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- PDB-7a2w: Crystal structure of the Fyn SH3 domain L112V-S114N-S115T-E121L-R... -

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Basic information

Entry
Database: PDB / ID: 7a2w
TitleCrystal structure of the Fyn SH3 domain L112V-S114N-S115T-E121L-R123H mutant in complex with VSL12 at pH 3.0
Components
  • Tyrosine-protein kinase Fyn
  • VSL12
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
CITRIC ACID / Tyrosine-protein kinase Fyn
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 0.99 Å
Model detailsFyn-SH3-SRC 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 in complex with VSL12 at pH 3.0
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
Revision 1.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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: VSL12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,3803
Polymers8,1882
Non-polymers1921
Water2,144119
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1370 Å2
ΔGint-7 kcal/mol
Surface area4960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)32.905, 32.884, 62.796
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: 6844.409 Da / Num. of mol.: 1 / Fragment: SH3 domain / 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: Protein/peptide VSL12


Mass: 1343.660 Da / Num. of mol.: 1 / Fragment: VSL12 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 119 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 2.07 Å3/Da / Density % sol: 40.6 % / Mosaicity: 0.1 °
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 3 / Details: 0.5 M ammonium sulfate, 0.1 sodium citrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 30, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 0.99→18.69 Å / Num. obs: 71263 / % possible obs: 99.9 % / Redundancy: 13.9 % / CC1/2: 0.996 / Rmerge(I) obs: 0.082 / Rpim(I) all: 0.023 / Rrim(I) all: 0.086 / Net I/σ(I): 19.6
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
0.99-1.0413.50.5257443455150.9460.1470.5462.999.5
3.13-18.6913.40.0691829913680.9920.020.07260.599.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.5.31data scaling
PHASERphasing
PHENIX1.17.1-3660refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3UA6

3ua6


Resolution: 0.99→18.69 Å / SU ML: 0.08 / Cross valid method: THROUGHOUT / σ(F): 0.16 / Phase error: 13.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1515 3454 4.85 %
Rwork0.1312 67809 -
obs0.1322 71263 97.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 50.81 Å2 / Biso mean: 15.3726 Å2 / Biso min: 7.25 Å2
Refinement stepCycle: final / Resolution: 0.99→18.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms582 0 18 119 719
Biso mean--13.55 25.42 -
Num. residues----74
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 25

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
0.99-10.21241030.2252631273495
1-1.020.22551810.19942772295399
1.02-1.030.25671230.18542752287598
1.03-1.050.23861420.16552723286598
1.05-1.070.16311330.1522794292799
1.07-1.080.15241190.14062766288599
1.08-1.10.13931250.12872775290099
1.1-1.130.13561170.118628572974100
1.13-1.150.13411100.121427912901100
1.15-1.170.12781530.11252734288799
1.17-1.20.12371640.114927592923100
1.2-1.230.14471330.1112781291499
1.23-1.260.10961270.113428532980100
1.26-1.30.12631240.112927632887100
1.3-1.340.13991840.110127442928100
1.34-1.390.13981590.116427642923100
1.39-1.450.13721620.11252796295899
1.45-1.510.14341480.107527292877100
1.51-1.590.13621480.11092761290999
1.59-1.690.12381590.10962754291399
1.69-1.820.15191330.12442746287997
1.82-2.010.14711180.12412374249286
2.01-2.30.13751190.13352242236180
2.3-2.890.1281190.15642554267392
2.89-18.690.19121510.13952594274593

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