+Open data
-Basic information
Entry | Database: PDB / ID: 6ipz | ||||||
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Title | Fyn SH3 domain R96W mutant, crystallized with 18-crown-6 | ||||||
Components | Tyrosine-protein kinase Fyn | ||||||
Keywords | PROTEIN BINDING / kinase / SH3 domain / 18-crown-6 / crown ether | ||||||
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 / Activated NTRK2 signals through FYN / heart process / cellular response to L-glutamate / growth factor receptor binding / 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 / Activated NTRK2 signals through FYN / heart process / cellular response to L-glutamate / growth factor receptor binding / regulation of glutamate receptor signaling pathway / regulation of calcium ion import across plasma membrane / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / Platelet Adhesion to exposed collagen / CD28 co-stimulation / G protein-coupled glutamate receptor signaling pathway / 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 / type 5 metabotropic glutamate receptor binding / Nef and signal transduction / Nephrin family interactions / DCC mediated attractive signaling / EPH-Ephrin signaling / dendrite morphogenesis / CD28 dependent Vav1 pathway / Ephrin signaling / dendritic spine maintenance / Regulation of KIT signaling / tau-protein kinase activity / CTLA4 inhibitory signaling / phospholipase activator activity / leukocyte migration / 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 / FCGR activation / cellular response to glycine / alpha-tubulin binding / positive regulation of protein targeting to membrane / EPH-ephrin mediated repulsion of cells / 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 / Signaling by ERBB2 / cell surface receptor protein tyrosine kinase signaling pathway / negative regulation of inflammatory response to antigenic stimulus / GPVI-mediated activation cascade / negative regulation of protein ubiquitination / cellular response to transforming growth factor beta stimulus / T cell costimulation / EPHB-mediated forward signaling / ephrin receptor binding / CD209 (DC-SIGN) signaling / NCAM signaling for neurite out-growth / 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 / axon guidance / actin filament / Regulation of signaling by CBL / Cell surface interactions at the vascular wall / FCGR3A-mediated phagocytosis / non-specific protein-tyrosine kinase / neuron migration / non-membrane spanning protein tyrosine kinase activity / modulation of chemical synaptic transmission / tau protein binding / protein catabolic process / Signaling by SCF-KIT / Schaffer collateral - CA1 synapse / negative regulation of protein catabolic process / VEGFA-VEGFR2 Pathway / positive regulation of neuron projection development / positive regulation of protein localization to nucleus / cellular response to hydrogen peroxide / peptidyl-tyrosine phosphorylation / cellular response to amyloid-beta / Signaling by CSF1 (M-CSF) in myeloid cells / Constitutive Signaling by Aberrant PI3K in Cancer / disordered domain specific binding / calcium ion transport / DAP12 signaling Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.576 Å | ||||||
Authors | Arold, S.T. / Aljedani, S.S. / Shahul Hameed, U.F. | ||||||
Funding support | Saudi Arabia, 1items
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Citation | Journal: Biochem.J. / Year: 2021 Title: Synergy and allostery in ligand binding by HIV-1 Nef. Authors: Aldehaiman, A. / Momin, A.A. / Restouin, A. / Wang, L. / Shi, X. / Aljedani, S. / Opi, S. / Lugari, A. / Shahul Hameed, U.F. / Ponchon, L. / Morelli, X. / Huang, M. / Dumas, C. / Collette, Y. / Arold, S.T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ipz.cif.gz | 53.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ipz.ent.gz | 38.8 KB | Display | PDB format |
PDBx/mmJSON format | 6ipz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ip/6ipz ftp://data.pdbj.org/pub/pdb/validation_reports/ip/6ipz | HTTPS FTP |
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-Related structure data
Related structure data | 3h0fSC 3h0hC 3h0iC 4d8dC 6ipyC 7d7sC S: Starting model for refinement C: citing same article (ref.) |
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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 on special symmetry positions |
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-Components
#1: Protein | Mass: 7849.575 Da / Num. of mol.: 1 / Fragment: UNP residues 82-144 / Mutation: R96W Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: FYN / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 References: UniProt: P06241, non-specific protein-tyrosine kinase | ||
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#2: Chemical | #3: 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: 2.22 Å3/Da / Density % sol: 44.62 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 4.6 Details: 0.08M Sodium acetate trihydrate pH 4.6, 1.6M Ammonium sulfate, 20%(v/v) Glycerol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.98 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Oct 5, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.576→36.536 Å / Num. obs: 10112 / % possible obs: 99.83 % / Redundancy: 25.6 % / Biso Wilson estimate: 34.14 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.06273 / Rpim(I) all: 0.01267 / Rrim(I) all: 0.06403 / Net I/σ(I): 29.66 |
Reflection shell | Resolution: 1.576→1.633 Å / Redundancy: 24.9 % / Rmerge(I) obs: 2.542 / Mean I/σ(I) obs: 0.91 / Num. unique obs: 988 / CC1/2: 0.565 / Rpim(I) all: 0.5147 / Rrim(I) all: 2.595 / % possible all: 98.38 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3H0F Resolution: 1.576→36.536 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 28.45
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 113.96 Å2 / Biso mean: 49.1487 Å2 / Biso min: 27.37 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.576→36.536 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 4
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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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