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- PDB-3bkb: Crystal structure of human Feline Sarcoma Viral Oncogene Homologu... -

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Basic information

Entry
Database: PDB / ID: 3bkb
TitleCrystal structure of human Feline Sarcoma Viral Oncogene Homologue (v-FES)
ComponentsProto-oncogene tyrosine-protein kinase Fes/Fps
KeywordsTRANSFERASE / FES / v-fes / Fujinami / avian sarcoma / viral / oncogene / feline sarcoma virus / SGC / Structural Genomics Consortium / ATP-binding / Kinase / Nucleotide-binding / Phosphoprotein / Proto-oncogene / SH2 domain / Tyrosine-protein kinase
Function / homology
Function and homology information


positive regulation of myeloid cell differentiation / regulation of mast cell degranulation / regulation of vesicle-mediated transport / cellular response to vitamin D / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / CRMPs in Sema3A signaling / microtubule bundle formation / positive regulation of monocyte differentiation / regulation of cell motility / centrosome cycle ...positive regulation of myeloid cell differentiation / regulation of mast cell degranulation / regulation of vesicle-mediated transport / cellular response to vitamin D / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / CRMPs in Sema3A signaling / microtubule bundle formation / positive regulation of monocyte differentiation / regulation of cell motility / centrosome cycle / myoblast proliferation / cardiac muscle cell proliferation / regulation of cell differentiation / immunoglobulin receptor binding / Sema3A PAK dependent Axon repulsion / regulation of cell adhesion / positive regulation of microtubule polymerization / phosphatidylinositol binding / non-specific protein-tyrosine kinase / non-membrane spanning protein tyrosine kinase activity / Signaling by SCF-KIT / positive regulation of neuron projection development / peptidyl-tyrosine phosphorylation / cytoplasmic side of plasma membrane / chemotaxis / microtubule cytoskeleton / regulation of cell population proliferation / regulation of cell shape / cytoplasmic vesicle / microtubule binding / protein tyrosine kinase activity / protein autophosphorylation / cell adhesion / focal adhesion / Golgi apparatus / ATP binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Tyrosine-protein kinase, Fes/Fps type / Fes/Fps/Fer, SH2 domain / Fes/CIP4, and EFC/F-BAR homology domain / Fes/CIP4 homology domain / FCH domain / F-BAR domain / F-BAR domain profile. / AH/BAR domain superfamily / SH2 domain / SHC Adaptor Protein ...Tyrosine-protein kinase, Fes/Fps type / Fes/Fps/Fer, SH2 domain / Fes/CIP4, and EFC/F-BAR homology domain / Fes/CIP4 homology domain / FCH domain / F-BAR domain / F-BAR domain profile. / AH/BAR domain superfamily / SH2 domain / SHC Adaptor Protein / : / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / SH2 domain superfamily / 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 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / 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 / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
STAUROSPORINE / Tyrosine-protein kinase Fes/Fps
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.78 Å
AuthorsFilippakopoulos, P. / Salah, E. / Fedorov, O. / Cooper, C. / Ugochukwu, E. / Pike, A.C.W. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Weigelt, J. ...Filippakopoulos, P. / Salah, E. / Fedorov, O. / Cooper, C. / Ugochukwu, E. / Pike, A.C.W. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Weigelt, J. / Knapp, S. / Structural Genomics Consortium (SGC)
CitationJournal: Cell(Cambridge,Mass.) / Year: 2008
Title: Structural Coupling of SH2-Kinase Domains Links Fes and Abl Substrate Recognition and Kinase Activation
Authors: Filippakopoulos, P. / Kofler, M. / Hantschel, O. / Gish, G.D. / Grebien, F. / Salah, E. / Neudecker, P. / Kay, L.E. / Turk, B.E. / Superti-Furga, G. / Pawson, T. / Knapp, S.
History
DepositionDec 6, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 25, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Proto-oncogene tyrosine-protein kinase Fes/Fps
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,00913
Polymers42,7581
Non-polymers1,25112
Water6,990388
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)80.404, 80.404, 131.411
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63
Components on special symmetry positions
IDModelComponents
11A-1-

SO4

21A-1-

SO4

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Components

#1: Protein Proto-oncogene tyrosine-protein kinase Fes/Fps / C-Fes


Mass: 42758.043 Da / Num. of mol.: 1 / Fragment: Residues 448-822
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FES, FPS / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)(R3)
References: UniProt: P07332, non-specific protein-tyrosine kinase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-STU / STAUROSPORINE


Mass: 466.531 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C28H26N4O3 / Comment: anticancer, antifungal, antibiotic, alkaloid*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 388 / 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: 2.87 Å3/Da / Density % sol: 57.11 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2M Na2SO4, 0.1M Bis-Tris-Propane, 20% PEG 3350, 10% Ethylene glycol, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.98074 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 20, 2007
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98074 Å / Relative weight: 1
ReflectionRedundancy: 14.1 % / Av σ(I) over netI: 4.4 / Number: 648377 / Rmerge(I) obs: 0.128 / Rsym value: 0.128 / D res high: 1.731 Å / D res low: 69.673 Å / Num. obs: 46019 / % possible obs: 100
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsRsym valueRedundancy
5.6369.6799.810.0610.06116.9
3.985.6310010.0770.07717.4
3.253.9810010.0910.09117.4
2.813.2510010.1060.10617.4
2.522.8110010.1560.15617.4
2.32.5210010.2240.22417.3
2.132.310010.320.3217.2
1.992.1310010.3860.38613.2
1.881.9910010.5230.5239.8
1.781.8810010.7870.7875.9
ReflectionResolution: 1.78→43.81 Å / Num. all: 46019 / Num. obs: 46019 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 14.1 % / Rmerge(I) obs: 0.128 / Rsym value: 0.128 / Net I/σ(I): 18.7
Reflection shellResolution: 1.78→1.88 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.787 / Mean I/σ(I) obs: 2 / Num. unique all: 6704 / Rsym value: 0.787 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å40.2 Å
Translation2 Å40.2 Å

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.004data extraction
CrystalCleardata collection
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: An ensemble of three kinase domains from the PDB entries 2HYY, 2G2I, 2G2H

2hyy

2g2i

2g2h


Resolution: 1.78→43.81 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.955 / SU B: 3.693 / SU ML: 0.063 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.091 / ESU R Free: 0.096 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.189 2312 5 %RANDOM
Rwork0.148 ---
all0.15 45977 --
obs0.15 45977 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.662 Å2
Baniso -1Baniso -2Baniso -3
1-0.39 Å20.19 Å20 Å2
2--0.39 Å20 Å2
3----0.58 Å2
Refinement stepCycle: LAST / Resolution: 1.78→43.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2927 0 82 388 3397
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_refined_d0.016
X-RAY DIFFRACTIONr_bond_other_d0.001
X-RAY DIFFRACTIONr_angle_refined_deg1.532
X-RAY DIFFRACTIONr_angle_other_deg1.118
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.941
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.042
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.098
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.284
X-RAY DIFFRACTIONr_chiral_restr0.105
X-RAY DIFFRACTIONr_gen_planes_refined0.006
X-RAY DIFFRACTIONr_gen_planes_other0.001
X-RAY DIFFRACTIONr_nbd_refined0.204
X-RAY DIFFRACTIONr_nbd_other0.202
X-RAY DIFFRACTIONr_nbtor_refined0.177
X-RAY DIFFRACTIONr_nbtor_other0.085
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.158
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.078
X-RAY DIFFRACTIONr_symmetry_vdw_other0.265
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.178
X-RAY DIFFRACTIONr_mcbond_it3.545
X-RAY DIFFRACTIONr_mcbond_other0.942
X-RAY DIFFRACTIONr_mcangle_it
LS refinement shellResolution: 1.78→1.826 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.318 153 -
Rwork0.22 3209 -
all-3362 -
obs--99.12 %
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)
11.82560.45880.35041.69210.36465.39050.0064-0.04-0.0305-0.0194-0.1026-0.06840.1125-0.03020.0962-0.0950.001-0.0469-0.07320.0138-0.065816.86434.29120.538
20.48020.20660.0381.0903-0.00731.0345-0.05410.02390.0464-0.07410.03420.1087-0.0867-0.01560.0199-0.15520.0012-0.0112-0.126-0.0094-0.056913.05131.09548.826
31.1786-0.3829-0.27931.42010.15881.0393-0.0201-0.0941-0.10910.16-0.01320.13870.0964-0.02330.0333-0.138-0.0140.0196-0.14680.0073-0.066119.04312.46162.168
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA449 - 5504 - 105
2X-RAY DIFFRACTION2AA551 - 650106 - 205
3X-RAY DIFFRACTION3AA651 - 821206 - 376

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