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- PDB-5oaz: Crystal structure of the Abl-SH3 domain at pH 7.5 -

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Basic information

Entry
Database: PDB / ID: 5oaz
TitleCrystal structure of the Abl-SH3 domain at pH 7.5
ComponentsTyrosine-protein kinase ABL1
KeywordsTRANSFERASE / beta shandwich
Function / homology
Function and homology information


negative regulation of ubiquitin-protein transferase activity / protein localization to cytoplasmic microtubule plus-end / DNA conformation change / DN4 thymocyte differentiation / response to epinephrine / phospholipase C-inhibiting G protein-coupled receptor signaling pathway / podocyte apoptotic process / transitional one stage B cell differentiation / positive regulation of phospholipase C/protein kinase C signal transduction / regulation of postsynaptic specialization assembly ...negative regulation of ubiquitin-protein transferase activity / protein localization to cytoplasmic microtubule plus-end / DNA conformation change / DN4 thymocyte differentiation / response to epinephrine / phospholipase C-inhibiting G protein-coupled receptor signaling pathway / podocyte apoptotic process / transitional one stage B cell differentiation / positive regulation of phospholipase C/protein kinase C signal transduction / regulation of postsynaptic specialization assembly / regulation of modification of synaptic structure / nicotinate-nucleotide adenylyltransferase activity / delta-catenin binding / cerebellum morphogenesis / Role of ABL in ROBO-SLIT signaling / B cell proliferation involved in immune response / neuroepithelial cell differentiation / 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 / mitochondrial depolarization / regulation of cell motility / bubble DNA binding / positive regulation of establishment of T cell polarity / cellular response to dopamine / activated T cell proliferation / 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 / positive regulation of dendrite development / syntaxin binding / alpha-beta T cell differentiation / regulation of axon extension / regulation of T cell differentiation / positive regulation of cell migration involved in sprouting angiogenesis / negative regulation of cell-cell adhesion / neuromuscular process controlling balance / Myogenesis / HDR through Single Strand Annealing (SSA) / positive regulation of osteoblast proliferation / 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 / Bergmann glial cell differentiation / regulation of endocytosis / regulation of microtubule polymerization / myoblast proliferation / negative regulation of cellular senescence / negative regulation of long-term synaptic potentiation / positive regulation of vasoconstriction / associative learning / actin monomer binding / positive regulation of focal adhesion assembly / negative regulation of BMP signaling pathway / RHO GTPases Activate WASPs and WAVEs / ephrin receptor signaling pathway / cardiac muscle cell proliferation / BMP signaling pathway / negative regulation of endothelial cell apoptotic process / cellular response to transforming growth factor beta stimulus / positive regulation of T cell migration / endothelial cell migration / negative regulation of double-strand break repair via homologous recombination / regulation of cell adhesion / positive regulation of interleukin-2 production / mismatch repair / ephrin receptor binding / spleen development / four-way junction DNA binding / ERK1 and ERK2 cascade / positive regulation of stress fiber assembly / ruffle / signal transduction in response to DNA damage / phosphotyrosine residue binding / actin filament polymerization / canonical NF-kappaB signal transduction / positive regulation of substrate adhesion-dependent cell spreading / substrate adhesion-dependent cell spreading / positive regulation of mitotic cell cycle / positive regulation of endothelial cell migration / SH2 domain binding / establishment of localization in cell / response to endoplasmic reticulum stress / Turbulent (oscillatory, disturbed) flow shear stress activates signaling by PIEZO1 and integrins in endothelial cells / thymus development / positive regulation of release of sequestered calcium ion into cytosol / protein kinase C binding / protein modification process / protein serine/threonine kinase activator activity / regulation of autophagy / B cell receptor signaling pathway / 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 / SH3 type barrels. / 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: 1.03 Å
AuthorsCamara-Artigas, A.
Funding support Spain, 1items
OrganizationGrant numberCountry
Spanish Ministry of Economy and CompetitivenessBIO2016-78020-R Spain
CitationJournal: to be published
Title: Crystal structure of the Abl-SH3 domain at pH 7.5
Authors: Camara-Artigas, A.
History
DepositionJun 25, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 12, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jan 24, 2018Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain
Revision 1.3Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,3385
Polymers14,0192
Non-polymers3183
Water2,234124
1
A: Tyrosine-protein kinase ABL1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,1162
Polymers7,0101
Non-polymers1061
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Tyrosine-protein kinase ABL1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,2223
Polymers7,0101
Non-polymers2122
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.919, 49.919, 45.046
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.: 2 / Fragment: SH3 DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ABL1, ABL, JTK7 / Plasmid: PET15B / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P00519, non-specific protein-tyrosine kinase
#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 124 / 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: 2.47 Å3/Da / Density % sol: 50.29 % / Mosaicity: 0.07 °
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1.65 M Ammonium sulphate, 0.1 M Hepes and 6% PEG 300

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 24, 2015 / Details: CHANNEL-CUT SI(111)
RadiationMonochromator: Si(111) channel-cut crystal monochromator and a pair of KB mirrors
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.03→20 Å / Num. obs: 118361 / % possible obs: 95.3 % / Redundancy: 4.9 % / Biso Wilson estimate: 13.01 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.036 / Rpim(I) all: 0.019 / Rrim(I) all: 0.04 / Net I/σ(I): 29.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Rpim(I) allRrim(I) all% possible all
1.03-1.052.60.5920.6910.4090.72689.5
5.64-19.974.30.0370.9910.0220.04396.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
Aimless0.5.17data scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4JJB

4jjb


Resolution: 1.03→20 Å / SU ML: 0.07 / Cross valid method: THROUGHOUT / σ(F): 0.06 / Phase error: 14.99
RfactorNum. reflection% reflection
Rfree0.1628 6209 5.25 %
Rwork0.1446 --
obs0.1455 118361 95.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 53.52 Å2 / Biso mean: 19.5644 Å2 / Biso min: 9.92 Å2
Refinement stepCycle: final / Resolution: 1.03→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms875 0 51 124 1050
Biso mean--43.82 32.95 -
Num. residues----115
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01930
X-RAY DIFFRACTIONf_angle_d1.1141267
X-RAY DIFFRACTIONf_chiral_restr0.095136
X-RAY DIFFRACTIONf_plane_restr0.007165
X-RAY DIFFRACTIONf_dihedral_angle_d12.863313
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.03-1.04170.2731520.28893605375789
1.0417-1.0540.26321240.24513586371091
1.054-1.06680.2438900.22113781387192
1.0668-1.08030.21422860.20833491377792
1.0803-1.09450.22462220.19033607382992
1.0945-1.10950.17852850.17533549383492
1.1095-1.12540.1851820.15943633381592
1.1254-1.14220.15262160.14333634385094
1.1422-1.160.16082300.14243750398093
1.16-1.1790.15992320.1363537376994
1.179-1.19940.17022420.12623681392395
1.1994-1.22120.16251340.12183806394094
1.2212-1.24460.14731760.1193699387594
1.2446-1.27010.11261840.11383736392095
1.2701-1.29770.13531740.10673676385094
1.2977-1.32780.13432160.10523698391495
1.3278-1.3610.13041500.10623834398495
1.361-1.39780.1192580.10313800405897
1.3978-1.4390.11651480.1063854400297
1.439-1.48540.13011720.11093762393496
1.4854-1.53850.14292180.10283784400297
1.5385-1.60.12433220.10933796411897
1.6-1.67280.12872420.11163759400198
1.6728-1.7610.12731840.12213890407498
1.761-1.87120.14361980.1283854405298
1.8712-2.01560.15492280.12263838406699
2.0156-2.21820.13252980.1333808410699
2.2182-2.53860.18852040.15133914411899
2.5386-3.19620.18672520.171739164168100
3.1962-19.97840.19611900.17013874406499

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