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- PDB-3eg0: Crystal structure of the N114T mutant of ABL-SH3 domain -

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Basic information

Entry
Database: PDB / ID: 3eg0
TitleCrystal structure of the N114T 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


positive regulation of actin filament binding / protein localization to cytoplasmic microtubule plus-end / DN4 thymocyte differentiation / response to epinephrine / phospholipase C-inhibiting G protein-coupled receptor signaling pathway / podocyte apoptotic process / transitional one stage B cell differentiation / delta-catenin binding / Role of ABL in ROBO-SLIT signaling / positive regulation of oxidoreductase activity ...positive regulation of actin filament binding / protein localization to cytoplasmic microtubule plus-end / DN4 thymocyte differentiation / response to epinephrine / phospholipase C-inhibiting G protein-coupled receptor signaling pathway / podocyte apoptotic process / transitional one stage B cell differentiation / delta-catenin binding / Role of ABL in ROBO-SLIT signaling / positive regulation of oxidoreductase activity / regulation of postsynaptic specialization assembly / nicotinate-nucleotide adenylyltransferase activity / regulation of modification of synaptic structure / positive regulation of microtubule binding / DNA conformation change / activation of protein kinase C activity / neuroepithelial cell differentiation / B cell proliferation involved in immune response / positive regulation of extracellular matrix organization / positive regulation of Wnt signaling pathway, planar cell polarity pathway / cerebellum morphogenesis / microspike assembly / positive regulation of blood vessel branching / B-1 B cell homeostasis / neuropilin signaling pathway / neuropilin binding / mitochondrial depolarization / negative regulation of ubiquitin-protein transferase activity / bubble DNA binding / negative regulation of protein serine/threonine kinase activity / activated T cell proliferation / cellular response to dopamine / regulation of cell motility / proline-rich region binding / regulation of Cdc42 protein signal transduction / syntaxin binding / mitogen-activated protein kinase binding / regulation of hematopoietic stem cell differentiation / myoblast proliferation / positive regulation of dendrite development / alpha-beta T cell differentiation / regulation of T cell differentiation / regulation of axon extension / cardiac muscle cell proliferation / HDR through Single Strand Annealing (SSA) / positive regulation of cell migration involved in sprouting angiogenesis / Fc-gamma receptor signaling pathway involved in phagocytosis / negative regulation of cell-cell adhesion / Myogenesis / positive regulation of osteoblast proliferation / platelet-derived growth factor receptor-beta signaling pathway / regulation of microtubule polymerization / RUNX2 regulates osteoblast differentiation / associative learning / Bergmann glial cell differentiation / regulation of endocytosis / neuromuscular process controlling balance / negative regulation of mitotic cell cycle / negative regulation of long-term synaptic potentiation / negative regulation of cellular senescence / negative regulation of BMP signaling pathway / actin monomer binding / endothelial cell migration / positive regulation of focal adhesion assembly / signal transduction in response to DNA damage / RHO GTPases Activate WASPs and WAVEs / positive regulation of T cell migration / BMP signaling pathway / regulation of cell adhesion / canonical NF-kappaB signal transduction / negative regulation of double-strand break repair via homologous recombination / mismatch repair / negative regulation of endothelial cell apoptotic process / four-way junction DNA binding / cellular response to transforming growth factor beta stimulus / spleen development / positive regulation of stress fiber assembly / peptidyl-tyrosine autophosphorylation / positive regulation of vasoconstriction / ruffle / positive regulation of establishment of T cell polarity / ephrin receptor binding / positive regulation of substrate adhesion-dependent cell spreading / phosphotyrosine residue binding / actin filament polymerization / positive regulation of endothelial cell migration / positive regulation of interleukin-2 production / ERK1 and ERK2 cascade / response to endoplasmic reticulum stress / positive regulation of mitotic cell cycle / SH2 domain binding / substrate adhesion-dependent cell spreading / positive regulation of release of sequestered calcium ion into cytosol / post-embryonic development / thymus development / regulation of autophagy / neural tube closure / integrin-mediated signaling pathway / establishment of localization in cell / regulation of actin cytoskeleton organization
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. / Src homology 2 domains ...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. / Src homology 2 domains / SH2 domain / Src homology 3 domains / SH2 domain superfamily / SH3 type barrels. / 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 / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / 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 / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 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 10, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 15, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 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 1.3Aug 30, 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: Proto-oncogene tyrosine-protein kinase ABL1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,0892
Polymers6,9971
Non-polymers921
Water30617
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.754, 49.754, 45.126
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: 6996.695 Da / Num. of mol.: 1 / Fragment: SH3 DOMAIN, RESIDUES 60-121 / Mutation: N114T
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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 17 / 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: 2.3 Å3/Da / Density % sol: 46.62 %
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: May 4, 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: 2.25→43.073 Å / Num. all: 3146 / Num. obs: 3153 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.38 % / Biso Wilson estimate: 37.169 Å2 / Rmerge(I) obs: 0.0734 / Rsym value: 0.0734
Reflection shellResolution: 2.25→2.35 Å / Redundancy: 3.48 % / Rmerge(I) obs: 0.4168 / Mean I/σ(I) obs: 3.48 / Num. unique all: 368 / Rsym value: 0.4168 / % possible all: 98.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SAINTdata scaling
MOLREPphasing
REFMAC5.2.0019refinement
PDB_EXTRACT3.006data extraction
PROTEUM PLUSdata collection
SAINTdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1ABQ

1abq


Resolution: 2.3→20 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.885 / Occupancy max: 1 / Occupancy min: 0 / SU B: 15.15 / SU ML: 0.19 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.401 / ESU R Free: 0.282 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.283 280 9.5 %RANDOM
Rwork0.221 ---
obs0.227 2942 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 43.78 Å2 / Biso mean: 17.919 Å2 / Biso min: 6.07 Å2
Baniso -1Baniso -2Baniso -3
1-1.05 Å20.53 Å20 Å2
2--1.05 Å20 Å2
3----1.58 Å2
Refinement stepCycle: LAST / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms438 0 6 17 461
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.022456
X-RAY DIFFRACTIONr_angle_refined_deg1.8181.929622
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.765557
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.57625.23821
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.3121565
X-RAY DIFFRACTIONr_dihedral_angle_4_deg7.249151
X-RAY DIFFRACTIONr_chiral_restr0.110.268
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02353
X-RAY DIFFRACTIONr_nbd_refined0.2660.2171
X-RAY DIFFRACTIONr_nbtor_refined0.3060.2305
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1780.227
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1830.225
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1370.24
X-RAY DIFFRACTIONr_mcbond_it0.5051.5288
X-RAY DIFFRACTIONr_mcangle_it0.8412450
X-RAY DIFFRACTIONr_scbond_it1.3953201
X-RAY DIFFRACTIONr_scangle_it2.1524.5172
LS refinement shellResolution: 2.3→2.359 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.446 19 -
Rwork0.31 199 -
all-218 -
obs--99.09 %
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)
17.16821.8425-7.45829.44772.760417.76990.079-0.23310.5486-0.95540.4875-0.3827-0.55551.0997-0.56650.1508-0.07420.0270.0268-0.0057-0.05686.3671-11.18016.8314
23.4273-3.574-3.3955.81150.954716.57920.10390.4707-0.0760.1835-0.38130.75810.975-0.55070.27740.08440.0064-0.0007-0.006-0.0216-0.0165-0.4979-18.84978.5962
36.73451.53230.65911.20692.90118.8836-0.1420.18950.0692-0.28450.1609-0.2711-0.51280.6838-0.01880.2873-0.02710.02220.0023-0.09610.07446.3879-14.91380.3842
44.4906-1.9371-1.17676.86633.49447.460.15070.09190.1368-0.3892-0.25380.4512-0.7038-0.3760.10310.12580.01070.0117-0.0036-0.0481-0.05812.0689-14.63572.1054
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A64 - 72
2X-RAY DIFFRACTION2A73 - 84
3X-RAY DIFFRACTION3A85 - 94
4X-RAY DIFFRACTION4A95 - 119

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