[English] 日本語
Yorodumi- PDB-7rnv: SH2 domain of guanine nucleotide exchange factor Vav2 in complex ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7rnv | ||||||
---|---|---|---|---|---|---|---|
Title | SH2 domain of guanine nucleotide exchange factor Vav2 in complex with an actin peptide with phosphorylated tyrosine 53 | ||||||
Components |
| ||||||
Keywords | PEPTIDE BINDING PROTEIN / phosphorylated tyrosine binding protein / actin peptide | ||||||
Function / homology | Function and homology information : / skeletal muscle fiber adaptation / : / Striated Muscle Contraction / Azathioprine ADME / response to steroid hormone / regulation of small GTPase mediated signal transduction / lamellipodium assembly / epidermal growth factor receptor binding / regulation of cell size ...: / skeletal muscle fiber adaptation / : / Striated Muscle Contraction / Azathioprine ADME / response to steroid hormone / regulation of small GTPase mediated signal transduction / lamellipodium assembly / epidermal growth factor receptor binding / regulation of cell size / RHOB GTPase cycle / small GTPase-mediated signal transduction / myosin binding / regulation of GTPase activity / Fc-gamma receptor signaling pathway involved in phagocytosis / NRAGE signals death through JNK / mesenchyme migration / RHOC GTPase cycle / Fc-epsilon receptor signaling pathway / skeletal muscle thin filament assembly / striated muscle thin filament / CDC42 GTPase cycle / RHOG GTPase cycle / RHOA GTPase cycle / EPH-ephrin mediated repulsion of cells / RAC2 GTPase cycle / RAC3 GTPase cycle / vascular endothelial growth factor receptor signaling pathway / skeletal muscle fiber development / muscle contraction / stress fiber / response to mechanical stimulus / GPVI-mediated activation cascade / RAC1 GTPase cycle / phosphotyrosine residue binding / sarcomere / FCERI mediated Ca+2 mobilization / VEGFR2 mediated vascular permeability / guanyl-nucleotide exchange factor activity / filopodium / Signal transduction by L1 / actin filament / FCERI mediated MAPK activation / FCGR3A-mediated phagocytosis / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / structural constituent of cytoskeleton / platelet activation / Regulation of actin dynamics for phagocytic cup formation / ADP binding / VEGFA-VEGFR2 Pathway / G alpha (12/13) signalling events / actin cytoskeleton / cellular response to xenobiotic stimulus / cell migration / DAP12 signaling / lamellipodium / cell body / angiogenesis / blood microparticle / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / hydrolase activity / positive regulation of gene expression / signal transduction / extracellular space / extracellular exosome / ATP binding / metal ion binding / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.15 Å | ||||||
Authors | Dai, S. / Horton, J.R. / Cheng, X. | ||||||
Funding support | United States, 1items
| ||||||
Citation | Journal: To Be Published Title: The Functional Analysis of a Major Tyrosine Phosphorylation Site on Actin Authors: Amelie, A. / Dai, S. / Shen, X. / Horton, J.R. / Zhang, X. / Cheng, X. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 7rnv.cif.gz | 46 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7rnv.ent.gz | 24.5 KB | Display | PDB format |
PDBx/mmJSON format | 7rnv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rn/7rnv ftp://data.pdbj.org/pub/pdb/validation_reports/rn/7rnv | HTTPS FTP |
---|
-Related structure data
Related structure data | 7rnsC 7rnuC 2iuiS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
Unit cell |
| ||||||||||||
Components on special symmetry positions |
|
-Components
#1: Protein | Mass: 13807.589 Da / Num. of mol.: 1 / Fragment: SH2 domain (UNP residues 665-774) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: VAV2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P52735 | ||||
---|---|---|---|---|---|
#2: Protein/peptide | Mass: 1063.975 Da / Num. of mol.: 1 / Fragment: UNP residues 52-60 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P68133 | ||||
#3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.37 Å3/Da / Density % sol: 48.06 % |
---|---|
Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.2 M sodium acetate trihydrate, 0.1 M Tris hydrochloride, pH 8.5, 30% PEG4000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SEALED TUBE / Type: RIGAKU MICROMAX-003 / Wavelength: 1.54184 Å |
Detector | Type: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: Mar 28, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54184 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→26.8 Å / Num. obs: 7715 / % possible obs: 96.1 % / Redundancy: 13.1 % / Biso Wilson estimate: 34.47 Å2 / CC1/2: 0.987 / Net I/σ(I): 10.3 |
Reflection shell | Resolution: 2.15→2.23 Å / Num. unique obs: 5024 / CC1/2: 0.312 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2IUI Resolution: 2.15→26.8 Å / SU ML: 0.3405 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 35.8157 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
| ||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 41.47 Å2 | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.15→26.8 Å
| ||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|