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- PDB-7a2o: Crystal structure of the Fyn SH3 domain L112V-S114N-S115T-E121L-R... -

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Basic information

Entry
Database: PDB / ID: 7a2o
TitleCrystal structure of the Fyn SH3 domain L112V-S114N-S115T-E121L-R123H mutant at pH 4.5
ComponentsTyrosine-protein kinase Fyn
KeywordsPROTEIN 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 / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion ...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 / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / regulation of glutamate receptor signaling pathway / regulation of calcium ion import across plasma membrane / Platelet Adhesion to exposed collagen / G protein-coupled glutamate receptor signaling pathway / 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 / feeding behavior / Nef and signal transduction / negative regulation of dendritic spine maintenance / 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 / 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 / glial cell projection / PECAM1 interactions / CD28 dependent PI3K/Akt signaling / phospholipase binding / response to amyloid-beta / Sema3A PAK dependent Axon repulsion / cellular response to glycine / alpha-tubulin binding / FCGR activation / 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 / forebrain development / positive regulation of tyrosine phosphorylation of STAT protein / 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 / EPHB-mediated forward signaling / T cell costimulation / NCAM signaling for neurite out-growth / CD209 (DC-SIGN) signaling / ephrin receptor binding / 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 / cell surface receptor protein tyrosine kinase signaling pathway / 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
: / 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 ...: / 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
TRIETHYLENE GLYCOL / Tyrosine-protein kinase Fyn
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 0.94 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-E121L-R123H mutant at pH 4.5
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,9382
Polymers6,7871
Non-polymers1501
Water1,53185
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area310 Å2
ΔGint5 kcal/mol
Surface area4050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)29.139, 32.127, 59.656
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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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: 6787.357 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 / Plasmid: pHTP1 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P06241, non-specific protein-tyrosine kinase
#2: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 85 / 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: 2.06 Å3/Da / Density % sol: 40.2 % / Mosaicity: 0.12 °
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 5% PEG 300, 1.5 ammonium sulfate, 0.1M sodium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97879 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 2, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97879 Å / Relative weight: 1
ReflectionResolution: 0.94→59.66 Å / Num. obs: 69035 / % possible obs: 98.8 % / Redundancy: 5.7 % / CC1/2: 0.997 / Rmerge(I) obs: 0.059 / Rpim(I) all: 0.026 / Rrim(I) all: 0.064 / Net I/σ(I): 16.4
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
0.94-0.993.70.5171818549710.750.2980.6012.592.1
2.96-59.665.90.056778813300.9950.0250.06133.199.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.5.32data scaling
PHASERphasing
PHENIX1.18.2-3874refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3UA6

3ua6


Resolution: 0.94→21.86 Å / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 0.44 / Phase error: 16.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1753 3362 4.87 %
Rwork0.151 65673 -
obs0.1522 69035 96.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 54.14 Å2 / Biso mean: 14.9456 Å2 / Biso min: 7.14 Å2
Refinement stepCycle: final / Resolution: 0.94→21.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms476 0 24 85 585
Biso mean--30.61 26.69 -
Num. residues----60
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 24

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
0.94-0.950.29611150.2791898201368
0.95-0.960.2821180.25922211232978
0.96-0.980.25111650.23232589275493
0.98-0.990.22021640.20362781294598
0.99-1.010.22891570.18422803296099
1.01-1.030.17951370.172728082945100
1.03-1.050.17551470.16128082955100
1.05-1.070.16391240.14642860298499
1.07-1.090.1651190.15112783290298
1.09-1.120.13121540.14362822297699
1.12-1.150.15831400.13872808294899
1.15-1.180.14371180.13128102928100
1.18-1.210.18021250.129728793004100
1.21-1.250.15381340.13842779291399
1.25-1.30.15941280.133428352963100
1.3-1.350.13651270.13832841296899
1.35-1.410.17621310.13542829296099
1.41-1.480.14971430.13712780292399
1.48-1.580.13251530.13522811296499
1.58-1.70.15991380.141728422980100
1.7-1.870.17681230.14992801292498
1.87-2.140.17661750.14612742291798
2.14-2.70.19481680.1622774294299
2.7-21.860.18141590.15482779293899

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