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- PDB-7a2s: Crystal structure of the Fyn SH3 domain L112V-S114N-S115T-E121L-R... -

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Basic information

Entry
Database: PDB / ID: 7a2s
TitleCrystal structure of the Fyn SH3 domain L112V-S114N-S115T-E121L-R123H mutant at pH 5.0
ComponentsTyrosine-protein kinase Fyn
KeywordsPROTEIN BINDING / 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 / growth factor receptor binding / heart process / regulation of glutamate receptor signaling pathway / Activated NTRK2 signals through FYN / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion ...negative regulation of hydrogen peroxide biosynthetic process / response to singlet oxygen / Reelin signalling pathway / perinuclear endoplasmic reticulum / NTRK2 activates RAC1 / growth factor receptor binding / heart process / regulation of glutamate receptor signaling pathway / Activated NTRK2 signals through FYN / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / regulation of calcium ion import across plasma membrane / reelin-mediated signaling pathway / Platelet Adhesion to exposed collagen / positive regulation of protein localization to membrane / cellular response to L-glutamate / G protein-coupled glutamate receptor signaling pathway / CRMPs in Sema3A signaling / activated T cell proliferation / FLT3 signaling through SRC family kinases / type 5 metabotropic glutamate receptor binding / Nef and signal transduction / negative regulation of dendritic spine maintenance / feeding behavior / Co-stimulation by CD28 / Nephrin family interactions / natural killer cell activation / DCC mediated attractive signaling / EPH-Ephrin signaling / Ephrin signaling / dendritic spine maintenance / CD28 dependent Vav1 pathway / dendrite morphogenesis / tau-protein kinase activity / Regulation of KIT signaling / leukocyte migration / phospholipase activator activity / Co-inhibition by CTLA4 / EPHA-mediated growth cone collapse / Dectin-2 family / stimulatory C-type lectin receptor signaling pathway / Fc-gamma receptor signaling pathway involved in phagocytosis / phospholipase binding / PECAM1 interactions / response to amyloid-beta / cellular response to glycine / FCGR activation / Sema3A PAK dependent Axon repulsion / glial cell projection / positive regulation of protein targeting to membrane / EPH-ephrin mediated repulsion of cells / ephrin receptor signaling pathway / CD28 dependent PI3K/Akt signaling / Role of LAT2/NTAL/LAB on calcium mobilization / alpha-tubulin binding / 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 / forebrain development / cellular response to transforming growth factor beta stimulus / GPVI-mediated activation cascade / cellular response to platelet-derived growth factor stimulus / ephrin receptor binding / T cell costimulation / Signaling by ERBB2 / EPHB-mediated forward signaling / negative regulation of protein ubiquitination / NCAM signaling for neurite out-growth / CD209 (DC-SIGN) signaling / FCGR3A-mediated IL10 synthesis / axon guidance / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / cell surface receptor protein tyrosine kinase signaling pathway / negative regulation of angiogenesis / learning / Cell surface interactions at the vascular wall / actin filament / non-membrane spanning protein tyrosine kinase activity / FCGR3A-mediated phagocytosis / Regulation of signaling by CBL / non-specific protein-tyrosine kinase / negative regulation of inflammatory response to antigenic stimulus / G protein-coupled receptor binding / modulation of chemical synaptic transmission / protein catabolic process / Signaling by SCF-KIT / Schaffer collateral - CA1 synapse / peptidyl-tyrosine phosphorylation / negative regulation of protein catabolic process / positive regulation of neuron projection development / positive regulation of protein localization to nucleus / tau protein binding / VEGFA-VEGFR2 Pathway / cellular response to hydrogen peroxide / cellular response to amyloid-beta / neuron migration / Signaling by CSF1 (M-CSF) in myeloid cells / calcium ion transport / Constitutive Signaling by Aberrant PI3K in Cancer / disordered domain specific binding
Similarity search - Function
: / Fyn/Yrk, SH3 domain / : / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / SH2 domain superfamily / Src homology 3 domains ...: / Fyn/Yrk, SH3 domain / : / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / SH2 domain superfamily / Src homology 3 domains / 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 / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / 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: 1.02 Å
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 L112V-S114N-S115T-E121L-R123H mutant at pH 5.0
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


Theoretical massNumber of molelcules
Total (without water)6,9311
Polymers6,9311
Non-polymers00
Water2,108117
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area4030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)28.134, 32.365, 60.196
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab

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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: 6931.487 Da / Num. of mol.: 1 / Mutation: L112V S114N S115T E121L R123H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FYN / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P06241, non-specific protein-tyrosine kinase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 117 / Source method: isolated from a natural source / Formula: H2O

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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: 1.98 Å3/Da / Density % sol: 37.78 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: 2.0 ammonium sulfate, 0.1M sodium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.966 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Aug 22, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.966 Å / Relative weight: 1
ReflectionResolution: 1.02→17.35 Å / Num. obs: 52930 / % possible obs: 97.9 % / Redundancy: 4.6 % / Biso Wilson estimate: 9.66 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.041 / Rpim(I) all: 0.021 / Rrim(I) all: 0.047 / Net I/σ(I): 15.5
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
1.02-1.043.30.45387711900.7970.2760.5322.285.1
5.59-17.354.40.0389152080.9970.0210.04345.196.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
Aimless0.7.4data scaling
PHASERphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3UA6

3ua6


Resolution: 1.02→17.35 Å / SU ML: 0.0843 / Cross valid method: FREE R-VALUE / σ(F): 0.22 / Phase error: 17.7212
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1748 2558 4.83 %
Rwork0.1593 50371 -
obs0.16 52929 97.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 12.53 Å2
Refinement stepCycle: LAST / Resolution: 1.02→17.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms477 0 0 117 594
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0078521
X-RAY DIFFRACTIONf_angle_d1.0429716
X-RAY DIFFRACTIONf_chiral_restr0.077777
X-RAY DIFFRACTIONf_plane_restr0.006393
X-RAY DIFFRACTIONf_dihedral_angle_d14.6085179
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.02-1.040.27271460.26092422X-RAY DIFFRACTION85.32
1.04-1.060.20891230.21512719X-RAY DIFFRACTION95.95
1.06-1.080.20231670.18592887X-RAY DIFFRACTION99.58
1.08-1.110.20171290.16232813X-RAY DIFFRACTION99.9
1.11-1.140.14961170.15392894X-RAY DIFFRACTION99.34
1.14-1.170.17541480.142816X-RAY DIFFRACTION99.1
1.17-1.20.16081290.15022848X-RAY DIFFRACTION98.9
1.2-1.240.15251120.14482862X-RAY DIFFRACTION99.23
1.24-1.280.16831480.14132860X-RAY DIFFRACTION99.57
1.29-1.340.17751360.15562868X-RAY DIFFRACTION99.7
1.34-1.40.18021400.14562836X-RAY DIFFRACTION99.67
1.4-1.470.19611370.14562894X-RAY DIFFRACTION99.51
1.47-1.560.16271650.14252769X-RAY DIFFRACTION98.85
1.56-1.680.17791490.14852839X-RAY DIFFRACTION99.6
1.68-1.850.16081520.15182851X-RAY DIFFRACTION99.87
1.85-2.120.13181560.15752502X-RAY DIFFRACTION88.9
2.12-2.670.20061370.16812860X-RAY DIFFRACTION99.3
2.67-17.350.17851670.16482831X-RAY DIFFRACTION99.63

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