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- PDB-6xr6: Abl 1b isoform active state -

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Basic information

Entry
Database: PDB / ID: 6xr6
TitleAbl 1b isoform active state
ComponentsTyrosine-protein kinase ABL1
KeywordsONCOPROTEIN / abl kinase
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 T cell differentiation / regulation of axon extension / 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 / regulation of autophagy / protein serine/threonine kinase activator activity / 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 domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain ...F-actin binding / F-actin binding / F-actin binding domain (FABD) / Tyrosine-protein kinase ABL, SH2 domain / : / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / 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 / 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 Alpha / Alpha Beta
Similarity search - Domain/homology
Tyrosine-protein kinase ABL1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / molecular dynamics
AuthorsXie, T. / Saleh, T. / Rossi, P. / Kalodimos, C.G.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)5R35GM122462-04 United States
CitationJournal: Science / Year: 2020
Title: Conformational states dynamically populated by a kinase determine its function.
Authors: Xie, T. / Saleh, T. / Rossi, P. / Kalodimos, C.G.
History
DepositionJul 11, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 7, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 14, 2020Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Oct 21, 2020Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.3Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.4May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tyrosine-protein kinase ABL1


Theoretical massNumber of molelcules
Total (without water)33,1811
Polymers33,1811
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function
RepresentativeModel #1lowest energy

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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: 33180.898 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ABL1, ABL, JTK7 / Production host: Escherichia coli (E. coli)
References: UniProt: P00519, non-specific protein-tyrosine kinase

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-13C HSQC aromatic
121isotropic12D HMQC methyl
131isotropic12D 15N TROSY
141isotropic13D 1H-13C SOFAST NOESY aliphatic
151isotropic23D 1H-13C SOFAST NOESY aromatic
1102isotropic23D HN(CA)CB
192isotropic23D HNCA
182isotropic23D HNCO
171isotropic23D 15N NOESY
161isotropic23D HMBC-HMQC
1111isotropic13D CCH NOESY

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Sample preparation

Details
TypeSolution-IDContentsDetailsLabelSolvent system
solution1250 uM [U-15N] Abl 1b isoform (Active), 25 mM sodium phosphate, 75 mM sodium chloride, 2.5 mM b-mercaptoethanol, 90% H2O/10% D2OU -15N U-2H U-1H-13C ILVMAT CH3 and Phe HE1,2-CE1,215N, Methyls and Phe90% H2O/10% D2O
solution2250 uM [U-100% 13C; U-100% 15N; U-100% 2H] Abl 1b isoform (Active), 25 mM sodium phosphate, 75 mM sodium chloride, 2.5 mM b-mercaptoethanol, 90% H2O/10% D2OU -15N U-2H U-13Ctriple90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
250 uMAbl 1b isoform (Active)[U-15N]1
25 mMsodium phosphatenatural abundance1
75 mMsodium chloridenatural abundance1
2.5 mMb-mercaptoethanolnatural abundance1
250 uMAbl 1b isoform (Active)[U-100% 13C; U-100% 15N; U-100% 2H]2
25 mMsodium phosphatenatural abundance2
75 mMsodium chloridenatural abundance2
2.5 mMb-mercaptoethanolnatural abundance2
Sample conditionsIonic strength: 100 mM / Label: 1 / pH: 7.1 / Pressure: 1 atm / Temperature: 283 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE11001
Bruker AVANCEBrukerAVANCE8502

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Processing

NMR software
NameDeveloperClassification
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
TALOSCornilescu, Delaglio and Baxgeometry optimization
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
I-PINELee, Bahrami, Dashti, Eghbalnia, Tonelli, Westler and Markleychemical shift assignment
SparkyGoddardpeak picking
PSVSBhattacharya and Montelionerefinement
TopSpinBruker Biospincollection
RefinementMethod: molecular dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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