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- PDB-4qt7: Crystal structure of the c-Src SH3 domain in complex with a pepti... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4qt7 | ||||||
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Title | Crystal structure of the c-Src SH3 domain in complex with a peptide from the Hepatitis C virus NS5A-protein | ||||||
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![]() | TRANSFERASE/TRANSFERASE ACTIVATOR / beta shandwich / SH3 domain / Proline rich motifs / VIRAL PROTEIN / TRANSFERASE-TRANSFERASE ACTIVATOR complex | ||||||
Function / homology | ![]() Signaling by ERBB2 / Nuclear signaling by ERBB4 / PIP3 activates AKT signaling / Signaling by SCF-KIT / Regulation of KIT signaling / Signaling by EGFR / GAB1 signalosome / Regulation of gap junction activity / FCGR activation / PECAM1 interactions ...Signaling by ERBB2 / Nuclear signaling by ERBB4 / PIP3 activates AKT signaling / Signaling by SCF-KIT / Regulation of KIT signaling / Signaling by EGFR / GAB1 signalosome / Regulation of gap junction activity / FCGR activation / PECAM1 interactions / CD28 co-stimulation / CTLA4 inhibitory signaling / 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 / RAF activation / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / RET signaling / Receptor Mediated Mitophagy / ADP signalling through P2Y purinoceptor 1 / Downregulation of ERBB4 signaling / EPH-ephrin mediated repulsion of cells / Cyclin D associated events in G1 / Regulation of RUNX3 expression and activity / Activated NTRK3 signals through PI3K / Downstream signal transduction / 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 / progesterone receptor signaling pathway / negative regulation of intrinsic apoptotic signaling pathway / ribonucleoside triphosphate phosphatase activity / negative regulation of extrinsic apoptotic signaling pathway / non-specific protein-tyrosine kinase / non-membrane spanning protein tyrosine kinase activity / epidermal growth factor receptor signaling pathway / cell junction / protein phosphatase binding / protein tyrosine kinase activity / mitochondrial inner membrane / cell differentiation / cytoskeleton / regulation of cell cycle / endosome membrane / cell adhesion / cysteine-type endopeptidase activity / serine-type endopeptidase activity / RNA-dependent RNA polymerase activity / innate immune response / focal adhesion / signaling receptor binding / heme binding / perinuclear region of cytoplasm / protein-containing complex / zinc ion binding / ATP binding / membrane / nucleus / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Camara-Artigas, A. / Bacarizo, J. | ||||||
![]() | ![]() Title: Structure of the c-Src-SH3 domain in complex with a proline-rich motif of NS5A protein from the hepatitis C virus. Authors: Bacarizo, J. / Martinez-Rodriguez, S. / 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 | ![]() | 51.2 KB | Display | ![]() |
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PDB format | ![]() | 35.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4jz4S 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
#1: Protein | Mass: 6905.498 Da / Num. of mol.: 1 / Fragment: SH3 domain, UNP residues 85-141 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: 1314.624 Da / Num. of mol.: 1 / Fragment: Proline rich peptide, UNP residues 349-359 / Source method: obtained synthetically / Details: The peptide was chemically synthesized. / Source: (synth.) ![]() |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.61 Å3/Da / Density % sol: 23.59 % Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS Mosaicity: 0.23 ° |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 2M Ammonium sulphate, 0.1M sodium chloride, 0.86mM methyl-beta-cyclodextrin, 0.1M Hepes, pH 7, vapor diffusion, hanging drop, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||
Detector | Detector: CCD / Date: Nov 28, 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: 0.9334 Å / Relative weight: 1 | ||||||||||||||||||||||||
Reflection | Resolution: 1.55→24.98 Å / Num. obs: 14570 / % possible obs: 98.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.6 % / Biso Wilson estimate: 7.42 Å2 / Rmerge(I) obs: 0.091 / Net I/σ(I): 23.7 / Scaling rejects: 6 | ||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4JZ4 Resolution: 1.55→24.979 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 0.01 / Phase error: 22.26 / Stereochemistry target values: ML Details: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS
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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: 42.62 Å2 / Biso mean: 10.5396 Å2 / Biso min: 3 Å2 | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.55→24.979 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: 5
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