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- PDB-7a2j: Crystal structure of the Fyn SH3 domain in space group C21 at pH 7.5 -

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Basic information

Entry
Database: PDB / ID: 7a2j
TitleCrystal structure of the Fyn SH3 domain in space group C21 at pH 7.5
ComponentsTyrosine-protein kinase Fyn
KeywordsPROTEIN BINDING / beta barrel / SH3 domain
Function / homology
Function and homology information


negative regulation of hydrogen peroxide biosynthetic process / response to singlet oxygen / Reelin signalling pathway / perinuclear endoplasmic reticulum / NTRK2 activates RAC1 / regulation of glutamate receptor signaling pathway / Activated NTRK2 signals through FYN / reelin-mediated signaling pathway / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / regulation of calcium ion import across plasma membrane ...negative regulation of hydrogen peroxide biosynthetic process / response to singlet oxygen / Reelin signalling pathway / perinuclear endoplasmic reticulum / NTRK2 activates RAC1 / regulation of glutamate receptor signaling pathway / Activated NTRK2 signals through FYN / reelin-mediated signaling pathway / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / regulation of calcium ion import across plasma membrane / Platelet Adhesion to exposed collagen / cellular response to L-glutamate / FLT3 signaling through SRC family kinases / CRMPs in Sema3A signaling / G protein-coupled glutamate receptor signaling pathway / heart process / CD4 receptor binding / feeding behavior / positive regulation of protein localization to membrane / Nef and signal transduction / Co-stimulation by CD28 / natural killer cell activation / EPH-Ephrin signaling / DCC mediated attractive signaling / Nephrin family interactions / type 5 metabotropic glutamate receptor binding / CD28 dependent Vav1 pathway / Ephrin signaling / dendritic spine maintenance / negative regulation of dendritic spine maintenance / leukocyte migration / Regulation of KIT signaling / growth factor receptor binding / cellular response to peptide hormone stimulus / phospholipase activator activity / tau-protein kinase activity / Co-inhibition by CTLA4 / EPHA-mediated growth cone collapse / negative regulation of T cell activation / Dectin-2 family / stimulatory C-type lectin receptor signaling pathway / peptide hormone receptor binding / Fc-gamma receptor signaling pathway involved in phagocytosis / PECAM1 interactions / CD8 receptor binding / response to amyloid-beta / FCGR activation / Sema3A PAK dependent Axon repulsion / EPH-ephrin mediated repulsion of cells / Role of LAT2/NTAL/LAB on calcium mobilization / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / vascular endothelial growth factor receptor signaling pathway / ephrin receptor signaling pathway / cellular response to glycine / positive regulation of protein targeting to membrane / negative regulation of T cell receptor signaling pathway / CD28 dependent PI3K/Akt signaling / glial cell projection / T cell costimulation / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / alpha-tubulin binding / ephrin receptor binding / postsynaptic density, intracellular component / phosphatidylinositol 3-kinase binding / GPVI-mediated activation cascade / T cell receptor binding / phospholipase binding / Signaling by ERBB2 / negative regulation of angiogenesis / EPHB-mediated forward signaling / peptidyl-tyrosine phosphorylation / NCAM signaling for neurite out-growth / CD209 (DC-SIGN) signaling / FCGR3A-mediated IL10 synthesis / axon guidance / learning / cell surface receptor protein tyrosine kinase signaling pathway / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / Cell surface interactions at the vascular wall / non-specific protein-tyrosine kinase / FCGR3A-mediated phagocytosis / response to cocaine / actin filament / negative regulation of inflammatory response to antigenic stimulus / non-membrane spanning protein tyrosine kinase activity / Regulation of signaling by CBL / Signaling by SCF-KIT / cellular response to growth factor stimulus / VEGFA-VEGFR2 Pathway / G protein-coupled receptor binding / Degradation of CDH1 / modulation of chemical synaptic transmission / cellular response to hydrogen peroxide / tau protein binding / Schaffer collateral - CA1 synapse / T cell receptor signaling pathway / cellular response to amyloid-beta / Constitutive Signaling by Aberrant PI3K in Cancer / calcium ion transport
Similarity search - Function
: / Fyn/Yrk, SH3 domain / : / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / Src homology 3 domains / SH2 domain superfamily ...: / Fyn/Yrk, SH3 domain / : / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / Src homology 3 domains / SH2 domain superfamily / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / Tyrosine-protein kinase, active site / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Tyrosine-protein kinase Fyn
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.5 Å
Model detailsC21 structure
AuthorsCamara-Artigas, A. / Plaza-Garrido, M. / Salinas-Garcia, M.C.
Funding support Spain, 1items
OrganizationGrant numberCountry
Spanish Ministry of Economy and CompetitivenessBIO2016-78020-R Spain
CitationJournal: To be published
Title: Crystal structure of the Fyn SH3 domain in space group C21 at pH 7.5
Authors: Camara-Artigas, A. / Plaza-Garrido, M. / Salinas-Garcia, M.C.
History
DepositionAug 18, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 25, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tyrosine-protein kinase Fyn
B: Tyrosine-protein kinase Fyn
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,6143
Polymers13,5912
Non-polymers231
Water1,40578
1
A: Tyrosine-protein kinase Fyn
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,8182
Polymers6,7951
Non-polymers231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Tyrosine-protein kinase Fyn


Theoretical massNumber of molelcules
Total (without water)6,7951
Polymers6,7951
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.011, 46.747, 42.818
Angle α, β, γ (deg.)90.000, 97.840, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-317-

HOH

21B-241-

HOH

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Components

#1: Protein Tyrosine-protein kinase Fyn / Proto-oncogene Syn / Proto-oncogene c-Fyn / Src-like kinase / SLK / p59-Fyn


Mass: 6795.336 Da / Num. of mol.: 2
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
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 78 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.66 Å3/Da / Density % sol: 53.81 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 4.5M sodium formate, 0.1M Hepes

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97879 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 14, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97879 Å / Relative weight: 1
ReflectionResolution: 1.5→19.63 Å / Num. obs: 22756 / % possible obs: 99.2 % / Redundancy: 3.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.028 / Rpim(I) all: 0.018 / Rrim(I) all: 0.033 / Net I/σ(I): 17.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.5-1.533.40.482376911010.9310.3030.5712.298.4
8.22-19.633.30.024551390.9990.0130.02448.691.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.7.4data scaling
PHASERphasing
PHENIX1.18.2-3874refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3UA6

3ua6


Resolution: 1.5→19.63 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 0.01 / Phase error: 37.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2466 2179 5.1 %
Rwork0.2121 40524 -
obs0.2138 22756 95.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 127.14 Å2 / Biso mean: 46.7575 Å2 / Biso min: 26.92 Å2
Refinement stepCycle: final / Resolution: 1.5→19.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms924 0 1 78 1003
Biso mean--68 45 -
Num. residues----116
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 16

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5-1.530.37921000.39872504260493
1.53-1.570.37031550.37282466262194
1.57-1.610.36381350.36022512264793
1.61-1.650.38891270.32432514264194
1.65-1.70.29681340.3142460259494
1.7-1.750.37311790.30132520269996
1.75-1.820.31771490.28832519266895
1.82-1.890.29461380.27792546268495
1.89-1.980.36421540.2522535268994
1.98-2.080.26691260.22932516264295
2.08-2.210.24361450.21982546269196
2.21-2.380.27191310.22062600273197
2.38-2.620.26131440.24122520266496
2.62-30.29271260.23282597272397
3-3.770.23241080.19282585269396
3.77-19.630.16621280.15122584271296

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