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- PDB-4u17: Swapped dimer of the human Fyn-SH2 domain -

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Basic information

Entry
Database: PDB / ID: 4u17
TitleSwapped dimer of the human Fyn-SH2 domain
ComponentsTyrosine-protein kinase Fyn
KeywordsTRANSFERASE / human Fyn-SH2 domain / domain swapping
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 / Activated NTRK2 signals through FYN / reelin-mediated signaling pathway / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / 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 / Activated NTRK2 signals through FYN / reelin-mediated signaling pathway / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / regulation of calcium ion import across plasma membrane / Platelet Adhesion to exposed collagen / cellular response to L-glutamate / FLT3 signaling through SRC family kinases / CRMPs in Sema3A signaling / G protein-coupled glutamate receptor signaling pathway / heart process / CD4 receptor binding / feeding behavior / positive regulation of protein localization to membrane / Nef and signal transduction / Co-stimulation by CD28 / natural killer cell activation / EPH-Ephrin signaling / DCC mediated attractive signaling / Nephrin family interactions / type 5 metabotropic glutamate receptor binding / CD28 dependent Vav1 pathway / Ephrin signaling / dendritic spine maintenance / negative regulation of dendritic spine maintenance / leukocyte migration / Regulation of KIT signaling / growth factor receptor binding / cellular response to peptide hormone stimulus / phospholipase activator activity / tau-protein kinase activity / Co-inhibition by CTLA4 / EPHA-mediated growth cone collapse / negative regulation of T cell activation / Dectin-2 family / stimulatory C-type lectin receptor signaling pathway / peptide hormone receptor binding / Fc-gamma receptor signaling pathway involved in phagocytosis / 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 / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / vascular endothelial growth factor receptor signaling pathway / ephrin receptor signaling pathway / cellular response to glycine / positive regulation of protein targeting to membrane / CD28 dependent PI3K/Akt signaling / negative regulation of T cell receptor signaling pathway / glial cell projection / T cell costimulation / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / alpha-tubulin binding / ephrin receptor binding / postsynaptic density, intracellular component / phosphatidylinositol 3-kinase binding / GPVI-mediated activation cascade / T cell receptor binding / phospholipase binding / Signaling by ERBB2 / negative regulation of angiogenesis / EPHB-mediated forward signaling / peptidyl-tyrosine phosphorylation / NCAM signaling for neurite out-growth / CD209 (DC-SIGN) signaling / FCGR3A-mediated IL10 synthesis / axon guidance / learning / cell surface receptor protein tyrosine kinase signaling pathway / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / Cell surface interactions at the vascular wall / non-specific protein-tyrosine kinase / FCGR3A-mediated phagocytosis / response to cocaine / actin filament / negative regulation of inflammatory response to antigenic stimulus / non-membrane spanning protein tyrosine kinase activity / Regulation of signaling by CBL / Signaling by SCF-KIT / cellular response to growth factor stimulus / VEGFA-VEGFR2 Pathway / G protein-coupled receptor binding / Degradation of CDH1 / modulation of chemical synaptic transmission / cellular response to hydrogen peroxide / tau protein binding / Schaffer collateral - CA1 synapse / T cell receptor signaling pathway / cellular response to amyloid-beta / Constitutive Signaling by Aberrant PI3K in Cancer / calcium ion transport
Similarity search - Function
: / Fyn/Yrk, SH3 domain / SH2 domain / SHC Adaptor Protein / : / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain ...: / Fyn/Yrk, SH3 domain / SH2 domain / SHC Adaptor Protein / : / 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 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Tyrosine-protein kinase Fyn
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 Å
AuthorsGarcia-Pino, A. / Huculeci, R. / Lenaerts, T. / van Nuland, N.A.J.
CitationJournal: To Be Published
Title: Swapped dimer of the human Fyn-SH2 domain
Authors: Garcia-Pino, A. / Huculeci, R. / Lenaerts, T. / van Nuland, N.A.J.
History
DepositionJul 15, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jul 29, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,61214
Polymers36,6993
Non-polymers91311
Water2,720151
1
A: Tyrosine-protein kinase Fyn
C: Tyrosine-protein kinase Fyn
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,12710
Polymers24,4662
Non-polymers6618
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6620 Å2
ΔGint-71 kcal/mol
Surface area11250 Å2
MethodPISA
2
B: Tyrosine-protein kinase Fyn
hetero molecules

B: Tyrosine-protein kinase Fyn
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,9708
Polymers24,4662
Non-polymers5046
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area6260 Å2
ΔGint-70 kcal/mol
Surface area10750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.965, 57.873, 101.188
Angle α, β, γ (deg.)90.00, 90.60, 90.00
Int Tables number5
Space group name H-MC121

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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: 12232.927 Da / Num. of mol.: 3 / Fragment: Fyn-SH2 domain (UNP residues 148-248)
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: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: PO4
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 151 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.55 Å3/Da / Density % sol: 65.34 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 50 mM sodium phosphate pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9801 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 4, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 1.99→34.92 Å / Num. obs: 35049 / % possible obs: 98.66 % / Redundancy: 3.6 % / Rsym value: 0.081 / Net I/σ(I): 7.7
Reflection shellResolution: 1.99→2.1 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.303 / Mean I/σ(I) obs: 3.2 / % possible all: 98.9

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
iMOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1G83

1g83


Resolution: 1.99→34.916 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 31.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2554 1743 4.98 %Random selection
Rwork0.2068 ---
obs0.2093 34985 98.48 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.99→34.916 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2434 0 51 151 2636
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0122539
X-RAY DIFFRACTIONf_angle_d1.4133424
X-RAY DIFFRACTIONf_dihedral_angle_d15.607900
X-RAY DIFFRACTIONf_chiral_restr0.057353
X-RAY DIFFRACTIONf_plane_restr0.006433
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9895-2.04810.32981440.312624X-RAY DIFFRACTION94
2.0481-2.11420.35451470.29592779X-RAY DIFFRACTION99
2.1142-2.18970.30341260.27082759X-RAY DIFFRACTION99
2.1897-2.27740.311400.25492773X-RAY DIFFRACTION99
2.2774-2.3810.29851370.25542789X-RAY DIFFRACTION99
2.381-2.50650.2661270.24232801X-RAY DIFFRACTION99
2.5065-2.66350.31681500.24212794X-RAY DIFFRACTION99
2.6635-2.8690.31091710.2332740X-RAY DIFFRACTION99
2.869-3.15760.29971560.23022764X-RAY DIFFRACTION99
3.1576-3.61410.25711570.18592782X-RAY DIFFRACTION99
3.6141-4.55180.19451470.16662769X-RAY DIFFRACTION98
4.5518-34.92120.22151410.1832868X-RAY DIFFRACTION98
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.8941.28972.95168.166-3.03024.86470.3612-1.1157-0.97730.6195-0.75620.18040.78331.2021-0.15650.69480.06190.06790.55410.1450.457517.3157-10.886943.8886
22.0522-0.62120.70176.10470.96858.11150.03930.1935-0.25340.1465-0.0626-0.28660.36390.6839-0.0060.2743-0.0793-0.02210.4955-0.02060.321517.4158-6.421332.9794
32.485-0.80681.16296.4456-2.68737.06940.227-0.52810.0898-0.1931-0.05990.01370.0039-0.55-0.20750.4106-0.1975-0.00960.5555-0.03690.26124.567814.372430.3981
43.5487-1.0726-3.39773.3312.06069.20050.1949-0.40380.3531-0.1373-0.0122-0.2719-0.19010.6205-0.21160.5688-0.0760.03830.33960.00220.284818.1148-3.30921.6035
55.0522-4.6725-4.89339.4227.7258.13060.45060.55030.4933-0.6236-0.2511-0.6718-0.2881-0.6577-0.27180.59950.0523-0.02280.30910.01320.313211.7031-0.7616-0.3356
65.98732.53576.3073.22192.32017.79290.19890.2851-0.10070.01270.2066-0.0490.32750.1585-0.49390.42530.00450.02680.60040.01620.26081.00831.29410.6794
77.89953.72940.55756.0309-2.11826.4172-0.51610.3648-0.7623-0.25160.2786-0.30361.24790.64450.30850.68540.13160.05230.4216-0.0170.3165-11.2054-9.6449-7.0086
84.5738-1.41021.28125.70052.5965.2139-0.098-0.23480.4977-0.2230.1772-0.4835-1.26420.2368-0.0020.5321-0.1041-0.01990.3203-0.06090.34430.22924.601232.2444
90.5022-0.6993-0.71512.7401-1.07913.42380.4991-0.43430.00220.5903-0.34590.0475-0.87820.2369-0.04760.6179-0.2316-0.0580.5076-0.00450.313420.12793.737637.4098
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 11:19)
2X-RAY DIFFRACTION2chain 'A' and (resseq 20:71)
3X-RAY DIFFRACTION3chain 'A' and (resseq 72:112)
4X-RAY DIFFRACTION4chain 'B' and (resseq 11:60)
5X-RAY DIFFRACTION5chain 'B' and (resseq 61:71)
6X-RAY DIFFRACTION6chain 'B' and (resseq 72:87)
7X-RAY DIFFRACTION7chain 'B' and (resseq 88:112)
8X-RAY DIFFRACTION8chain 'C' and (resseq 10:71)
9X-RAY DIFFRACTION9chain 'C' and (resseq 72:112)

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