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- PDB-7a2v: Crystal structure of the Fyn SH3 domain L112V-S114N-S115T-E129Q a... -

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Basic information

Entry
Database: PDB / ID: 7a2v
TitleCrystal structure of the Fyn SH3 domain L112V-S114N-S115T-E129Q at pH 4.0
ComponentsTyrosine-protein kinase Fyn
KeywordsPROTEIN BINDING / beta barrel / SH3 domain
Function / homology
Function and homology information


response to singlet oxygen / negative regulation of hydrogen peroxide biosynthetic process / Reelin signalling pathway / perinuclear endoplasmic reticulum / NTRK2 activates RAC1 / heart process / Activated NTRK2 signals through FYN / growth factor receptor binding / positive regulation of cysteine-type endopeptidase activity / regulation of glutamate receptor signaling pathway ...response to singlet oxygen / negative regulation of hydrogen peroxide biosynthetic process / Reelin signalling pathway / perinuclear endoplasmic reticulum / NTRK2 activates RAC1 / heart process / Activated NTRK2 signals through FYN / growth factor receptor binding / positive regulation of cysteine-type endopeptidase activity / regulation of glutamate receptor signaling pathway / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / regulation of calcium ion import across plasma membrane / negative regulation of dendritic spine maintenance / Platelet Adhesion to exposed collagen / CD28 co-stimulation / cellular response to L-glutamate / G protein-coupled glutamate receptor signaling pathway / FLT3 signaling through SRC family kinases / CRMPs in Sema3A signaling / positive regulation of protein localization to membrane / activated T cell proliferation / Nef and signal transduction / type 5 metabotropic glutamate receptor binding / feeding behavior / Nephrin family interactions / DCC mediated attractive signaling / EPH-Ephrin signaling / CD28 dependent Vav1 pathway / Ephrin signaling / dendrite morphogenesis / dendritic spine maintenance / Fc-gamma receptor signaling pathway involved in phagocytosis / Regulation of KIT signaling / leukocyte migration / CTLA4 inhibitory signaling / tau-protein kinase activity / phospholipase activator activity / EPHA-mediated growth cone collapse / Dectin-2 family / stimulatory C-type lectin receptor signaling pathway / cellular response to platelet-derived growth factor stimulus / PECAM1 interactions / response to amyloid-beta / CD28 dependent PI3K/Akt signaling / phospholipase binding / glial cell projection / Sema3A PAK dependent Axon repulsion / FCGR activation / cellular response to glycine / positive regulation of protein targeting to membrane / EPH-ephrin mediated repulsion of cells / ephrin receptor signaling pathway / alpha-tubulin binding / detection of mechanical stimulus involved in sensory perception of pain / Role of LAT2/NTAL/LAB on calcium mobilization / vascular endothelial growth factor receptor signaling pathway / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / cell surface receptor protein tyrosine kinase signaling pathway / regulation of peptidyl-tyrosine phosphorylation / positive regulation of tyrosine phosphorylation of STAT protein / cellular response to transforming growth factor beta stimulus / forebrain development / Signaling by ERBB2 / GPVI-mediated activation cascade / negative regulation of protein ubiquitination / 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 / Regulation of signaling by CBL / actin filament / negative regulation of inflammatory response to antigenic stimulus / Cell surface interactions at the vascular wall / non-specific protein-tyrosine kinase / FCGR3A-mediated phagocytosis / non-membrane spanning protein tyrosine kinase activity / neuron migration / modulation of chemical synaptic transmission / protein catabolic process / tau protein binding / Signaling by SCF-KIT / negative regulation of protein catabolic process / Schaffer collateral - CA1 synapse / VEGFA-VEGFR2 Pathway / positive regulation of neuron projection development / peptidyl-tyrosine phosphorylation / positive regulation of protein localization to nucleus / cellular response to hydrogen peroxide / Signaling by CSF1 (M-CSF) in myeloid cells / Constitutive Signaling by Aberrant PI3K in Cancer / cellular response to amyloid-beta / calcium ion transport / disordered domain specific binding / PIP3 activates AKT signaling
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 / 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: 1.81 Å
Model detailsFyn-SH3-RT chimeric construction
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-E129Q at pH 4.0
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)6,8211
Polymers6,8211
Non-polymers00
Water66737
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)45.542, 45.542, 58.595
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61

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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: 6821.375 Da / Num. of mol.: 1 / Mutation: L112V S114N S115T E129Q
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 37 / 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: 2.57 Å3/Da / Density % sol: 52.17 % / Mosaicity: 0.09 °
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4 / Details: 1.5 M ammonium sulfate, 0.1 sodium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 14, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.81→19.72 Å / Num. obs: 11188 / % possible obs: 92.9 % / Redundancy: 10.8 % / CC1/2: 0.998 / Rmerge(I) obs: 0.119 / Rpim(I) all: 0.037 / Rrim(I) all: 0.125 / Net I/σ(I): 13.6
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
1.81-1.856.80.91623453440.5940.3740.9942.594
9.05-19.7210.80.07453420.9990.0220.07430.275.9

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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: 1.81→19.72 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.93 / Phase error: 29.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2195 531 4.75 %
Rwork0.2111 10657 -
obs0.2117 11188 90.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 106.98 Å2 / Biso mean: 33.253 Å2 / Biso min: 15.54 Å2
Refinement stepCycle: final / Resolution: 1.81→19.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms484 0 0 37 521
Biso mean---41.34 -
Num. residues----60
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.81-1.990.31451680.30572848301698
1.99-2.280.25391250.23632906303198
2.28-2.870.21961410.20822694283592
2.87-19.720.1761970.17712209230675

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