cell spreading by IPP complex components / 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 / Localization of the PINCH-ILK-PARVIN complex to focal adhesions / Regulation of cytoskeletal remodeling and cell spreading by IPP complex components / 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 / Z disc / beta-catenin binding / cellular response to reactive oxygen species / VEGFA-VEGFR2 Pathway / 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 / metal ion binding / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Lorenz, S. / Vakonakis, I. / Lowe, E.D. / Campbell, I.D. / Noble, M.E.M. / Hoellerer, M.K. | ||||||
Citation | Journal: Structure / Year: 2008 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2vzi.cif.gz | 48.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2vzi.ent.gz | 34.1 KB | Display | PDB format |
PDBx/mmJSON format | 2vzi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vz/2vzi ftp://data.pdbj.org/pub/pdb/validation_reports/vz/2vzi | HTTPS FTP |
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-Related structure data
Related structure data | 2vzcSC 2vzdC 2vzgC 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/peptide / Protein , 2 types, 2 molecules AB
#1: Protein/peptide | Mass: 2305.626 Da / Num. of mol.: 1 Fragment: PAXILLIN LD4 MOTIF, RESIDUES 262-277 AND 312-315 OF PAXILLIN ISOFORM BETA,PAXILLIN LD4 MOTIF, RESIDUES 262-277 AND 312-315 OF PAXILLIN ISOFORM BETA Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PXN / Plasmid: PGEX-6P1 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P49023 |
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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.) Homo sapiens (human) / Gene: PARVA, MXRA2 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q9NVD7 |
-Non-polymers , 4 types, 44 molecules
#3: Chemical | ChemComp-PG4 / | ||||
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#4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
-Details
Sequence details | LD4 MOTIF OF PAXILLIN ISOFORM BETA (EXCLUDING RESIDUES 278-311 OF UNIPROT ENTRY P49023 PROTEIN SEQUENCE) |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 45 % / Description: NONE |
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Crystal grow | Temperature: 286 K / Method: vapor diffusion, sitting drop / pH: 5.2 / Details: 40%(W/V) PEG 300, 0.1M CITRATE PH 5.2 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.976 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Sep 1, 2007 / Details: MIRRORS |
Radiation | Monochromator: SI(311), SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→37.72 Å / Num. obs: 7929 / % possible obs: 99.5 % / Observed criterion σ(I): 2 / Redundancy: 3.5 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 9.7 |
Reflection shell | Resolution: 2.2→2.32 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.63 / Mean I/σ(I) obs: 2.2 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2VZC Resolution: 2.2→58.93 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.905 / SU B: 15.117 / SU ML: 0.203 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.396 / ESU R Free: 0.252 / 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: 31.7 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→58.93 Å
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Refine LS restraints |
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