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- PDB-1opk: Structural basis for the auto-inhibition of c-Abl tyrosine kinase -

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Basic information

Entry
Database: PDB / ID: 1opk
TitleStructural basis for the auto-inhibition of c-Abl tyrosine kinase
ComponentsProto-oncogene tyrosine-protein kinase ABL1
KeywordsTRANSFERASE
Function / homology
Function and homology information


transitional one stage B cell differentiation / Role of ABL in ROBO-SLIT signaling / cerebellum morphogenesis / regulation of extracellular matrix organization / HDR through Single Strand Annealing (SSA) / B cell proliferation involved in immune response / B-1 B cell homeostasis / RHO GTPases Activate WASPs and WAVEs / neuroepithelial cell differentiation / positive regulation of Wnt signaling pathway, planar cell polarity pathway ...transitional one stage B cell differentiation / Role of ABL in ROBO-SLIT signaling / cerebellum morphogenesis / regulation of extracellular matrix organization / HDR through Single Strand Annealing (SSA) / B cell proliferation involved in immune response / B-1 B cell homeostasis / RHO GTPases Activate WASPs and WAVEs / neuroepithelial cell differentiation / positive regulation of Wnt signaling pathway, planar cell polarity pathway / alpha-beta T cell differentiation / microspike assembly / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / Turbulent (oscillatory, disturbed) flow shear stress activates signaling by PIEZO1 and integrins in endothelial cells / activated T cell proliferation / protein localization to cytoplasmic microtubule plus-end / DNA conformation change / regulation of cellular senescence / Cyclin D associated events in G1 / response to epinephrine / phospholipase C-inhibiting G protein-coupled receptor signaling pathway / negative regulation of ubiquitin-protein transferase activity / podocyte apoptotic process / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / Bergmann glial cell differentiation / regulation of postsynaptic specialization assembly / positive regulation of phospholipase C/protein kinase C signal transduction / regulation of modification of synaptic structure / delta-catenin binding / RUNX1 regulates transcription of genes involved in differentiation of HSCs / circulatory system development / positive regulation of extracellular matrix organization / Regulation of actin dynamics for phagocytic cup formation / neuropilin signaling pathway / neuropilin binding / Myogenesis / negative regulation of mitotic cell cycle / bubble DNA binding / spleen development / positive regulation of establishment of T cell polarity / neuromuscular process controlling balance / regulation of T cell differentiation / positive regulation of blood vessel branching / proline-rich region binding / post-embryonic development / platelet-derived growth factor receptor signaling pathway / positive regulation of dendrite development / B cell proliferation / regulation of Cdc42 protein signal transduction / negative regulation of cell-cell adhesion / syntaxin binding / negative regulation of cellular senescence / regulation of axon extension / mitogen-activated protein kinase binding / positive regulation of cell migration involved in sprouting angiogenesis / positive regulation of osteoblast proliferation / neural tube closure / thymus development / platelet-derived growth factor receptor-beta signaling pathway / cell leading edge / negative regulation of endothelial cell apoptotic process / myoblast proliferation / negative regulation of BMP signaling pathway / negative regulation of long-term synaptic potentiation / cardiac muscle cell proliferation / regulation of microtubule polymerization / associative learning / phagocytosis / ephrin receptor signaling pathway / cellular response to transforming growth factor beta stimulus / positive regulation of focal adhesion assembly / positive regulation of vasoconstriction / positive regulation of substrate adhesion-dependent cell spreading / endothelial cell migration / positive regulation of stress fiber assembly / substrate adhesion-dependent cell spreading / negative regulation of double-strand break repair via homologous recombination / positive regulation of T cell migration / ephrin receptor binding / positive regulation of mitotic cell cycle / four-way junction DNA binding / positive regulation of interleukin-2 production / ruffle / signal transduction in response to DNA damage / phosphotyrosine residue binding / actin filament polymerization / peptidyl-tyrosine phosphorylation / SH2 domain binding / positive regulation of endothelial cell migration / B cell receptor signaling pathway / integrin-mediated signaling pathway / response to endoplasmic reticulum stress / positive regulation of fibroblast proliferation / protein serine/threonine kinase activator activity / positive regulation of release of sequestered calcium ion into cytosol / regulation of actin cytoskeleton organization / protein kinase C binding / non-specific protein-tyrosine kinase / non-membrane spanning protein tyrosine kinase activity / positive regulation of type II interferon production
Similarity search - Function
F-actin binding / F-actin binding / F-actin binding domain (FABD) / Tyrosine-protein kinase ABL, SH2 domain / SH2 domain / SHC Adaptor Protein / SH3 Domains / : / SH3 domain / SH2 domain ...F-actin binding / F-actin binding / F-actin binding domain (FABD) / Tyrosine-protein kinase ABL, SH2 domain / SH2 domain / SHC Adaptor Protein / SH3 Domains / : / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / SH3 type barrels. / Src homology 2 domains / 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 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
MYRISTIC ACID / Chem-P16 / Tyrosine-protein kinase ABL1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsNagar, B. / Hantschel, O. / Young, M.A. / Scheffzek, K. / Veach, D. / Bornmann, W. / Clarkson, B. / Superti-Furga, G. / Kuriyan, J.
Citation
Journal: Cell(Cambridge,Mass.) / Year: 2003
Title: Structural basis for the autoinhibition of c-Abl tyrosine kinase
Authors: Nagar, B. / Hantschel, O. / Young, M.A. / Scheffzek, K. / Veach, D. / Bornmann, W. / Clarkson, B. / Superti-Furga, G. / Kuriyan, J.
#1: Journal: Cell(Cambridge,Mass.) / Year: 2003
Title: A myristoyl/phosphotyrosine switch regulates c-Abl
Authors: Hantschel, O. / Nagar, B. / Guettler, S. / Kretzschmar, J. / Dorey, K. / Kuriyan, J. / Superti-Furga, G.
History
DepositionMar 6, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 8, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations / Category: database_2 / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 16, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Remark 999SEQUENCE Numbering of the residues corresponds to the sequence database numbering of the isoform IV ...SEQUENCE Numbering of the residues corresponds to the sequence database numbering of the isoform IV of the protein.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Proto-oncogene tyrosine-protein kinase ABL1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,9374
Polymers56,1891
Non-polymers7483
Water4,864270
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)118.328, 123.943, 74.798
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Proto-oncogene tyrosine-protein kinase ABL1 / p150 / c-ABL


Mass: 56189.164 Da / Num. of mol.: 1 / Fragment: SH3-SH2-kinase domain / Mutation: D382N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: ABL1 / Plasmid: PFASTBAC / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P00520, 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
#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.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 270 / 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: 2.49 Å3/Da / Density % sol: 50.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 20% PEG 3350, 200 mM potassium nitrate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails (eV)Chemical formula
120 %(w/v)PEG33501reservoir
2200 mMpotassium nitrate1reservoir
320 mMTris-HCl1droppH8.0
4100 mM1dropNaCl
55 mMdithiothreitol1drop
635 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1.0781 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 20, 2002 / Details: mirrors
RadiationMonochromator: Double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0781 Å / Relative weight: 1
ReflectionResolution: 1.8→38 Å / Num. all: 50963 / Num. obs: 50963 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.1 % / Biso Wilson estimate: 22 Å2 / Rsym value: 0.057 / Net I/σ(I): 29.6
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 6.7 % / Mean I/σ(I) obs: 3.5 / Num. unique all: 5078 / Rsym value: 0.584 / % possible all: 100
Reflection
*PLUS
Lowest resolution: 38 Å / Num. measured all: 560273 / Rmerge(I) obs: 0.057
Reflection shell
*PLUS
Highest resolution: 1.8 Å / % possible obs: 100 % / Rmerge(I) obs: 0.584

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 1M52, 2ABL

1m52

2abl


Resolution: 1.8→37.59 Å / Rfactor Rfree error: 0.004 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.221 2966 6 %RANDOM
Rwork0.196 ---
obs0.196 49297 96.5 %-
all-49297 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 35.0282 Å2 / ksol: 0.366818 e/Å3
Displacement parametersBiso mean: 30.9 Å2
Baniso -1Baniso -2Baniso -3
1--3.83 Å20 Å20 Å2
2---1.25 Å20 Å2
3---5.07 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.17 Å0.14 Å
Refinement stepCycle: LAST / Resolution: 1.8→37.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3612 0 51 270 3933
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d23
X-RAY DIFFRACTIONc_improper_angle_d0.89
X-RAY DIFFRACTIONc_mcbond_it1.531.5
X-RAY DIFFRACTIONc_mcangle_it2.482
X-RAY DIFFRACTIONc_scbond_it2.352
X-RAY DIFFRACTIONc_scangle_it3.592.5
LS refinement shellResolution: 1.8→1.91 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.282 463 6.3 %
Rwork0.265 6894 -
obs-6894 87.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAM&_1_TOPOLOGY_INFILE_1
X-RAY DIFFRACTION2P16.PAR&_1_TOPOLOGY_INFILE_2
X-RAY DIFFRACTION3MYR.PAR&_1_TOPOLOGY_INFILE_3
X-RAY DIFFRACTION4WATER_REP.PARAM&_1_TOPOLOGY_INFILE_4
X-RAY DIFFRACTION5GOL.PAR&_1_TOPOLOGY_INFILE_5
Refinement
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 38 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.89

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