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- PDB-7jt9: Fgr SH3 domain crystal structure -

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Basic information

Entry
Database: PDB / ID: 7jt9
TitleFgr SH3 domain crystal structure
ComponentsTyrosine-protein kinase Fgr
KeywordsONCOPROTEIN / Src Family Kinase / SH3 domain
Function / homology
Function and homology information


immune response-regulating cell surface receptor signaling pathway / negative regulation of natural killer cell activation / positive regulation of mast cell degranulation / Fc-gamma receptor I complex binding / regulation of phagocytosis / aggresome / regulation of protein kinase activity / skeletal system morphogenesis / myoblast proliferation / Platelet sensitization by LDL ...immune response-regulating cell surface receptor signaling pathway / negative regulation of natural killer cell activation / positive regulation of mast cell degranulation / Fc-gamma receptor I complex binding / regulation of phagocytosis / aggresome / regulation of protein kinase activity / skeletal system morphogenesis / myoblast proliferation / Platelet sensitization by LDL / Fc-gamma receptor signaling pathway involved in phagocytosis / regulation of innate immune response / bone mineralization / FCGR activation / negative regulation of inflammatory response to antigenic stimulus / extrinsic component of cytoplasmic side of plasma membrane / immunoglobulin receptor binding / cell surface receptor protein tyrosine kinase signaling pathway / phosphotyrosine residue binding / FCGR3A-mediated IL10 synthesis / positive regulation of cytokine production / integrin-mediated signaling pathway / FCGR3A-mediated phagocytosis / non-specific protein-tyrosine kinase / non-membrane spanning protein tyrosine kinase activity / response to virus / mitochondrial intermembrane space / ruffle membrane / peptidyl-tyrosine phosphorylation / actin cytoskeleton / regulation of cell shape / protein tyrosine kinase activity / secretory granule lumen / protein autophosphorylation / mitochondrial inner membrane / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / cell differentiation / defense response to Gram-positive bacterium / positive regulation of cell migration / protein phosphorylation / innate immune response / signaling receptor binding / Neutrophil degranulation / protein kinase binding / extracellular exosome / extracellular region / ATP binding / plasma membrane / cytosol
Similarity search - Function
Tyrosine-protein kinase Fgr, SH2 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. ...Tyrosine-protein kinase Fgr, SH2 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
Tyrosine-protein kinase Fgr
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 Å
AuthorsPerez, I. / Berndt, S. / Gurevich, V.V. / Iverson, T.M.
Funding support United States, 5items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM120569 United States
National Institutes of Health/National Institute on Drug Abuse (NIH/NIDA)R21 DA043680 United States
National Institutes of Health/National Eye Institute (NIH/NEI)R01 EY011500 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 GM122491 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)2T32GM008320-31 United States
CitationJournal: J.Mol.Biol. / Year: 2022
Title: A Model for the Signal Initiation Complex Between Arrestin-3 and the Src Family Kinase Fgr.
Authors: Perez, I. / Berndt, S. / Agarwal, R. / Castro, M.A. / Vishnivetskiy, S.A. / Smith, J.C. / Sanders, C.R. / Gurevich, V.V. / Iverson, T.M.
History
DepositionAug 17, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 26, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: 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 Fgr


Theoretical massNumber of molelcules
Total (without water)8,1521
Polymers8,1521
Non-polymers00
Water50428
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area5100 Å2
Unit cell
Length a, b, c (Å)35.553, 53.287, 67.483
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-228-

HOH

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Components

#1: Protein Tyrosine-protein kinase Fgr / Gardner-Rasheed feline sarcoma viral (v-fgr) oncogene homolog / Proto-oncogene c-Fgr / p55-Fgr / ...Gardner-Rasheed feline sarcoma viral (v-fgr) oncogene homolog / Proto-oncogene c-Fgr / p55-Fgr / p58-Fgr / p58c-Fgr


Mass: 8151.982 Da / Num. of mol.: 1 / Fragment: SH3 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FGR, SRC2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P09769
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 28 / 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: 1.96 Å3/Da / Density % sol: 37.26 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.1 M Sodium citrate tribasic, 0.1 M citric acid, 40% (v/v) PEG 600

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 19, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.93→50 Å / Num. obs: 4945 / % possible obs: 97.5 % / Redundancy: 4.6 % / CC1/2: 1 / Rmerge(I) obs: 0.092 / Net I/σ(I): 15.875
Reflection shellResolution: 1.93→1.96 Å / Rmerge(I) obs: 0.468 / Num. unique obs: 227 / CC1/2: 0.778

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2HDA

2hda


Resolution: 1.93→33.74 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 21.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2172 495 10.01 %
Rwork0.1863 4450 -
obs0.1894 4945 97.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 65.68 Å2 / Biso mean: 27.7945 Å2 / Biso min: 15.85 Å2
Refinement stepCycle: final / Resolution: 1.93→33.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms565 0 0 28 593
Biso mean---37.39 -
Num. residues----71
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 (%)
1.93-2.130.23291180.19841067118596
2.13-2.430.22091220.19461090121298
2.43-3.060.24161230.20421108123198
3.07-33.740.20231320.17391185131799

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