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Yorodumi- PDB-3cd3: Crystal structure of phosphorylated human feline sarcoma viral on... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3cd3 | ||||||
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Title | Crystal structure of phosphorylated human feline sarcoma viral oncogene homologue (v-FES) in complex with staurosporine and a consensus peptide | ||||||
Components |
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Keywords | TRANSFERASE / FES / v-fes / Fujinami / avian sarcoma / viral / oncogene / feline sarcoma virus / active / SGC / Structural Genomics Consortium / ATP-binding / Kinase / Nucleotide-binding / Phosphoprotein / Proto-oncogene / SH2 domain / Tyrosine-protein kinase | ||||||
Function / homology | Function and homology information positive regulation of myeloid cell differentiation / regulation of mast cell degranulation / regulation of vesicle-mediated transport / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / cellular response to vitamin D / CRMPs in Sema3A signaling / microtubule bundle formation / positive regulation of monocyte differentiation / regulation of cell motility / centrosome cycle ...positive regulation of myeloid cell differentiation / regulation of mast cell degranulation / regulation of vesicle-mediated transport / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / cellular response to vitamin D / CRMPs in Sema3A signaling / microtubule bundle formation / positive regulation of monocyte differentiation / regulation of cell motility / centrosome cycle / myoblast proliferation / cardiac muscle cell proliferation / immunoglobulin receptor binding / regulation of cell differentiation / Sema3A PAK dependent Axon repulsion / regulation of cell adhesion / positive regulation of microtubule polymerization / phosphatidylinositol binding / non-specific protein-tyrosine kinase / non-membrane spanning protein tyrosine kinase activity / Signaling by SCF-KIT / cytoplasmic side of plasma membrane / positive regulation of neuron projection development / peptidyl-tyrosine phosphorylation / microtubule cytoskeleton / chemotaxis / regulation of cell population proliferation / regulation of cell shape / cytoplasmic vesicle / microtubule binding / protein tyrosine kinase activity / protein autophosphorylation / cell adhesion / focal adhesion / Golgi apparatus / ATP binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.98 Å | ||||||
Authors | Filippakopoulos, P. / Salah, E. / Cooper, C. / Picaud, S.S. / Elkins, J.M. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Weigelt, J. / Bountra, C. ...Filippakopoulos, P. / Salah, E. / Cooper, C. / Picaud, S.S. / Elkins, J.M. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Weigelt, J. / Bountra, C. / Knapp, S. / Structural Genomics Consortium (SGC) | ||||||
Citation | Journal: Cell(Cambridge,Mass.) / Year: 2008 Title: Structural Coupling of SH2-Kinase Domains Links Fes and Abl Substrate Recognition and Kinase Activation Authors: Filippakopoulos, P. / Kofler, M. / Hantschel, O. / Gish, G.D. / Grebien, F. / Salah, E. / Neudecker, P. / Kay, L.E. / Turk, B.E. / Superti-Furga, G. / Pawson, T. / Knapp, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3cd3.cif.gz | 98.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3cd3.ent.gz | 72.2 KB | Display | PDB format |
PDBx/mmJSON format | 3cd3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cd/3cd3 ftp://data.pdbj.org/pub/pdb/validation_reports/cd/3cd3 | HTTPS FTP |
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-Related structure data
Related structure data | 3bkbSC 3cblC 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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Details | THE BIOLOGICAL UNIT IS A MONOMERIC COMPLEX BETWEEN PROTEIN (CHAIN A) AND THE CONSENSUS PEPTIDE (CHAIN B). |
-Components
#1: Protein | Mass: 42838.023 Da / Num. of mol.: 1 / Fragment: Residues 448-822 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: FES, FPS / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-R3-Yop-PPase References: UniProt: P07332, non-specific protein-tyrosine kinase | ||||
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#2: Protein/peptide | Mass: 649.734 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Synthetic peptide / References: PDB-3CBL | ||||
#3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.36 Å3/Da / Density % sol: 47.93 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 30% PEG MME 2000, 0.15M Sodium bromide, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.54178 Å |
Detector | Type: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Jan 25, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 |
Reflection | Resolution: 1.98→15.347 Å / Num. all: 29652 / Num. obs: 29000 / % possible obs: 97.8 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.082 / Rsym value: 0.082 / Net I/σ(I): 10.2 |
Reflection shell | Resolution: 1.98→2.09 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.472 / Mean I/σ(I) obs: 2.3 / Num. unique all: 4265 / Rsym value: 0.472 / % possible all: 100 |
-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 3BKB Resolution: 1.98→15.347 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.905 / SU B: 7.831 / SU ML: 0.129 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.178 / ESU R Free: 0.173 / 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: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 37.689 Å2
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Refinement step | Cycle: LAST / Resolution: 1.98→15.347 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.98→2.031 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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