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- PDB-4j9f: Crystal structure of the Abl-SH3 domain complexed with the high a... -

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Basic information

Entry
Database: PDB / ID: 4j9f
TitleCrystal structure of the Abl-SH3 domain complexed with the high affinity peptide P0
Components
  • P0
  • Tyrosine-protein kinase ABL1
KeywordsTransferase/unknown function / beta shandwich / SH3 domain / kinase / poly proline rich motifs / Transferase / Transferase-unknown function complex
Function / homology
Function and homology information


regulation of actin filament depolymerization / negative regulation of small GTPase mediated signal transduction / semaphorin receptor binding / negative regulation of phospholipase C activity / positive regulation of actin filament binding / positive regulation of oxidoreductase activity / transitional one stage B cell differentiation / protein localization to cytoplasmic microtubule plus-end / DNA conformation change / podocyte apoptotic process ...regulation of actin filament depolymerization / negative regulation of small GTPase mediated signal transduction / semaphorin receptor binding / negative regulation of phospholipase C activity / positive regulation of actin filament binding / positive regulation of oxidoreductase activity / transitional one stage B cell differentiation / protein localization to cytoplasmic microtubule plus-end / DNA conformation change / podocyte apoptotic process / DN4 thymocyte differentiation / Role of ABL in ROBO-SLIT signaling / response to epinephrine / activation of protein kinase C activity / nicotinate-nucleotide adenylyltransferase activity / ruffle assembly / regulation of modification of synaptic structure / regulation of Rac protein signal transduction / positive regulation of microtubule binding / delta-catenin binding / B cell proliferation involved in immune response / positive regulation of extracellular matrix organization / neuroepithelial cell differentiation / microspike assembly / positive regulation of Wnt signaling pathway, planar cell polarity pathway / cerebellum morphogenesis / positive regulation of blood vessel branching / regulation of blood vessel endothelial cell migration / B-1 B cell homeostasis / mitochondrial depolarization / negative regulation of ubiquitin-protein transferase activity / neuropilin signaling pathway / neuropilin binding / bubble DNA binding / negative regulation of protein serine/threonine kinase activity / cell junction assembly / filopodium assembly / activated T cell proliferation / cellular response to dopamine / establishment of epithelial cell apical/basal polarity / regulation of cell motility / regulation of Cdc42 protein signal transduction / proline-rich region binding / positive regulation of dendrite development / mitogen-activated protein kinase binding / myoblast proliferation / regulation of small GTPase mediated signal transduction / alpha-beta T cell differentiation / regulation of hematopoietic stem cell differentiation / syntaxin binding / cardiac muscle cell proliferation / regulation of T cell differentiation / regulation of axon extension / HDR through Single Strand Annealing (SSA) / phagocytic cup / phagocytosis, engulfment / negative regulation of double-strand break repair via homologous recombination / positive regulation of cell migration involved in sprouting angiogenesis / Fc-gamma receptor signaling pathway involved in phagocytosis / negative regulation of cell-cell adhesion / Myogenesis / regulation of microtubule polymerization / positive regulation of osteoblast proliferation / cell leading edge / RUNX2 regulates osteoblast differentiation / platelet-derived growth factor receptor-beta signaling pathway / positive regulation of focal adhesion assembly / negative regulation of cellular senescence / Bergmann glial cell differentiation / associative learning / semaphorin-plexin signaling pathway / neuromuscular process controlling balance / regulation of endocytosis / actin monomer binding / negative regulation of BMP signaling pathway / negative regulation of mitotic cell cycle / negative regulation of long-term synaptic potentiation / mismatch repair / endothelial cell migration / RHO GTPases Activate WASPs and WAVEs / bicellular tight junction / positive regulation of T cell migration / canonical NF-kappaB signal transduction / BMP signaling pathway / negative regulation of endothelial cell apoptotic process / regulation of cell adhesion / four-way junction DNA binding / signal transduction in response to DNA damage / positive regulation of substrate adhesion-dependent cell spreading / peptidyl-tyrosine autophosphorylation / positive regulation of vasoconstriction / positive regulation of stress fiber assembly / spleen development / ERK1 and ERK2 cascade / ruffle / cellular response to transforming growth factor beta stimulus / RAC1 GTPase cycle / positive regulation of establishment of T cell polarity / actin filament polymerization / positive regulation of interleukin-2 production
Similarity search - Function
: / BAR domain / BAR domain profile. / BAR / BAR domain / F-actin binding / F-actin binding / F-actin binding domain (FABD) / Tyrosine-protein kinase ABL, SH2 domain / AH/BAR domain superfamily ...: / BAR domain / BAR domain profile. / BAR / BAR domain / F-actin binding / F-actin binding / F-actin binding domain (FABD) / Tyrosine-protein kinase ABL, SH2 domain / AH/BAR domain superfamily / Rho GTPase-activating protein domain / RhoGAP domain / Rho GTPase-activating proteins domain profile. / GTPase-activator protein for Rho-like GTPases / Rho GTPase activation protein / 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 / 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 / SH3 domain-binding protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.094 Å
AuthorsCamara-Artigas, A.
Citation
Journal: To be Published
Title: Crystal structure of the Abl-SH3 domain complexed with the high affinity peptide P0
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

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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: P0
C: Tyrosine-protein kinase ABL1
D: P0
E: Tyrosine-protein kinase ABL1
F: P0
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,4438
Polymers24,2556
Non-polymers1882
Water3,999222
1
A: Tyrosine-protein kinase ABL1
B: P0


Theoretical massNumber of molelcules
Total (without water)8,0852
Polymers8,0852
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1140 Å2
ΔGint-8 kcal/mol
Surface area4750 Å2
MethodPISA
2
C: Tyrosine-protein kinase ABL1
D: P0


Theoretical massNumber of molelcules
Total (without water)8,0852
Polymers8,0852
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1140 Å2
ΔGint-7 kcal/mol
Surface area4170 Å2
MethodPISA
3
E: Tyrosine-protein kinase ABL1
F: P0
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,2734
Polymers8,0852
Non-polymers1882
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1510 Å2
ΔGint-22 kcal/mol
Surface area4200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.429, 86.429, 45.160
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-222-

HOH

31A-250-

HOH

41A-255-

HOH

Detailsbiological unit is the complex between one molecule of SH3 domain and the peptide

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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) / 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: Protein/peptide P0


Mass: 1075.255 Da / Num. of mol.: 3 / Source method: obtained synthetically / References: UniProt: Q9Y3L3*PLUS
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


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


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


Mass: 18.015 Da / Num. of mol.: 222 / 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: 2.01 Å3/Da / Density % sol: 38.73 %
Crystal growTemperature: 298 K / pH: 7
Details: 2M Ammonium sulphate, 5% PEG300, 0.05M Litium Formate, 10 % glycerol, 0.1M MOPS , pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.97
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 28, 2011
RadiationMonochromator: CHANNEL CUT ESRF MONOCHROMATOR AND TORODIAL FOCUSING MIRROR
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.094→74.85 Å / Num. obs: 77433 / % possible obs: 97 % / Observed criterion σ(I): 0 / Redundancy: 8.8 % / Biso Wilson estimate: 6.9 Å2 / Rmerge(I) obs: 0.061 / Rsym value: 0.061 / Net I/σ(I): 19.2
Reflection shellResolution: 1.09→1.15 Å / Redundancy: 8.7 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 4.9 / % possible all: 94.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALA3.3.16data scaling
PHASERphasing
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.11data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2O88

2o88


Resolution: 1.094→21.84 Å / Occupancy max: 1 / Occupancy min: 0.1 / SU ML: 0.09 / σ(F): 0 / Phase error: 13.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.169 3893 5.03 %
Rwork0.147 --
obs0.148 77420 96.7 %
all-80070 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 13.54 Å2
Refinement stepCycle: LAST / Resolution: 1.094→21.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1637 0 11 222 1870
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011726
X-RAY DIFFRACTIONf_angle_d1.3862370
X-RAY DIFFRACTIONf_dihedral_angle_d11.608624
X-RAY DIFFRACTIONf_chiral_restr0.08250
X-RAY DIFFRACTIONf_plane_restr0.007316
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.094-1.10740.26291210.2182567X-RAY DIFFRACTION94
1.1074-1.12140.19941400.18272511X-RAY DIFFRACTION94
1.1214-1.13610.16731360.14722539X-RAY DIFFRACTION95
1.1361-1.15170.17211390.13532547X-RAY DIFFRACTION95
1.1517-1.16810.15461410.1392592X-RAY DIFFRACTION96
1.1681-1.18560.13371210.1372555X-RAY DIFFRACTION95
1.1856-1.20410.18061310.1352599X-RAY DIFFRACTION96
1.2041-1.22380.18421440.14982553X-RAY DIFFRACTION95
1.2238-1.24490.17061550.14162569X-RAY DIFFRACTION97
1.2449-1.26760.14161310.13392608X-RAY DIFFRACTION96
1.2676-1.2920.15391400.12442608X-RAY DIFFRACTION96
1.292-1.31830.16861390.1222608X-RAY DIFFRACTION97
1.3183-1.3470.13161190.12242616X-RAY DIFFRACTION97
1.347-1.37830.15781320.11892644X-RAY DIFFRACTION97
1.3783-1.41280.15511410.11482641X-RAY DIFFRACTION97
1.4128-1.4510.14341320.11362642X-RAY DIFFRACTION98
1.451-1.49370.14441500.11792645X-RAY DIFFRACTION98
1.4937-1.54190.14671470.1152645X-RAY DIFFRACTION98
1.5419-1.59690.16791470.12092675X-RAY DIFFRACTION98
1.5969-1.66090.15691410.12662651X-RAY DIFFRACTION98
1.6609-1.73640.15131340.12582694X-RAY DIFFRACTION98
1.7364-1.82790.14921390.13012683X-RAY DIFFRACTION99
1.8279-1.94240.15341440.13432727X-RAY DIFFRACTION99
1.9424-2.09230.14931520.13042682X-RAY DIFFRACTION99
2.0923-2.30260.16021570.13822712X-RAY DIFFRACTION99
2.3026-2.63530.18181460.15882704X-RAY DIFFRACTION97
2.6353-3.31830.18161490.1722727X-RAY DIFFRACTION99
3.3183-21.84310.2141250.20112583X-RAY DIFFRACTION90

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