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- PDB-4jjb: Crystal structure of the Abl-SH3 domain at pH3 -

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Basic information

Entry
Database: PDB / ID: 4jjb
TitleCrystal structure of the Abl-SH3 domain at pH3
ComponentsTyrosine-protein kinase ABL1
KeywordsTRANSFERASE / beta shandwich / SH3 DOMAIN / KINASE / POLY PROLINE RICH MOTIFS
Function / homology
Function and homology information


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 ...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 / mitochondrial depolarization / 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 / 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 / regulation of T cell differentiation / 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 / negative regulation of long-term synaptic potentiation / regulation of microtubule polymerization / associative learning / cardiac muscle cell proliferation / positive regulation of focal adhesion assembly / actin monomer binding / ephrin receptor signaling pathway / cellular response to transforming growth factor beta stimulus / positive regulation of vasoconstriction / regulation of cell adhesion / endothelial cell migration / 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 / positive regulation of stress fiber assembly / four-way junction DNA binding / ruffle / signal transduction in response to DNA damage / phosphotyrosine residue binding / positive regulation of substrate adhesion-dependent cell spreading / actin filament polymerization / positive regulation of endothelial cell migration / integrin-mediated signaling pathway / SH2 domain binding / 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 autophagy / protein serine/threonine kinase activator activity / regulation of actin cytoskeleton organization / non-specific protein-tyrosine kinase / FCGR3A-mediated phagocytosis / non-membrane spanning protein tyrosine kinase activity / Regulation of actin dynamics for phagocytic cup formation / intrinsic apoptotic signaling pathway in response to DNA damage / positive regulation of fibroblast proliferation / cellular response to hydrogen peroxide / epidermal growth factor receptor signaling pathway / enzyme activator activity / autophagy / sequence-specific double-stranded DNA binding / kinase activity / Cyclin D associated events in G1 / actin filament binding / actin cytoskeleton / positive regulation of neuron apoptotic process / manganese ion binding / mitotic cell cycle / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / positive regulation of cytosolic calcium ion concentration / 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 / nuclear membrane / RUNX1 regulates transcription of genes involved in differentiation of HSCs / cellular response to oxidative stress / actin cytoskeleton organization / protein tyrosine kinase activity / 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
DI(HYDROXYETHYL)ETHER / Tyrosine-protein kinase ABL1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.65 Å
AuthorsCamara-Artigas, A. / Martin-Garcia, J.M.
Citation
Journal: To be Published
Title: Crystal structure of the Abl-SH3 domain at pH3
Authors: Camara-Artigas, A. / Martin-Garcia, J.M.
#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.
#2: 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.
History
DepositionMar 7, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 12, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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

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Assembly

Deposited unit
A: Tyrosine-protein kinase ABL1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,3184
Polymers7,0101
Non-polymers3083
Water63135
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.470, 50.470, 45.120
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number153
Space group name H-MP3212
Components on special symmetry positions
IDModelComponents
11A-302-

HOH

21A-325-

HOH

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Components

#1: Protein Tyrosine-protein kinase ABL1 / PROTO-ONCOGENE TYROSINE-PROTEIN KINASE ABL1 / Abelson murine leukemia viral oncogene homolog 1 / ...PROTO-ONCOGENE TYROSINE-PROTEIN KINASE ABL1 / Abelson murine leukemia viral oncogene homolog 1 / Abelson tyrosine-protein kinase 1 / Proto-oncogene c-Abl / p150


Mass: 7009.694 Da / Num. of mol.: 1 / Fragment: SH3 domain, UNP residues 60-121
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ABL, ABL1, JTK7 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P00519, non-specific protein-tyrosine kinase
#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 35 / 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: 2.37 Å3/Da / Density % sol: 48.03 % / Mosaicity: 0.46 °
Crystal growTemperature: 298 K / Method: capillary counterdiffusion / pH: 3
Details: 3M ammonium sulphate, 5% PEG 200, 0.05M glycine, capillary counterdiffusion, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.97 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 26, 2010 / Details: TORODIAL FOCUSING MIRROR
RadiationMonochromator: CHANNEL CUT ESRF MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.65→43.708 Å / Num. all: 7859 / Num. obs: 7859 / % possible obs: 97.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.1 % / Biso Wilson estimate: 17.3 Å2 / Rmerge(I) obs: 0.139 / Rsym value: 0.139 / Net I/σ(I): 7.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allDiffraction-ID% possible all
1.65-1.745.30.1414.81131196.9
5.22-19.674.30.1579.3237187.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.3.16data scaling
PHASERphasing
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.11data extraction
ADSCQuantumdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3EG3

3eg3


Resolution: 1.65→16.52 Å / Occupancy max: 1 / Occupancy min: 0 / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Phase error: 25.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2247 363 4.62 %RANDOM
Rwork0.1648 ---
all0.1675 8055 --
obs0.1675 7854 97.5 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 80.48 Å2 / Biso mean: 25.1 Å2 / Biso min: 5.93 Å2
Refinement stepCycle: LAST / Resolution: 1.65→16.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms447 0 19 35 501
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009478
X-RAY DIFFRACTIONf_angle_d1.071647
X-RAY DIFFRACTIONf_chiral_restr0.0668
X-RAY DIFFRACTIONf_plane_restr0.00582
X-RAY DIFFRACTIONf_dihedral_angle_d12.927169
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 3

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection allNum. reflection obs% reflection obs (%)
1.65-1.890.21491180.12524402558244097
1.89-2.380.17921240.167425012625250198
2.38-16.520.25011210.173225502671255098

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