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- PDB-4j9h: Crystal structure of the ABL-SH3 domain complexed with the design... -

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Basic information

Entry
Database: PDB / ID: 4j9h
TitleCrystal structure of the ABL-SH3 domain complexed with the designed high-affinity peptide ligand P7 at pH 8
Components
  • P7
  • 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


positive regulation of actin filament binding / negative regulation of ubiquitin-protein transferase activity / positive regulation of oxidoreductase activity / protein localization to cytoplasmic microtubule plus-end / 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 ...positive regulation of actin filament binding / negative regulation of ubiquitin-protein transferase activity / positive regulation of oxidoreductase activity / protein localization to cytoplasmic microtubule plus-end / 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 / DNA conformation change / : / neuroepithelial cell differentiation / B cell proliferation involved in immune response / cerebellum morphogenesis / positive regulation of Wnt signaling pathway, planar cell polarity pathway / positive regulation of extracellular matrix organization / microspike assembly / B-1 B cell homeostasis / neuropilin signaling pathway / neuropilin binding / bubble DNA binding / mitochondrial depolarization / regulation of cell motility / activated T cell proliferation / positive regulation of establishment of T cell polarity / cellular response to dopamine / positive regulation of blood vessel branching / 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 / alpha-beta T cell differentiation / positive regulation of dendrite development / regulation of axon extension / regulation of T cell differentiation / cardiac muscle cell proliferation / positive regulation of cell migration involved in sprouting angiogenesis / HDR through Single Strand Annealing (SSA) / negative regulation of cell-cell adhesion / positive regulation of peptidyl-tyrosine phosphorylation / Myogenesis / platelet-derived growth factor receptor-beta signaling pathway / positive regulation of osteoblast proliferation / RUNX2 regulates osteoblast differentiation / regulation of microtubule polymerization / Fc-gamma receptor signaling pathway involved in phagocytosis / associative learning / vascular endothelial cell response to oscillatory fluid shear stress / Bergmann glial cell differentiation / regulation of endocytosis / neuromuscular process controlling balance / negative regulation of cellular senescence / negative regulation of long-term synaptic potentiation / negative regulation of mitotic cell cycle / negative regulation of BMP signaling pathway / actin monomer binding / canonical NF-kappaB signal transduction / signal transduction in response to DNA damage / positive regulation of focal adhesion assembly / RHO GTPases Activate WASPs and WAVEs / BMP signaling pathway / endothelial cell migration / positive regulation of T cell migration / negative regulation of double-strand break repair via homologous recombination / mismatch repair / negative regulation of endothelial cell apoptotic process / regulation of cell adhesion / peptidyl-tyrosine autophosphorylation / four-way junction DNA binding / cellular response to transforming growth factor beta stimulus / spleen development / positive regulation of stress fiber assembly / ruffle / positive regulation of vasoconstriction / ephrin receptor binding / actin filament polymerization / positive regulation of substrate adhesion-dependent cell spreading / phosphotyrosine residue binding / positive regulation of endothelial cell migration / ERK1 and ERK2 cascade / positive regulation of interleukin-2 production / positive regulation of mitotic cell cycle / substrate adhesion-dependent cell spreading / SH2 domain binding / response to endoplasmic reticulum stress / positive regulation of release of sequestered calcium ion into cytosol / thymus development / protein kinase C binding / Turbulent (oscillatory, disturbed) flow shear stress activates signaling by PIEZO1 and integrins in endothelial cells / post-embryonic development / integrin-mediated signaling pathway / establishment of localization in cell
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 / SH2 domain superfamily / Src homology 3 domains / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.7 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 P7
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 20, 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: Tyrosine-protein kinase ABL1
C: Tyrosine-protein kinase ABL1
D: Tyrosine-protein kinase ABL1
E: Tyrosine-protein kinase ABL1
F: Tyrosine-protein kinase ABL1
G: P7
H: P7
I: P7
J: P7
K: P7
L: P7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,50913
Polymers48,41312
Non-polymers961
Water6,918384
1
A: Tyrosine-protein kinase ABL1
G: P7


Theoretical massNumber of molelcules
Total (without water)8,0692
Polymers8,0692
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1140 Å2
ΔGint-8 kcal/mol
Surface area4170 Å2
MethodPISA
2
B: Tyrosine-protein kinase ABL1
H: P7


Theoretical massNumber of molelcules
Total (without water)8,0692
Polymers8,0692
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1150 Å2
ΔGint-8 kcal/mol
Surface area3990 Å2
MethodPISA
3
C: Tyrosine-protein kinase ABL1
L: P7


Theoretical massNumber of molelcules
Total (without water)8,0692
Polymers8,0692
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1150 Å2
ΔGint-8 kcal/mol
Surface area3970 Å2
MethodPISA
4
D: Tyrosine-protein kinase ABL1
K: P7


Theoretical massNumber of molelcules
Total (without water)8,0692
Polymers8,0692
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1150 Å2
ΔGint-7 kcal/mol
Surface area4020 Å2
MethodPISA
5
E: Tyrosine-protein kinase ABL1
J: P7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,1653
Polymers8,0692
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1340 Å2
ΔGint-23 kcal/mol
Surface area4040 Å2
MethodPISA
6
F: Tyrosine-protein kinase ABL1
I: P7


Theoretical massNumber of molelcules
Total (without water)8,0692
Polymers8,0692
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1140 Å2
ΔGint-8 kcal/mol
Surface area3960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.553, 86.553, 45.261
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number145
Space group name H-MP32

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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.: 6 / Fragment: SH3 domain
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
P7


Mass: 1059.212 Da / Num. of mol.: 6 / Source method: obtained synthetically
Details: This sequence has been optimized to increase the affinity
#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.: 384 / 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: 2.02 Å3/Da / Density % sol: 39.16 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 2M ammonium sulphate, 10% glicerol and 0.1 M Tris-HCl , pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 288K

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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: 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: 1.7→74.957 Å / Num. all: 41520 / Num. obs: 41520 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Biso Wilson estimate: 10.76 Å2 / Rmerge(I) obs: 0.059 / Rsym value: 0.059 / Net I/σ(I): 18.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique all% possible all
1.7-1.734.10.5013.19432228498.6
8.83-19.524.20.01748112827191.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
Aimless0.1.26data scaling
PHASERphasing
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.11data extraction
ADSCQuantumdata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2O88

2o88


Resolution: 1.7→19.522 Å / Occupancy max: 1 / Occupancy min: 0 / SU ML: 0.21 / σ(F): 0 / σ(I): 0 / Phase error: 21.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2094 2040 5.03 %RANDOM
Rwork0.1579 ---
all0.1605 ---
obs0.1605 41520 97.82 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 87.8 Å2 / Biso mean: 21.5558 Å2 / Biso min: 4.16 Å2
Refinement stepCycle: LAST / Resolution: 1.7→19.522 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3150 0 5 384 3539
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033272
X-RAY DIFFRACTIONf_angle_d0.924491
X-RAY DIFFRACTIONf_chiral_restr0.045471
X-RAY DIFFRACTIONf_plane_restr0.006598
X-RAY DIFFRACTIONf_dihedral_angle_d11.0991169
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 29

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7-1.720.34831370.24822716285397
1.72-1.7410.29441390.24062631277095
1.741-1.7630.27841360.22062649278598
1.763-1.78620.28231290.20172660278997
1.7862-1.81060.25221540.22631278596
1.8106-1.83650.28721250.19032628275398
1.8365-1.86390.24871580.18392671282997
1.8639-1.8930.25221600.16922584274496
1.893-1.9240.24531100.15892765287598
1.924-1.95710.19011490.15842676282597
1.9571-1.99270.23881450.15592602274798
1.9927-2.0310.19751070.1482662276998
2.031-2.07240.21431360.14162603273997
2.0724-2.11740.26221580.14172725288398
2.1174-2.16660.22041280.14312717284597
2.1666-2.22070.19631360.14172706284298
2.2207-2.28070.22721690.13992628279798
2.2807-2.34770.17841470.14722615276299
2.3477-2.42330.21421510.14232677282898
2.4233-2.50970.22961600.15072683284398
2.5097-2.610.18941660.14072696286299
2.61-2.72850.20131560.14072652280898
2.7285-2.87190.20821320.14052725285798
2.8719-3.05120.19081390.14162645278498
3.0512-3.28580.19421120.14412732284498
3.2858-3.61460.16171480.13782696284499
3.6146-4.13330.16111320.14362704283699
4.1333-5.19120.1751580.151827082866100
5.1912-19.52330.24131320.227627372869100

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