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- PDB-7a2n: Crystal structure of the Fyn SH3 domain A95S-D99T mutant in space... -

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Basic information

Entry
Database: PDB / ID: 7a2n
TitleCrystal structure of the Fyn SH3 domain A95S-D99T mutant in space group P21
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 / heart process / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / Activated NTRK2 signals through FYN / 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 / heart process / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / Activated NTRK2 signals through FYN / regulation of calcium ion import across plasma membrane / Platelet Adhesion to exposed collagen / reelin-mediated signaling pathway / CRMPs in Sema3A signaling / FLT3 signaling through SRC family kinases / G protein-coupled glutamate receptor signaling pathway / activated T cell proliferation / CD4 receptor binding / feeding behavior / positive regulation of protein localization to membrane / Nef and signal transduction / Co-stimulation by CD28 / EPH-Ephrin signaling / natural killer cell activation / DCC mediated attractive signaling / cellular response to L-glutamate / Nephrin family interactions / type 5 metabotropic glutamate receptor binding / CD28 dependent Vav1 pathway / Ephrin signaling / negative regulation of dendritic spine maintenance / dendritic spine maintenance / leukocyte migration / Regulation of KIT signaling / growth factor receptor binding / cellular response to peptide hormone stimulus / phospholipase activator activity / EPHA-mediated growth cone collapse / tau-protein kinase activity / Co-inhibition by CTLA4 / dendrite morphogenesis / Dectin-2 family / negative regulation of T cell activation / peptide hormone receptor binding / stimulatory C-type lectin receptor signaling pathway / Fc-gamma receptor signaling pathway involved in phagocytosis / forebrain development / 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 / CD28 dependent PI3K/Akt signaling / cellular response to glycine / vascular endothelial growth factor receptor signaling pathway / ephrin receptor signaling pathway / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / negative regulation of T cell receptor signaling pathway / positive regulation of protein targeting to membrane / cellular response to transforming growth factor beta stimulus / glial cell projection / detection of mechanical stimulus involved in sensory perception of pain / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / alpha-tubulin binding / phosphatidylinositol 3-kinase binding / postsynaptic density, intracellular component / ephrin receptor binding / GPVI-mediated activation cascade / phospholipase binding / T cell costimulation / T cell receptor binding / cellular response to platelet-derived growth factor stimulus / Signaling by ERBB2 / peptidyl-tyrosine phosphorylation / EPHB-mediated forward signaling / negative regulation of protein ubiquitination / NCAM signaling for neurite out-growth / CD209 (DC-SIGN) signaling / FCGR3A-mediated IL10 synthesis / cell surface receptor protein tyrosine kinase signaling pathway / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / negative regulation of angiogenesis / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / axon guidance / Cell surface interactions at the vascular wall / protein catabolic process / learning / FCGR3A-mediated phagocytosis / non-specific protein-tyrosine kinase / actin filament / response to cocaine / Regulation of signaling by CBL / negative regulation of inflammatory response to antigenic stimulus / non-membrane spanning protein tyrosine kinase activity / Signaling by SCF-KIT / positive regulation of neuron projection development / negative regulation of protein catabolic process / G protein-coupled receptor binding / Degradation of CDH1
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
FORMIC ACID / Tyrosine-protein kinase Fyn
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.4 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 A95S-D99T mutant in space group P21
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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)27,88025
Polymers27,1894
Non-polymers69021
Water4,378243
1
A: Tyrosine-protein kinase Fyn
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,9356
Polymers6,7971
Non-polymers1385
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Tyrosine-protein kinase Fyn
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,9355
Polymers6,7971
Non-polymers1384
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Tyrosine-protein kinase Fyn
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,0047
Polymers6,7971
Non-polymers2076
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Tyrosine-protein kinase Fyn
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,0047
Polymers6,7971
Non-polymers2076
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.176, 47.795, 73.089
Angle α, β, γ (deg.)90.000, 98.350, 90.000
Int Tables number4
Space group name H-MP1211

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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: 6797.352 Da / Num. of mol.: 4 / Mutation: A95S D99T
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-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: CH2O2
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 243 / 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: 2.68 Å3/Da / Density % sol: 54.12 % / Mosaicity: 0.12 °
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4 / Details: 4.5 M sodium formate, 0.1 sodium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.976251 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 11, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976251 Å / Relative weight: 1
ReflectionResolution: 1.4→19.94 Å / Num. obs: 104035 / % possible obs: 98.8 % / Redundancy: 3.4 % / CC1/2: 0.998 / Rmerge(I) obs: 0.08 / Rpim(I) all: 0.049 / Rrim(I) all: 0.094 / Net I/σ(I): 8.5
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
1.4-1.423.50.845975227960.6670.5240.9991.499.6
7.67-19.943.30.04211753590.9980.0260.052193.6

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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: 1.4→19.94 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.97 / Phase error: 21.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2035 5413 5.2 %
Rwork0.1698 98622 -
obs0.1715 104035 93.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 50.57 Å2 / Biso mean: 18.4293 Å2 / Biso min: 9.17 Å2
Refinement stepCycle: final / Resolution: 1.4→19.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1880 0 57 243 2180
Biso mean--24.29 29.82 -
Num. residues----235
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.4-1.420.36722120.3033331354395
1.42-1.430.28181960.28293302349895
1.43-1.450.2971850.27043406359194
1.45-1.470.29331650.25483208337394
1.47-1.490.29651660.24563323348993
1.49-1.510.28921840.23973241342592
1.51-1.530.25131740.22963120329489
1.53-1.550.24731750.21773303347893
1.55-1.580.26031630.22853205336893
1.58-1.60.27631860.22123266345292
1.6-1.630.23212050.2193227343293
1.63-1.660.23051340.20093202333691
1.66-1.690.26171790.20193241342091
1.69-1.730.23261690.19993203337291
1.73-1.760.22822040.19433159336389
1.76-1.80.20711790.19353061324089
1.8-1.850.21372020.16983373357596
1.85-1.90.17981890.16153368355796
1.9-1.960.20991910.1543310350196
1.96-2.020.16811850.14763410359597
2.02-2.090.18011970.13643382357996
2.09-2.170.21141730.13833370354395
2.17-2.270.20291660.14363298346493
2.27-2.390.16091740.1513325349995
2.39-2.540.21131660.16723412357896
2.54-2.740.2032040.17583359356396
2.74-3.010.21132200.17063311353194
3.01-3.450.16441620.14973272343493
3.45-4.330.14021390.12253308344793
4.34-19.940.18781690.1663326349594

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