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- PDB-4hvu: Crystal structure of the T98D c-Src-SH3 domain mutant in complex ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4hvu | ||||||
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Title | Crystal structure of the T98D c-Src-SH3 domain mutant in complex with the high affinity peptide APP12 | ||||||
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![]() | Signaling Protein/Peptide / beta shandwich / SH3 like barrel / Kinase / Proline Rich Motifs / Signaling Protein-Peptide complex | ||||||
Function / homology | ![]() Signaling by ERBB2 / Nuclear signaling by ERBB4 / Signaling by SCF-KIT / Regulation of KIT signaling / Signaling by EGFR / GAB1 signalosome / Regulation of gap junction activity / FCGR activation / PECAM1 interactions / Co-stimulation by CD28 ...Signaling by ERBB2 / Nuclear signaling by ERBB4 / Signaling by SCF-KIT / Regulation of KIT signaling / Signaling by EGFR / GAB1 signalosome / Regulation of gap junction activity / FCGR activation / PECAM1 interactions / Co-stimulation by CD28 / Co-inhibition by CTLA4 / EPHA-mediated growth cone collapse / Ephrin signaling / G alpha (i) signalling events / GP1b-IX-V activation signalling / Thrombin signalling through proteinase activated receptors (PARs) / VEGFR2 mediated cell proliferation / RET signaling / Receptor Mediated Mitophagy / ADP signalling through P2Y purinoceptor 1 / RAF activation / PIP3 activates AKT signaling / EPH-ephrin mediated repulsion of cells / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / Activated NTRK3 signals through PI3K / Downstream signal transduction / Downregulation of ERBB4 signaling / Cyclin D associated events in G1 / Regulation of RUNX3 expression and activity / MAP2K and MAPK activation / Integrin signaling / GRB2:SOS provides linkage to MAPK signaling for Integrins / DCC mediated attractive signaling / MET activates PTK2 signaling / Extra-nuclear estrogen signaling / EPHB-mediated forward signaling / p130Cas linkage to MAPK signaling for integrins / VEGFA-VEGFR2 Pathway / connexin binding / negative regulation of intrinsic apoptotic signaling pathway / progesterone receptor signaling pathway / negative regulation of extrinsic apoptotic signaling pathway / non-membrane spanning protein tyrosine kinase activity / non-specific protein-tyrosine kinase / epidermal growth factor receptor signaling pathway / cell junction / cell-cell junction / protein tyrosine kinase activity / protein phosphatase binding / histone H3Y41 kinase activity / histone H2AXY142 kinase activity / cell differentiation / mitochondrial inner membrane / cytoskeleton / regulation of cell cycle / cell adhesion / endosome membrane / signaling receptor binding / innate immune response / focal adhesion / heme binding / perinuclear region of cytoplasm / protein-containing complex / ATP binding / nucleus / membrane / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Camara-Artigas, A. | ||||||
![]() | ![]() Title: Atomic resolution structures of the c-Src SH3 domain in complex with two high-affinity peptides from classes I and II. Authors: Bacarizo, J. / Camara-Artigas, A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 57.5 KB | Display | ![]() |
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PDB format | ![]() | 41.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 451.7 KB | Display | ![]() |
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Full document | ![]() | 452.8 KB | Display | |
Data in XML | ![]() | 6.2 KB | Display | |
Data in CIF | ![]() | 7.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4hvvC ![]() 4hvwC ![]() 3fj5S 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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Details | biological unit is the same as asym. |
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Components
#1: Protein | Mass: 6948.547 Da / Num. of mol.: 1 / Fragment: SH3 domain / Mutation: T98D, Q128R Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P00523, non-specific protein-tyrosine kinase | ||
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#2: Protein/peptide | Mass: 1142.353 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: High affinity peptide designed from phage display experiments | ||
#3: Chemical | ChemComp-SO4 / | ||
#4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.89 Å3/Da / Density % sol: 34.89 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 1.7 M Ammonium sulphate, 10% PEG 300, 10% glycerol and 0.1 M sodium acetate, pH 5, vapor diffusion, hanging drop, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 13, 2012 Details: vertical focusing mirror (VFM) and a horizontal focusing mirror(HFM), manufactured by IRELEC. | |||||||||||||||||||||
Radiation | Monochromator: Si(111) channel-cut crystal monochromator and a pair of KB mirrors Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97951 Å / Relative weight: 1 | |||||||||||||||||||||
Reflection | Resolution: 0.98→35.57 Å / Num. all: 36286 / Num. obs: 35524 / % possible obs: 97.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.8 % / Biso Wilson estimate: 10.023 Å2 / Rmerge(I) obs: 0.037 / Net I/σ(I): 29.5 | |||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 3FJ5 Resolution: 0.98→19.074 Å / Occupancy max: 1 / Occupancy min: 0.1 / FOM work R set: 0.9381 / SU ML: 0.07 / Cross valid method: THROUGHOUT / σ(F): 1.44 / σ(I): 0 / Phase error: 11.54 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 48.09 Å2 / Biso mean: 18.5467 Å2 / Biso min: 6.32 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 0.98→19.074 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 23
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