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Yorodumi- PDB-7a2x: Crystal structure of the Fyn SH3 domain L112V-S114N-S115T-E121L-R... -
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-Basic information
Entry | Database: PDB / ID: 7a2x | ||||||
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Title | Crystal structure of the Fyn SH3 domain L112V-S114N-S115T-E121L-R123H mutant in complex with VSL12 at pH 5.0 | ||||||
Components |
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Keywords | PROTEIN BINDING / beta barrel / SH3 domain | ||||||
Function / homology | Function and homology information response to singlet oxygen / Reelin signalling pathway / negative regulation of hydrogen peroxide biosynthetic process / perinuclear endoplasmic reticulum / NTRK2 activates RAC1 / growth factor receptor binding / Activated NTRK2 signals through FYN / heart process / cellular response to L-glutamate / regulation of glutamate receptor signaling pathway ...response to singlet oxygen / Reelin signalling pathway / negative regulation of hydrogen peroxide biosynthetic process / perinuclear endoplasmic reticulum / NTRK2 activates RAC1 / growth factor receptor binding / Activated NTRK2 signals through FYN / heart process / cellular response to L-glutamate / regulation of glutamate receptor signaling pathway / regulation of calcium ion import across plasma membrane / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / G protein-coupled glutamate receptor signaling pathway / Platelet Adhesion to exposed collagen / CD28 co-stimulation / positive regulation of protein localization to membrane / activated T cell proliferation / CRMPs in Sema3A signaling / positive regulation of cysteine-type endopeptidase activity / FLT3 signaling through SRC family kinases / negative regulation of dendritic spine maintenance / feeding behavior / Nef and signal transduction / type 5 metabotropic glutamate receptor binding / Nephrin family interactions / DCC mediated attractive signaling / dendrite morphogenesis / EPH-Ephrin signaling / CD28 dependent Vav1 pathway / Ephrin signaling / dendritic spine maintenance / Regulation of KIT signaling / tau-protein kinase activity / CTLA4 inhibitory signaling / leukocyte migration / phospholipase activator activity / Fc-gamma receptor signaling pathway involved in phagocytosis / EPHA-mediated growth cone collapse / cellular response to platelet-derived growth factor stimulus / Dectin-2 family / stimulatory C-type lectin receptor signaling pathway / PECAM1 interactions / CD28 dependent PI3K/Akt signaling / phospholipase binding / response to amyloid-beta / glial cell projection / Sema3A PAK dependent Axon repulsion / cellular response to glycine / FCGR activation / alpha-tubulin binding / EPH-ephrin mediated repulsion of cells / positive regulation of protein targeting to membrane / ephrin receptor signaling pathway / Role of LAT2/NTAL/LAB on calcium mobilization / vascular endothelial growth factor receptor signaling pathway / detection of mechanical stimulus involved in sensory perception of pain / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / regulation of peptidyl-tyrosine phosphorylation / positive regulation of tyrosine phosphorylation of STAT protein / forebrain development / negative regulation of inflammatory response to antigenic stimulus / extrinsic component of cytoplasmic side of plasma membrane / Signaling by ERBB2 / negative regulation of protein ubiquitination / GPVI-mediated activation cascade / cellular response to transforming growth factor beta stimulus / cell surface receptor protein tyrosine kinase signaling pathway / T cell costimulation / EPHB-mediated forward signaling / ephrin receptor binding / NCAM signaling for neurite out-growth / CD209 (DC-SIGN) signaling / FCGR3A-mediated IL10 synthesis / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / learning / actin filament / Regulation of signaling by CBL / Cell surface interactions at the vascular wall / FCGR3A-mediated phagocytosis / axon guidance / non-specific protein-tyrosine kinase / neuron migration / non-membrane spanning protein tyrosine kinase activity / Schaffer collateral - CA1 synapse / protein catabolic process / modulation of chemical synaptic transmission / tau protein binding / Signaling by SCF-KIT / negative regulation of protein catabolic process / VEGFA-VEGFR2 Pathway / positive regulation of neuron projection development / cellular response to hydrogen peroxide / positive regulation of protein localization to nucleus / peptidyl-tyrosine phosphorylation / cellular response to amyloid-beta / Constitutive Signaling by Aberrant PI3K in Cancer / calcium ion transport / Signaling by CSF1 (M-CSF) in myeloid cells / disordered domain specific binding Similarity search - Function | ||||||
Biological species | Homo sapiens (human) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 0.92 Å | ||||||
Model details | Fyn-SH3-SRC chimeric construction | ||||||
Authors | Camara-Artigas, A. / Plaza-Garrido, M. / Salinas-Garcia, M.C. | ||||||
Funding support | Spain, 1items
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Citation | Journal: To be published Title: Crystal structure of the Fyn SH3 domain L112V-S114N-S115T-E121L-R123H mutant in complex with VSL12 at pH 5.0 Authors: Camara-Artigas, A. / Plaza-Garrido, M. / Salinas-Garcia, M.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7a2x.cif.gz | 66.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7a2x.ent.gz | 49.1 KB | Display | PDB format |
PDBx/mmJSON format | 7a2x.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7a2x_validation.pdf.gz | 288.4 KB | Display | wwPDB validaton report |
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Full document | 7a2x_full_validation.pdf.gz | 288.4 KB | Display | |
Data in XML | 7a2x_validation.xml.gz | 6.9 KB | Display | |
Data in CIF | 7a2x_validation.cif.gz | 9.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a2/7a2x ftp://data.pdbj.org/pub/pdb/validation_reports/a2/7a2x | HTTPS FTP |
-Related structure data
Related structure data | 3ua6S 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
#1: Protein | Mass: 6787.357 Da / Num. of mol.: 1 / Fragment: SH3 domain / Mutation: L112V S114N S115T E121L R123H Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: FYN / Plasmid: pHTP1 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: P06241, non-specific protein-tyrosine kinase |
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#2: Protein/peptide | Mass: 1343.660 Da / Num. of mol.: 1 / Fragment: VSL12 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#3: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.09 Å3/Da / Density % sol: 41.23 % / Mosaicity: 0.05 ° |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: 0.5 M ammonium sulfate, 0.1 sodium acetate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.9792 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 30, 2017 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 0.92→17.66 Å / Num. obs: 46882 / % possible obs: 98.2 % / Redundancy: 22.4 % / CC1/2: 1 / Rmerge(I) obs: 0.067 / Rpim(I) all: 0.014 / Rrim(I) all: 0.069 / Net I/σ(I): 33 / Num. measured all: 1048999 / Scaling rejects: 3158 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3UA6 Resolution: 0.92→17.66 Å / SU ML: 0.07 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 12.15 / 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: 55.22 Å2 / Biso mean: 15.5553 Å2 / Biso min: 6.59 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 0.92→17.66 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 17
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