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Entry
Database: PDB / ID: 2fo0
TitleOrganization of the SH3-SH2 Unit in Active and Inactive Forms of the c-Abl Tyrosine Kinase
ComponentsProto-oncogene tyrosine-protein kinase ABL1 (1B ISOFORM)
KeywordsTRANSFERASE / N-terminal cap / autoinhibition / myristoylation / SH3-SH2 clamp / phosphoserine
Function / homology
Function and homology information


Role of ABL in ROBO-SLIT signaling / Regulation of actin dynamics for phagocytic cup formation / Myogenesis / HDR through Single Strand Annealing (SSA) / RHO GTPases Activate WASPs and WAVEs / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / Factors involved in megakaryocyte development and platelet production / Cyclin D associated events in G1 / RUNX1 regulates transcription of genes involved in differentiation of HSCs / RUNX2 regulates osteoblast differentiation ...Role of ABL in ROBO-SLIT signaling / Regulation of actin dynamics for phagocytic cup formation / Myogenesis / HDR through Single Strand Annealing (SSA) / RHO GTPases Activate WASPs and WAVEs / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / Factors involved in megakaryocyte development and platelet production / Cyclin D associated events in G1 / RUNX1 regulates transcription of genes involved in differentiation of HSCs / RUNX2 regulates osteoblast differentiation / mitochondrial depolarization / transitional one stage B cell differentiation / positive regulation of actin filament binding / activation of protein kinase C activity / DNA conformation change / negative regulation of phospholipase C activity / actin filament branching / positive regulation of interleukin-2 secretion / positive regulation blood vessel branching / nicotinate-nucleotide adenylyltransferase activity / B cell proliferation involved in immune response / positive regulation of microtubule binding / neuroepithelial cell differentiation / positive regulation of Wnt signaling pathway, planar cell polarity pathway / regulation of extracellular matrix organization / microspike assembly / regulation of modification of synaptic structure / cerebellum morphogenesis / collateral sprouting / B-1 B cell homeostasis / cardiovascular system development / positive regulation of oxidoreductase activity / alpha-beta T cell differentiation / activated T cell proliferation / bubble DNA binding / neuropilin signaling pathway / neuropilin binding / regulation of T cell differentiation / regulation of Cdc42 protein signal transduction / negative regulation of protein serine/threonine kinase activity / negative regulation of ubiquitin-protein transferase activity / regulation of microtubule polymerization / regulation of actin cytoskeleton reorganization / negative regulation of BMP signaling pathway / mitogen-activated protein kinase binding / sequence-specific double-stranded DNA binding / proline-rich region binding / positive regulation of interferon-gamma secretion / negative regulation of cell-cell adhesion / cellular response to dopamine / syntaxin binding / regulation of response to DNA damage stimulus / DNA damage induced protein phosphorylation / negative regulation of cellular senescence / positive regulation of osteoblast proliferation / cell leading edge / regulation of axon extension / actin monomer binding / positive regulation of cell migration involved in sprouting angiogenesis / platelet-derived growth factor receptor-beta signaling pathway / negative regulation of long-term synaptic potentiation / neuromuscular process controlling balance / Bergmann glial cell differentiation / positive regulation of focal adhesion assembly / regulation of hematopoietic stem cell differentiation / mismatch repair / positive regulation of muscle cell differentiation / positive regulation of actin cytoskeleton reorganization / regulation of endocytosis / negative regulation of mitotic cell cycle / regulation of cell adhesion / positive regulation of substrate adhesion-dependent cell spreading / regulation of cell motility / negative regulation of endothelial cell apoptotic process / four-way junction DNA binding / endothelial cell migration / positive regulation of stress fiber assembly / regulation of actin cytoskeleton organization / signal transduction in response to DNA damage / substrate adhesion-dependent cell spreading / regulation of autophagy / positive regulation of endothelial cell migration / cellular protein modification process / spleen development / SH2 domain binding / post-embryonic development / neural tube closure / positive regulation of mitotic cell cycle / negative regulation of I-kappaB kinase/NF-kappaB signaling / positive regulation of release of sequestered calcium ion into cytosol / thymus development / protein kinase C binding / negative regulation of ERK1 and ERK2 cascade / phosphotyrosine residue binding / ephrin receptor binding / integrin-mediated signaling pathway / actin cytoskeleton organization / autophagy / non-specific protein-tyrosine kinase / peptidyl-tyrosine autophosphorylation
SH2 domain superfamily / SH2 domain / Protein kinase domain profile. / Src homology 3 (SH3) domain profile. / Src homology 2 (SH2) domain profile. / Tyrosine protein kinases specific active-site signature. / SH2 domain / F-actin binding / Protein tyrosine kinase / SH3 domain ...SH2 domain superfamily / SH2 domain / Protein kinase domain profile. / Src homology 3 (SH3) domain profile. / Src homology 2 (SH2) domain profile. / Tyrosine protein kinases specific active-site signature. / SH2 domain / F-actin binding / Protein tyrosine kinase / SH3 domain / Protein kinase domain / Serine-threonine/tyrosine-protein kinase, catalytic domain / SH3 domain / Tyrosine-protein kinase, active site / Protein kinase-like domain superfamily / F-actin binding / Protein kinase, ATP binding site / Tyrosine-protein kinase, catalytic domain / Tyrosine-protein kinase ABL1/transforming protein Abl / Tyrosine-protein kinase ABL, SH2 domain / SH3-like domain superfamily / Protein kinases ATP-binding region signature.
Tyrosine-protein kinase ABL1 / Tyrosine-protein kinase ABL1
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.27 Å
AuthorsNagar, B. / Hantschel, O. / Seeliger, M. / Davies, J.M. / Weis, W.I. / Superti-Furga, G. / Kuriyan, J.
CitationJournal: Mol.Cell / Year: 2006
Title: Organization of the SH3-SH2 unit in active and inactive forms of the c-Abl tyrosine kinase.
Authors: Nagar, B. / Hantschel, O. / Seeliger, M. / Davies, J.M. / Weis, W.I. / Superti-Furga, G. / Kuriyan, J.
Validation Report
SummaryFull reportAbout validation report
History
DepositionJan 12, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 21, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Aug 2, 2017Group: Source and taxonomy / Category: entity_src_gen
Remark 999SEQUENCE Residues 15-56 of the original protein sequence were deleted. Myristoyl group (MYR) is ...SEQUENCE Residues 15-56 of the original protein sequence were deleted. Myristoyl group (MYR) is covalently attached to the N-terminus of the protein.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Proto-oncogene tyrosine-protein kinase ABL1 (1B ISOFORM)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,2925
Polymers56,4521
Non-polymers8404
Water2,612145
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
γ
α
β
Length a, b, c (Å)79.688, 117.266, 60.416
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein/peptide Proto-oncogene tyrosine-protein kinase ABL1 (1B ISOFORM)


Mass: 56452.371 Da / Num. of mol.: 1
Fragment: Abl N-cap (residues 1-531, residues 15-56 deleted)
Mutation: D382N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: c-Abl / Plasmid: PFASTBAC1 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: P00519-2, UniProt: P00519*PLUS, EC: 2.7.1.112
#2: Chemical ChemComp-MYR / MYRISTIC ACID


Mass: 228.371 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H28O2 / Myristic acid
#3: Chemical ChemComp-P16 / 6-(2,6-DICHLOROPHENYL)-2-{[3-(HYDROXYMETHYL)PHENYL]AMINO}-8-METHYLPYRIDO[2,3-D]PYRIMIDIN-7(8H)-ONE / PD166326


Mass: 427.283 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H16Cl2N4O2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 145 / Source method: isolated from a natural source / Formula: H2O / Water

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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: 2.5 Å3/Da / Density % sol: 50.78 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20% PEG 10000, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 24, 2003
RadiationMonochromator: Double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.27→48.14 Å / Num. all: 25639 / Num. obs: 25639 / % possible obs: 94.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.1 % / Biso Wilson estimate: 17.2 Å2 / Rsym value: 0.095 / Net I/σ(I): 14.6
Reflection shellResolution: 2.27→2.35 Å / Redundancy: 2.5 % / Mean I/σ(I) obs: 3.2 / Num. unique all: 2026 / Rsym value: 0.289 / % possible all: 76.5

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1OPK
Resolution: 2.27→48.14 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 318702.33 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.246 1656 6.8 %RANDOM
Rwork0.21 ---
Obs0.21 24283 90.3 %-
All-24283 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 33.6955 Å2 / ksol: 0.376791 e/Å3
Displacement parametersBiso mean: 38.8 Å2
Baniso -1Baniso -2Baniso -3
1--9.32 Å20 Å20 Å2
2---10.46 Å20 Å2
3---19.77 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.33 Å0.35 Å
Refinement stepCycle: LAST / Resolution: 2.27→48.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3748 0 56 145 3949
Refine LS restraints

Refinement-ID: X-RAY DIFFRACTION

TypeDev idealDev ideal target
c_bond_d0.007
c_angle_deg1.3
c_dihedral_angle_d22.7
c_improper_angle_d0.85
c_mcbond_it1.581.5
c_mcangle_it2.682
c_scbond_it2.232
c_scangle_it3.42.5
LS refinement shellResolution: 2.27→2.41 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.28 235 7.3 %
Rwork0.27 3000 -
Obs-3235 73.5 %
Xplor file

Refinement-ID: X-RAY DIFFRACTION

Serial noParam fileTopol file
1protein_rep.paramprotein_rep.top
2ligands.parligands.top
3water_rep.paramwater_rep.top

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