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- PDB-4j9i: Crystal structure of the ABL-SH3 domain complexed with the design... -

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Basic information

Entry
Database: PDB / ID: 4j9i
TitleCrystal structure of the ABL-SH3 domain complexed with the designed high-affinity peptide ligand P17
Components
  • P17
  • Tyrosine-protein kinase ABL1
KeywordsTransferase/unknown function / beta shandwich / SH3 domain / kinase / poly proline rich motifs / Transferase-unknown function complex
Function / homology
Function and homology information


: / positive regulation of actin filament binding / negative regulation of ubiquitin-protein transferase activity / protein localization to cytoplasmic microtubule plus-end / DNA conformation change / DN4 thymocyte differentiation / response to epinephrine / activation of protein kinase C activity / phospholipase C-inhibiting G protein-coupled receptor signaling pathway / podocyte apoptotic process ...: / positive regulation of actin filament binding / negative regulation of ubiquitin-protein transferase activity / protein localization to cytoplasmic microtubule plus-end / DNA conformation change / DN4 thymocyte differentiation / response to epinephrine / activation of protein kinase C activity / phospholipase C-inhibiting G protein-coupled receptor signaling pathway / podocyte apoptotic process / delta-catenin binding / Role of ABL in ROBO-SLIT signaling / transitional one stage B cell differentiation / regulation of postsynaptic specialization assembly / regulation of modification of synaptic structure / nicotinate-nucleotide adenylyltransferase activity / cerebellum morphogenesis / 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 / microspike assembly / B-1 B cell homeostasis / neuropilin signaling pathway / neuropilin binding / bubble DNA binding / mitochondrial depolarization / regulation of cell motility / positive regulation of establishment of T cell polarity / activated T cell proliferation / cellular response to dopamine / positive regulation of blood vessel branching / proline-rich region binding / negative regulation of mitotic cell cycle / regulation of Cdc42 protein signal transduction / mitogen-activated protein kinase binding / regulation of hematopoietic stem cell differentiation / syntaxin binding / positive regulation of dendrite development / alpha-beta T cell differentiation / positive regulation of cell migration involved in sprouting angiogenesis / peptidyl-tyrosine autophosphorylation / regulation of axon extension / regulation of T cell differentiation / positive regulation of peptidyl-tyrosine phosphorylation / negative regulation of cell-cell adhesion / neuromuscular process controlling balance / HDR through Single Strand Annealing (SSA) / Myogenesis / positive regulation of osteoblast proliferation / platelet-derived growth factor receptor-beta signaling pathway / RUNX2 regulates osteoblast differentiation / positive regulation of vasoconstriction / Fc-gamma receptor signaling pathway involved in phagocytosis / vascular endothelial cell response to oscillatory fluid shear stress / regulation of endocytosis / Bergmann glial cell differentiation / regulation of microtubule polymerization / negative regulation of long-term synaptic potentiation / myoblast proliferation / associative learning / negative regulation of cellular senescence / actin monomer binding / signal transduction in response to DNA damage / positive regulation of focal adhesion assembly / canonical NF-kappaB signal transduction / negative regulation of BMP signaling pathway / RHO GTPases Activate WASPs and WAVEs / ephrin receptor signaling pathway / cardiac muscle cell proliferation / positive regulation of T cell migration / BMP signaling pathway / cellular response to transforming growth factor beta stimulus / endothelial cell migration / negative regulation of endothelial cell apoptotic process / negative regulation of double-strand break repair via homologous recombination / regulation of cell adhesion / mismatch repair / ephrin receptor binding / spleen development / four-way junction DNA binding / positive regulation of stress fiber assembly / ruffle / ERK1 and ERK2 cascade / phosphotyrosine residue binding / actin filament polymerization / positive regulation of substrate adhesion-dependent cell spreading / positive regulation of endothelial cell migration / positive regulation of interleukin-2 production / substrate adhesion-dependent cell spreading / positive regulation of mitotic cell cycle / SH2 domain binding / protein kinase C binding / peptidyl-tyrosine phosphorylation / response to endoplasmic reticulum stress / thymus development / Turbulent (oscillatory, disturbed) flow shear stress activates signaling by PIEZO1 and integrins in endothelial cells / positive regulation of release of sequestered calcium ion into cytosol / integrin-mediated signaling pathway / post-embryonic development
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 / SH3 type barrels. / 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 / 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: 2.2 Å
AuthorsCamara-Artigas, A.
Citation
Journal: To be Published
Title: Crystal structure of the ABL-SH3 domain complexed with the designed high-affinity peptide ligand P17
Authors: Camara-Artigas, A.
#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
DepositionFeb 16, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 29, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 20, 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_conn / 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_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tyrosine-protein kinase ABL1
B: P17
C: Tyrosine-protein kinase ABL1
D: P17
E: Tyrosine-protein kinase ABL1
F: P17
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,4098
Polymers24,2256
Non-polymers1842
Water1,24369
1
A: Tyrosine-protein kinase ABL1
B: P17


Theoretical massNumber of molelcules
Total (without water)8,0752
Polymers8,0752
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1180 Å2
ΔGint-8 kcal/mol
Surface area4050 Å2
MethodPISA
2
C: Tyrosine-protein kinase ABL1
D: P17


Theoretical massNumber of molelcules
Total (without water)8,0752
Polymers8,0752
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1150 Å2
ΔGint-8 kcal/mol
Surface area4140 Å2
MethodPISA
3
E: Tyrosine-protein kinase ABL1
F: P17
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,2594
Polymers8,0752
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1440 Å2
ΔGint-8 kcal/mol
Surface area4170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.029, 88.029, 45.801
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-202-

HOH

21A-204-

HOH

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Components

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


Mass: 7009.694 Da / Num. of mol.: 3 / Fragment: SH3 domain (unp residues 60-121)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Strain: PBAT4 / Gene: ABL, ABL1, JTK7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P00519, non-specific protein-tyrosine kinase
#2: Protein/peptide P17


Mass: 1065.218 Da / Num. of mol.: 3 / Source method: obtained synthetically
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 69 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.11 Å3/Da / Density % sol: 41.83 %
Crystal growTemperature: 298 K / pH: 7
Details: 2.8 M ammonium sulphate, 5% PEG300, 0.1 M LiCl, 0.1 M Hepes, capillary, pH 7, LIQUID DIFFUSION, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.54
DetectorDetector: CCD / Date: Oct 26, 2010
RadiationMonochromator: MONTEL OPTIC / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.999→76.227 Å / Num. obs: 14549 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 15.9 % / Biso Wilson estimate: 24.1 Å2 / Rmerge(I) obs: 0.1565 / Rsym value: 0.1565 / Net I/σ(I): 14.32
Reflection shellResolution: 1.98→2.08 Å / Redundancy: 7.28 % / Rmerge(I) obs: 0.013 / Mean I/σ(I) obs: 2 / % possible all: 99.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SAINTdata scaling
SCALAdata scaling
MOLREPphasing
PHENIX1.7.3_928refinement
PDB_EXTRACT3.11data extraction
SAINTdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2O88

2o88


Resolution: 2.2→19.84 Å / Occupancy max: 1 / Occupancy min: 0.1 / SU ML: 0.28 / σ(F): 0 / Phase error: 26.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.233 502 4.74 %
Rwork0.197 --
obs0.198 10583 99.8 %
all-10609 -
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 31.39 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 26.12 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.2→19.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1556 0 12 69 1637
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011623
X-RAY DIFFRACTIONf_angle_d1.1212209
X-RAY DIFFRACTIONf_dihedral_angle_d13.303570
X-RAY DIFFRACTIONf_chiral_restr0.076235
X-RAY DIFFRACTIONf_plane_restr0.005285
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2009-2.42210.32511260.25162475X-RAY DIFFRACTION100
2.4221-2.77170.30751360.24242475X-RAY DIFFRACTION100
2.7717-3.4890.22931150.19112536X-RAY DIFFRACTION100
3.489-19.8370.17431250.16492595X-RAY DIFFRACTION100

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