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- PDB-10fs: Crystal Structure of Human Fgr SH3-SH2-High Affinity Linker Mutan... -

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Basic information

Entry
Database: PDB / ID: 10fs
TitleCrystal Structure of Human Fgr SH3-SH2-High Affinity Linker Mutant 1 (HAL1) Domains.
ComponentsTyrosine-protein kinase Fgr
KeywordsTRANSFERASE / FGR / SIGNALING PROTEIN / SH3 / SH2
Function / homology
Function and homology information


negative regulation of natural killer cell activation / positive regulation of mast cell degranulation / immune response-regulating cell surface receptor signaling pathway / regulation of protein kinase activity / regulation of phagocytosis / Fc-gamma receptor I complex binding / immunoglobulin receptor binding / Platelet sensitization by LDL / regulation of innate immune response / Fc-gamma receptor signaling pathway involved in phagocytosis ...negative regulation of natural killer cell activation / positive regulation of mast cell degranulation / immune response-regulating cell surface receptor signaling pathway / regulation of protein kinase activity / regulation of phagocytosis / Fc-gamma receptor I complex binding / immunoglobulin receptor binding / Platelet sensitization by LDL / regulation of innate immune response / Fc-gamma receptor signaling pathway involved in phagocytosis / FCGR activation / phosphotyrosine residue binding / peptidyl-tyrosine phosphorylation / FCGR3A-mediated IL10 synthesis / cell surface receptor protein tyrosine kinase signaling pathway / integrin-mediated signaling pathway / positive regulation of cytokine production / non-specific protein-tyrosine kinase / FCGR3A-mediated phagocytosis / negative regulation of inflammatory response to antigenic stimulus / non-membrane spanning protein tyrosine kinase activity / mitochondrial intermembrane space / ruffle membrane / response to virus / protein autophosphorylation / regulation of cell shape / actin cytoskeleton / protein tyrosine kinase activity / secretory granule lumen / protein phosphorylation / cell differentiation / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / mitochondrial inner membrane / defense response to Gram-positive bacterium / positive regulation of cell migration / signaling receptor binding / innate immune response / 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 ...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
DI(HYDROXYETHYL)ETHER / Tyrosine-protein kinase Fgr
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsAlvarado, J.J. / Gonzalez-Areizaga, G. / Smithgall, T.E.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)CA233576 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)CA291724 United States
CitationJournal: Cell Rep / Year: 2026
Title: Constraining regulatory domain dynamics of the Src kinase Fgr increases ATP-site inhibitor sensitivity and impairs bone marrow engraftment.
Authors: Gonzalez-Areizaga, G. / Shu, S.T. / Alvarado, J.J. / Shi, H. / Chen, L. / Smithgall, T.E.
History
DepositionJan 17, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 15, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tyrosine-protein kinase Fgr
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,4069
Polymers19,6411
Non-polymers7658
Water1,982110
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.443, 34.794, 61.677
Angle α, β, γ (deg.)90, 101.051, 90
Int Tables number4
Space group name H-MP1211

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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: 19641.049 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Human Fgr SH3, SH2 and Linker domains; a mutation in the linker domain has been engineered to change the wild-type residue T252 to P252. N-terminal serine residue (S83) originates from Sumo Ulp1 cleavage site.
Source: (gene. exp.) Homo sapiens (human) / Gene: FGR, SRC2 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): STAR
References: UniProt: P09769, non-specific protein-tyrosine kinase
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 110 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 2.32 Å3/Da / Density % sol: 47.1 %
Crystal growTemperature: 298.15 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 0.2 M sodium chloride, 0.1 M MES monohydrate, pH 6.0, 20% (w/v) polyethylene glycol 6,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.033 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 28, 2025 / Details: KB bent focusing mirror
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 1.3→39.12 Å / Num. obs: 45366 / % possible obs: 99 % / Redundancy: 13.4 % / CC1/2: 1 / Rmerge(I) obs: 0.068 / Rpim(I) all: 0.019 / Rrim(I) all: 0.07 / Χ2: 0.93 / Net I/σ(I): 14.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
7.12-39.1212.80.04262.33090.9980.0120.0441.3199.4
1.3-1.3213.23.5910.922170.61.0053.7320.8598.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0431 (refmacat 0.4.126)refinement
Cootmodel building
PHASERphasing
Aimlessdata scaling
xia2data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.3→39.12 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.969 / WRfactor Rfree: 0.196 / WRfactor Rwork: 0.181 / SU B: 2.776 / SU ML: 0.051 / Average fsc free: 0.9498 / Average fsc work: 0.954 / Cross valid method: FREE R-VALUE / ESU R: 0.05 / ESU R Free: 0.05
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.1979 2331 5.14 %RANDOM
Rwork0.1819 43020 --
all0.183 ---
obs-45351 98.836 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 27.609 Å2
Baniso -1Baniso -2Baniso -3
1--0.457 Å2-0 Å2-1.326 Å2
2---1.136 Å2-0 Å2
3---1.961 Å2
Refinement stepCycle: LAST / Resolution: 1.3→39.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1357 0 50 110 1517
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0121477
X-RAY DIFFRACTIONr_bond_other_d0.0060.0161349
X-RAY DIFFRACTIONr_angle_refined_deg1.91.8141994
X-RAY DIFFRACTIONr_angle_other_deg0.9791.7623125
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.5015185
X-RAY DIFFRACTIONr_dihedral_angle_2_deg12.95259
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.07910241
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.9861071
X-RAY DIFFRACTIONr_chiral_restr0.1050.2211
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021749
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02347
X-RAY DIFFRACTIONr_nbd_refined0.1770.2199
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1450.21111
X-RAY DIFFRACTIONr_nbtor_refined0.1690.2669
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0710.2769
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1080.288
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1670.213
X-RAY DIFFRACTIONr_nbd_other0.1260.250
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0890.211
X-RAY DIFFRACTIONr_mcbond_it1.6921.644704
X-RAY DIFFRACTIONr_mcbond_other1.6921.644704
X-RAY DIFFRACTIONr_mcangle_it2.5772.952883
X-RAY DIFFRACTIONr_mcangle_other2.5762.962884
X-RAY DIFFRACTIONr_scbond_it2.8991.986773
X-RAY DIFFRACTIONr_scbond_other2.8971.991774
X-RAY DIFFRACTIONr_scangle_it4.1673.4221105
X-RAY DIFFRACTIONr_scangle_other4.1653.4271106
X-RAY DIFFRACTIONr_lrange_it7.31917.8911550
X-RAY DIFFRACTIONr_lrange_other7.2917.5191534
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.3-1.3340.3561580.32731890.32833880.8630.87498.78980.338
1.334-1.370.2941650.330420.29932410.8950.89798.95090.306
1.37-1.410.2911850.29329840.29331990.9120.90999.06220.291
1.41-1.4530.2831490.2629480.26131230.9260.9399.16750.255
1.453-1.5010.251640.23727750.23729950.9350.94698.13020.225
1.501-1.5530.241490.2226880.22129080.9550.95597.55850.205
1.553-1.6120.2051300.20626640.20628120.9570.96699.35990.191
1.612-1.6780.231350.18725440.1926980.9640.97399.29580.175
1.678-1.7520.191390.18124570.18126160.970.97899.23550.165
1.752-1.8370.181030.16723740.16724910.9780.98199.4380.154
1.837-1.9370.2011120.16722340.16923660.9780.98299.15470.156
1.937-2.0540.1841180.15520350.15722220.9830.98596.89470.148
2.054-2.1950.1811120.16519800.16621140.980.98598.95930.16
2.195-2.370.1961110.17118540.17219780.9780.98399.34280.167
2.37-2.5960.2151060.1716980.17318110.9780.98299.61350.168
2.596-2.9010.154940.16815470.16716530.9850.98299.2740.171
2.901-3.3460.17840.15713750.15814630.9820.98599.72660.163
3.346-4.0910.169510.15911390.15912460.9860.98495.50560.174
4.091-5.7540.213470.1759390.1779860.980.9841000.195
5.754-39.120.247190.2425540.2425730.9790.9651000.266
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)
12.61680.16420.09793.533-0.46842.62680.071-0.02740.0793-0.0135-0.10550.1897-0.0002-0.12720.03450.00850.0024-0.00720.0118-0.01230.02415.8908-2.477-0.4526
23.75160.51870.98323.09180.56551.88950.030.0647-0.02150.0438-0.04820.20330.05-0.10280.01820.0482-0.019-0.02320.06110.00840.02854.5609-14.955221.637
30.1169-0.71180.05135.7291-0.47910.0456-0.0099-0.00250.04010.16150.04250.0108-0.0252-0.0105-0.03260.1849-0.00050.0090.1967-0.00350.18844.3262-7.0080.4151
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLA83 - 146
2X-RAY DIFFRACTION2ALLA147 - 246
3X-RAY DIFFRACTION3ALLA247 - 254

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