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- PDB-3egu: Crystal structure of the N114A mutant of ABL-SH3 domain -

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Basic information

Entry
Database: PDB / ID: 3egu
TitleCrystal structure of the N114A mutant of ABL-SH3 domain
ComponentsProto-oncogene tyrosine-protein kinase ABL1
KeywordsTRANSFERASE / beta / ATP-binding / Cell adhesion / Cytoskeleton / Kinase / Lipoprotein / Magnesium / Manganese / Metal-binding / Myristate / Nucleotide-binding / Nucleus / Phosphoprotein / Proto-oncogene / SH2 domain / SH3 domain / Tyrosine-protein kinase
Function / homology
Function and homology information


mitochondrial depolarization / protein localization to cytoplasmic microtubule plus-end / DNA conformation change / response to epinephrine / phospholipase C-inhibiting G protein-coupled receptor signaling pathway / negative regulation of ubiquitin-protein transferase activity / podocyte apoptotic process / regulation of postsynaptic specialization assembly / positive regulation of phospholipase C/protein kinase C signal transduction / regulation of modification of synaptic structure ...mitochondrial depolarization / protein localization to cytoplasmic microtubule plus-end / DNA conformation change / response to epinephrine / phospholipase C-inhibiting G protein-coupled receptor signaling pathway / negative regulation of ubiquitin-protein transferase activity / podocyte apoptotic process / regulation of postsynaptic specialization assembly / positive regulation of phospholipase C/protein kinase C signal transduction / regulation of modification of synaptic structure / nicotinate-nucleotide adenylyltransferase activity / delta-catenin binding / Role of ABL in ROBO-SLIT signaling / positive regulation of extracellular matrix organization / neuropilin signaling pathway / neuropilin binding / regulation of cell motility / bubble DNA binding / positive regulation of establishment of T cell polarity / regulation of T cell differentiation / cellular response to dopamine / positive regulation of blood vessel branching / proline-rich region binding / positive regulation of dendrite development / mitogen-activated protein kinase binding / regulation of Cdc42 protein signal transduction / regulation of hematopoietic stem cell differentiation / syntaxin binding / regulation of axon extension / positive regulation of cell migration involved in sprouting angiogenesis / Myogenesis / HDR through Single Strand Annealing (SSA) / platelet-derived growth factor receptor-beta signaling pathway / RUNX2 regulates osteoblast differentiation / Fc-gamma receptor signaling pathway involved in phagocytosis / vascular endothelial cell response to oscillatory fluid shear stress / myoblast proliferation / regulation of endocytosis / cardiac muscle cell proliferation / regulation of microtubule polymerization / negative regulation of long-term synaptic potentiation / associative learning / positive regulation of focal adhesion assembly / actin monomer binding / cellular response to transforming growth factor beta stimulus / ephrin receptor signaling pathway / positive regulation of vasoconstriction / regulation of cell adhesion / positive regulation of substrate adhesion-dependent cell spreading / endothelial cell migration / positive regulation of stress fiber assembly / RHO GTPases Activate WASPs and WAVEs / negative regulation of double-strand break repair via homologous recombination / positive regulation of T cell migration / mismatch repair / ephrin receptor binding / four-way junction DNA binding / ruffle / signal transduction in response to DNA damage / phosphotyrosine residue binding / actin filament polymerization / positive regulation of endothelial cell migration / SH2 domain binding / integrin-mediated signaling pathway / protein serine/threonine kinase activator activity / positive regulation of fibroblast proliferation / response to endoplasmic reticulum stress / Turbulent (oscillatory, disturbed) flow shear stress activates signaling by PIEZO1 and integrins in endothelial cells / protein kinase C binding / protein modification process / regulation of actin cytoskeleton organization / intrinsic apoptotic signaling pathway in response to DNA damage / non-specific protein-tyrosine kinase / FCGR3A-mediated phagocytosis / non-membrane spanning protein tyrosine kinase activity / regulation of autophagy / Regulation of actin dynamics for phagocytic cup formation / cellular response to hydrogen peroxide / epidermal growth factor receptor signaling pathway / enzyme activator activity / autophagy / positive regulation of neuron apoptotic process / sequence-specific double-stranded DNA binding / kinase activity / Cyclin D associated events in G1 / actin filament binding / actin cytoskeleton organization / actin cytoskeleton / manganese ion binding / mitotic cell cycle / positive regulation of cytosolic calcium ion concentration / nuclear membrane / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / Factors involved in megakaryocyte development and platelet production / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / growth cone / RUNX1 regulates transcription of genes involved in differentiation of HSCs / response to oxidative stress / protein tyrosine kinase activity / cellular response to oxidative stress
Similarity search - Function
F-actin binding / F-actin binding / F-actin binding domain (FABD) / Tyrosine-protein kinase ABL, SH2 domain / SH3 Domains / : / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / SH3 type barrels. ...F-actin binding / F-actin binding / F-actin binding domain (FABD) / Tyrosine-protein kinase ABL, SH2 domain / SH3 Domains / : / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / SH3 type barrels. / 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 / Roll / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Mainly Beta
Similarity search - Domain/homology
Tyrosine-protein kinase ABL1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2.25 Å
AuthorsCamara-Artigas, A.
Citation
Journal: J.Biol.Chem. / Year: 2010
Title: Role of interfacial water molecules in proline-rich ligand recognition by the Src homology 3 domain of Abl.
Authors: Palencia, A. / Camara-Artigas, A. / Pisabarro, M.T. / Martinez, J.C. / Luque, I.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2007
Title: Crystallization by capillary counter-diffusion and structure determination of the N114A mutant of the SH3 domain of Abl tyrosine kinase complexed with a high-affinity peptide ligand
Authors: Camara-Artigas, A. / Palencia, A. / Martinez, J.C. / Luque, I. / Gavira, J.A. / Garcia-Ruiz, J.M.
History
DepositionSep 11, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 15, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / 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
Revision 1.4Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Proto-oncogene tyrosine-protein kinase ABL1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,1553
Polymers6,9671
Non-polymers1882
Water34219
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)51.350, 51.350, 46.386
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number153
Space group name H-MP3212

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Components

#1: Protein Proto-oncogene tyrosine-protein kinase ABL1 / p150 / c- ABL / Abelson murine leukemia viral oncogene homolog 1


Mass: 6966.669 Da / Num. of mol.: 1 / Fragment: SH3 DOMAIN, RESIDUES 60-121 / Mutation: N114A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Strain: PBAT4 / Gene: ABL1, ABL, JTK7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P00519, non-specific protein-tyrosine kinase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 19 / 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: 2.53 Å3/Da / Density % sol: 51.46 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 2M ammonium sulphate, 5% PEG300, 10% glycerol, and 0.1 M of buffer solution, pH 7, vapor diffusion, hanging drop, temperature 288K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.54 Å
DetectorType: BRUKER SMART 6000 / Detector: CCD / Date: Feb 2, 2006 / Details: Montel Optics
RadiationMonochromator: BRUKER MICROSTAR MICRO-FOCUS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.15→44.47 Å / Num. all: 3938 / Num. obs: 3936 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.85 % / Biso Wilson estimate: 24.173 Å2 / Rmerge(I) obs: 0.0531 / Rsym value: 0.0531
Reflection shellResolution: 2.15→2.25 Å / Redundancy: 4.07 % / Rmerge(I) obs: 0.303 / Mean I/σ(I) obs: 3.97 / Num. unique all: 491 / Rsym value: 0.303 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
SAINTdata scaling
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.2.0019refinement
PDB_EXTRACT3.006data extraction
PROTEUM PLUSdata collection
SAINTdata reduction
SCALAdata scaling
MOLREPphasing
RefinementResolution: 2.25→13.61 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.903 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 6.721 / SU ML: 0.165 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.297 / ESU R Free: 0.233 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.267 153 4.5 %RANDOM
Rwork0.22 ---
obs0.222 3411 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 55.09 Å2 / Biso mean: 20.071 Å2 / Biso min: 5.33 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.25→13.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms443 0 11 19 473
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.022465
X-RAY DIFFRACTIONr_angle_refined_deg2.1021.946633
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.26556
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.07725.23821
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.6471567
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.775151
X-RAY DIFFRACTIONr_chiral_restr0.130.268
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02353
X-RAY DIFFRACTIONr_nbd_refined0.2450.2117
X-RAY DIFFRACTIONr_nbtor_refined0.3050.2275
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2260.213
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2340.217
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2790.24
X-RAY DIFFRACTIONr_mcbond_it2.112295
X-RAY DIFFRACTIONr_mcangle_it3.1613452
X-RAY DIFFRACTIONr_scbond_it2.0392208
X-RAY DIFFRACTIONr_scangle_it2.8983181
LS refinement shellResolution: 2.25→2.308 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.346 11 -
Rwork0.254 240 -
all-251 -
obs--100 %

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