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- PDB-6xr7: Abl isoform 1b inactive1 state -

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Basic information

Entry
Database: PDB / ID: 6xr7
TitleAbl isoform 1b inactive1 state
ComponentsTyrosine-protein kinase ABL1
KeywordsONCOPROTEIN / abl kinase 1b isoform
Function / homology
Function and homology information


positive regulation of actin filament binding / phospholipase C-inhibiting G protein-coupled receptor signaling pathway / positive regulation of oxidoreductase activity / protein localization to cytoplasmic microtubule plus-end / DN4 thymocyte differentiation / response to epinephrine / podocyte apoptotic process / transitional one stage B cell differentiation / Role of ABL in ROBO-SLIT signaling / activation of protein kinase C activity ...positive regulation of actin filament binding / phospholipase C-inhibiting G protein-coupled receptor signaling pathway / positive regulation of oxidoreductase activity / protein localization to cytoplasmic microtubule plus-end / DN4 thymocyte differentiation / response to epinephrine / podocyte apoptotic process / transitional one stage B cell differentiation / Role of ABL in ROBO-SLIT signaling / activation of protein kinase C activity / nicotinate-nucleotide adenylyltransferase activity / regulation of modification of synaptic structure / positive regulation of microtubule binding / delta-catenin binding / DNA conformation change / microspike assembly / neuroepithelial cell differentiation / B cell proliferation involved in immune response / positive regulation of Wnt signaling pathway, planar cell polarity pathway / positive regulation of extracellular matrix organization / cerebellum morphogenesis / positive regulation of blood vessel branching / B-1 B cell homeostasis / negative regulation of ubiquitin-protein transferase activity / neuropilin signaling pathway / neuropilin binding / mitochondrial depolarization / bubble DNA binding / negative regulation of protein serine/threonine kinase activity / activated T cell proliferation / cellular response to dopamine / regulation of hematopoietic stem cell differentiation / regulation of cell motility / regulation of Cdc42 protein signal transduction / proline-rich region binding / mitogen-activated protein kinase binding / positive regulation of dendrite development / myoblast proliferation / syntaxin binding / alpha-beta T cell differentiation / regulation of T cell differentiation / cardiac muscle cell proliferation / regulation of axon extension / Fc-gamma receptor signaling pathway involved in phagocytosis / HDR through Single Strand Annealing (SSA) / positive regulation of cell migration involved in sprouting angiogenesis / negative regulation of cell-cell adhesion / Myogenesis / positive regulation of osteoblast proliferation / regulation of microtubule polymerization / RUNX2 regulates osteoblast differentiation / platelet-derived growth factor receptor-beta signaling pathway / negative regulation of cellular senescence / positive regulation of focal adhesion assembly / associative learning / Bergmann glial cell differentiation / regulation of endocytosis / neuromuscular process controlling balance / negative regulation of mitotic cell cycle / actin monomer binding / negative regulation of long-term synaptic potentiation / negative regulation of BMP signaling pathway / negative regulation of double-strand break repair via homologous recombination / endothelial cell migration / signal transduction in response to DNA damage / RHO GTPases Activate WASPs and WAVEs / positive regulation of T cell migration / mismatch repair / regulation of cell adhesion / BMP signaling pathway / negative regulation of endothelial cell apoptotic process / canonical NF-kappaB signal transduction / peptidyl-tyrosine autophosphorylation / positive regulation of substrate adhesion-dependent cell spreading / four-way junction DNA binding / spleen development / cellular response to transforming growth factor beta stimulus / positive regulation of vasoconstriction / positive regulation of stress fiber assembly / ruffle / positive regulation of establishment of T cell polarity / phosphotyrosine residue binding / response to endoplasmic reticulum stress / positive regulation of interleukin-2 production / ephrin receptor binding / actin filament polymerization / ERK1 and ERK2 cascade / positive regulation of endothelial cell migration / post-embryonic development / SH2 domain binding / positive regulation of mitotic cell cycle / substrate adhesion-dependent cell spreading / thymus development / positive regulation of release of sequestered calcium ion into cytosol / regulation of autophagy / integrin-mediated signaling pathway / neural tube closure / establishment of localization in cell / regulation of actin cytoskeleton organization / non-specific protein-tyrosine kinase
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 / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
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 support1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)5R35GM122462-04
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 BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
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 TROSY aromatic
121isotropic22D 1H-15N TROSY
131isotropic12D 1H-13C HMQC
1101isotropic23D 15N NOESY
191isotropic13D CCH-NOESY
181isotropic13D 1H-13C NOESY aliphatic
171isotropic13D 1H-13C NOESY aromatic

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Sample preparation

Details
TypeSolution-IDContentsDetailsLabelSolvent system
solution1250 uM U-15N U-2H U-1H13C ILVMAT CH3 and Phe HE12-CE12 Abl M309L/H415P Variant, 5 mM beta-mercaptoethanol, 25 mM sodium phosphate, 75 mM sodium chloride, 90% H2O/10% D2OU-15N,2H 1-13C ILVMAT CH3 and HE12-CE12 Phe15N + methyl + phe90% H2O/10% D2O
solution2250 uM U-15N U-2H U-1H13C ILVMAT CH3 and Phe HE12-CE12 Abl M309L/H415P, 5 mM beta-mercaptoethanol, 25 mM sodium phosphate, 75 mM sodium chloride, 90% H2O/10% D2OU-2H,15N 13Ctriple90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
250 uMAbl M309L/H415P VariantU-15N U-2H U-1H13C ILVMAT CH3 and Phe HE12-CE121
5 mMbeta-mercaptoethanolnatural abundance1
25 mMsodium phosphatenatural abundance1
75 mMsodium chloridenatural abundance1
250 uMAbl M309L/H415PU-15N U-2H U-1H13C ILVMAT CH3 and Phe HE12-CE122
5 mMbeta-mercaptoethanolnatural abundance2
25 mMsodium phosphatenatural abundance2
75 mMsodium chloridenatural abundance2
Sample conditionsIonic strength: 100 mM / Label: 1 / pH: 6.5 / 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
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
I-PINELee, Bahrami, Dashti, Eghbalnia, Tonelli, Westler and Markleychemical shift assignment
SparkyGoddardpeak picking
TALOSCornilescu, Delaglio and Baxgeometry optimization
TopSpinBruker Biospincollection
PSVSBhattacharya and Montelionerefinement
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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