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- PDB-1zzp: Solution structure of the F-actin binding domain of Bcr-Abl/c-Abl -

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Basic information

Entry
Database: PDB / ID: 1zzp
TitleSolution structure of the F-actin binding domain of Bcr-Abl/c-Abl
ComponentsProto-oncogene tyrosine-protein kinase ABL1
KeywordsTRANSFERASE / four helix bundle / nuclear export signal
Function / homology
Function and homology information


mitochondrial depolarization / positive regulation of interleukin-2 production => GO:0032743 / transitional one stage B cell differentiation / positive regulation of actin filament binding / DNA conformation change / negative regulation of phospholipase C activity / regulation of extracellular matrix organization / activation of protein kinase C activity / positive regulation blood vessel branching / nicotinate-nucleotide adenylyltransferase activity ...mitochondrial depolarization / positive regulation of interleukin-2 production => GO:0032743 / transitional one stage B cell differentiation / positive regulation of actin filament binding / DNA conformation change / negative regulation of phospholipase C activity / regulation of extracellular matrix organization / activation of protein kinase C activity / positive regulation blood vessel branching / nicotinate-nucleotide adenylyltransferase activity / alpha-beta T cell differentiation / B cell proliferation involved in immune response / regulation of modification of synaptic structure / positive regulation of microtubule binding / positive regulation of Wnt signaling pathway, planar cell polarity pathway / microspike assembly / neuroepithelial cell differentiation / cerebellum morphogenesis / collateral sprouting / B-1 B cell homeostasis / actin filament branching / positive regulation of oxidoreductase activity / activated T cell proliferation / circulatory system development => GO:0072359 / neuropilin binding / neuropilin signaling pathway / bubble DNA binding / regulation of Cdc42 protein signal transduction / negative regulation of protein serine/threonine kinase activity / regulation of T cell differentiation / negative regulation of ubiquitin-protein transferase activity / negative regulation of BMP signaling pathway / regulation of microtubule polymerization / regulation of actin cytoskeleton reorganization / mitogen-activated protein kinase binding / positive regulation of interferon-gamma production => GO:0032729 / proline-rich region binding / syntaxin binding / DNA damage induced protein phosphorylation / cellular response to dopamine / positive regulation of osteoblast proliferation / negative regulation of cell-cell adhesion / negative regulation of cellular senescence / regulation of response to DNA damage stimulus / regulation of axon extension / platelet-derived growth factor receptor-beta signaling pathway / positive regulation of cell migration involved in sprouting angiogenesis / cell leading edge / negative regulation of long-term synaptic potentiation / actin monomer binding / neuromuscular process controlling balance / Bergmann glial cell differentiation / positive regulation of focal adhesion assembly / positive regulation of actin cytoskeleton reorganization / regulation of endocytosis / mismatch repair / regulation of hematopoietic stem cell differentiation / negative regulation of endothelial cell apoptotic process / regulation of cell adhesion / regulation of cell motility / negative regulation of mitotic cell cycle / positive regulation of substrate adhesion-dependent cell spreading / endothelial cell migration / positive regulation of muscle cell differentiation / four-way junction DNA binding / positive regulation of stress fiber assembly / signal transduction in response to DNA damage / regulation of actin cytoskeleton organization / positive regulation of endothelial cell migration / substrate adhesion-dependent cell spreading / sequence-specific double-stranded DNA binding / regulation of autophagy / cellular protein modification process / spleen development / negative regulation of I-kappaB kinase/NF-kappaB signaling / post-embryonic development / positive regulation of mitotic cell cycle / positive regulation of release of sequestered calcium ion into cytosol / SH2 domain binding / negative regulation of ERK1 and ERK2 cascade / thymus development / phosphotyrosine residue binding / protein kinase C binding / neural tube closure / ephrin receptor binding / integrin-mediated signaling pathway / peptidyl-tyrosine autophosphorylation / actin cytoskeleton organization / non-specific protein-tyrosine kinase / non-membrane spanning protein tyrosine kinase activity / establishment of protein localization / SH3 domain binding / autophagy / postsynapse / cell cycle arrest / epidermal growth factor receptor signaling pathway / cellular response to hydrogen peroxide / positive regulation of neuron death / B cell receptor signaling pathway / Fc-gamma receptor signaling pathway involved in phagocytosis
Tyrosine-protein kinase, catalytic domain / Tyrosine-protein kinase, active site / F-actin binding / Protein kinase, ATP binding site / SH3 domain / Tyrosine-protein kinase ABL1/transforming protein Abl / Tyrosine-protein kinase ABL, SH2 domain / Serine-threonine/tyrosine-protein kinase, catalytic domain / SH2 domain / SH3-like domain superfamily ...Tyrosine-protein kinase, catalytic domain / Tyrosine-protein kinase, active site / F-actin binding / Protein kinase, ATP binding site / SH3 domain / Tyrosine-protein kinase ABL1/transforming protein Abl / Tyrosine-protein kinase ABL, SH2 domain / Serine-threonine/tyrosine-protein kinase, catalytic domain / SH2 domain / SH3-like domain superfamily / SH2 domain superfamily / F-actin binding / Protein kinase domain / Protein kinase-like domain superfamily / Nucleotidyltransferases domain 2 / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha
Tyrosine-protein kinase ABL1
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR
AuthorsHantschel, O. / Wiesner, S. / Guttler, T. / Mackereth, C.D. / Rix, L.L.R. / Mikes, Z. / Dehne, J. / Gorlich, D. / Sattler, M. / Superti-Furga, G.
CitationJournal: Mol.Cell / Year: 2005
Title: Structural Basis for the Cytoskeletal Association of Bcr-Abl/c-Abl.
Authors: Hantschel, O. / Wiesner, S. / Guttler, T. / Mackereth, C.D. / Rix, L.L.R. / Mikes, Z. / Dehne, J. / Gorlich, D. / Sattler, M. / Superti-Furga, G.
Validation Report
SummaryFull reportAbout validation report
History
DepositionJun 14, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 30, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Remark 999SEQUENCE Two additional C-terminal residues (LE) result from primer design.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)14,1501
Polymers14,1501
Non-polymers00
Water0
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

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


Mass: 14150.119 Da / Num. of mol.: 1 / Fragment: F-actin binding domain (residues 1007-1130)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ABL1, ABL, JTK7 / Plasmid: modified pET24d / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P00519, EC: 2.7.1.112

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
2223D 13C-separated NOESY
131HNHA

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Sample preparation

Details
Solution-IDContentsSolvent system
11mM U-15N,13C Bcr-Abl/c-Abl FABD, 20mM phosphate buffer, 100mM NaCl, 0.02% NaN3, 5mM DTT, 90% H2O, 10% D2O90% H2O/10% D2O
21mM U-15N,13C Bcr-Abl/c-Abl FABD, 20mM phosphate buffer, 100mM NaCl, 0.02% NaN3, 5mM DTT, 100% D2O100% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (Pa)Temperature (K)
120mM sodium phosphate, 150mM NaCl, 0.02% (w/v) NaN3 6.3 ambient 295 K
220mM sodium phosphate, 150mM NaCl, 0.02% (w/v) NaN3 6.3 ambient 295 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DMXBrukerDMX5001
Bruker DMXBrukerDMX6002
Bruker DMXBrukerDMX9003

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Processing

NMR software
NameVersionDeveloperClassification
XWINNMRBrukercollection
NMRPipeDelaglio, F.processing
XEASYBartels, M.data analysis
NMRView5.0.4Johnson, B.data analysis
Aria1.2Nilges, M.refinement
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 10

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