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- PDB-1awo: THE SOLUTION NMR STRUCTURE OF ABL SH3 AND ITS RELATIONSHIP TO SH2... -

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Entry
Database: PDB / ID: 1awo
TitleTHE SOLUTION NMR STRUCTURE OF ABL SH3 AND ITS RELATIONSHIP TO SH2 IN THE SH(32) CONSTRUCT, 20 STRUCTURES
ComponentsABL TYROSINE KINASE
KeywordsKINASE / SH3 DOMAIN / TRANSFERASE / PHOSPHOTRANSFERASE / PROTO-ONCOGENE / MULTIPLE DOMAIN / LEUKEMIA
Function / homology
Function and homology information


: / positive regulation of actin filament binding / negative regulation of ubiquitin-protein transferase activity / protein localization to cytoplasmic microtubule plus-end / DNA conformation change / DN4 thymocyte differentiation / response to epinephrine / activation of protein kinase C activity / phospholipase C-inhibiting G protein-coupled receptor signaling pathway / podocyte apoptotic process ...: / positive regulation of actin filament binding / negative regulation of ubiquitin-protein transferase activity / protein localization to cytoplasmic microtubule plus-end / DNA conformation change / DN4 thymocyte differentiation / response to epinephrine / activation of protein kinase C activity / phospholipase C-inhibiting G protein-coupled receptor signaling pathway / podocyte apoptotic process / delta-catenin binding / Role of ABL in ROBO-SLIT signaling / transitional one stage B cell differentiation / regulation of postsynaptic specialization assembly / regulation of modification of synaptic structure / nicotinate-nucleotide adenylyltransferase activity / cerebellum morphogenesis / neuroepithelial cell differentiation / B cell proliferation involved in immune response / 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 / bubble DNA binding / mitochondrial depolarization / regulation of cell motility / positive regulation of establishment of T cell polarity / activated T cell proliferation / cellular response to dopamine / 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 / syntaxin binding / alpha-beta T cell differentiation / positive regulation of dendrite development / positive regulation of cell migration involved in sprouting angiogenesis / peptidyl-tyrosine autophosphorylation / regulation of axon extension / regulation of T cell differentiation / positive regulation of peptidyl-tyrosine phosphorylation / negative regulation of cell-cell adhesion / HDR through Single Strand Annealing (SSA) / neuromuscular process controlling balance / Myogenesis / positive regulation of osteoblast proliferation / platelet-derived growth factor receptor-beta signaling pathway / positive regulation of vasoconstriction / RUNX2 regulates osteoblast differentiation / Fc-gamma receptor signaling pathway involved in phagocytosis / vascular endothelial cell response to oscillatory fluid shear stress / regulation of endocytosis / Bergmann glial cell differentiation / regulation of microtubule polymerization / negative regulation of long-term synaptic potentiation / myoblast proliferation / associative learning / negative regulation of cellular senescence / actin monomer binding / signal transduction in response to DNA damage / positive regulation of focal adhesion assembly / canonical NF-kappaB signal transduction / negative regulation of BMP signaling pathway / RHO GTPases Activate WASPs and WAVEs / cardiac muscle cell proliferation / ephrin receptor signaling pathway / positive regulation of T cell migration / endothelial cell migration / BMP signaling pathway / negative regulation of double-strand break repair via homologous recombination / cellular response to transforming growth factor beta stimulus / negative regulation of endothelial cell apoptotic process / regulation of cell adhesion / mismatch repair / ephrin receptor binding / four-way junction DNA binding / spleen development / positive regulation of stress fiber assembly / ruffle / ERK1 and ERK2 cascade / actin filament polymerization / phosphotyrosine residue binding / positive regulation of substrate adhesion-dependent cell spreading / positive regulation of interleukin-2 production / positive regulation of endothelial cell migration / SH2 domain binding / substrate adhesion-dependent cell spreading / positive regulation of mitotic cell cycle / protein kinase C binding / peptidyl-tyrosine phosphorylation / response to endoplasmic reticulum stress / thymus development / positive regulation of release of sequestered calcium ion into cytosol / Turbulent (oscillatory, disturbed) flow shear stress activates signaling by PIEZO1 and integrins in endothelial cells / 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 Domains / : / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains ...F-actin binding / F-actin binding / F-actin binding domain (FABD) / Tyrosine-protein kinase ABL, SH2 domain / SH3 Domains / : / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / SH3 type barrels. / 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 / Roll / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Mainly Beta
Similarity search - Domain/homology
Tyrosine-protein kinase ABL1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / VARIABLE TARGET FUNCTION TORSION ANGLE SIMULATED ANNEALING
AuthorsCowburn, D.
Citation
Journal: Structure / Year: 1995
Title: The solution structure of Abl SH3, and its relationship to SH2 in the SH(32) construct.
Authors: Gosser, Y.Q. / Zheng, J. / Overduin, M. / Mayer, B.J. / Cowburn, D.
#1: Journal: Mol.Cell.Biol. / Year: 1994
Title: Mutagenic Analysis of the Roles of Sh2 and SH3 Domains in Regulation of the Abl Tyrosine Kinase
Authors: Mayer, B.J. / Baltimore, D.
#2: Journal: Nat.Struct.Biol. / Year: 1994
Title: High-Resolution Crystal Structures of Tyrosine Kinase SH3 Domains Complexed with Proline-Rich Peptides
Authors: Musacchio, A. / Saraste, M. / Wilmanns, M.
#3: Journal: Science / Year: 1993
Title: Identification of a Ten-Amino Acid Proline-Rich SH3 Binding Site
Authors: Ren, R. / Mayer, B.J. / Cicchetti, P. / Baltimore, D.
#4: Journal: Embo J. / Year: 1993
Title: Crystal Structure of the SH3 Domain in Human Fyn; Comparison of the Three-Dimensional Structures of SH3 Domains in Tyrosine Kinases and Spectrin
Authors: Noble, M.E. / Musacchio, A. / Saraste, M. / Courtneidge, S.A. / Wierenga, R.K.
#5: Journal: Cell(Cambridge,Mass.) / Year: 1992
Title: Three-Dimensional Solution Structure of the Src Homology 2 Domain of C-Abl
Authors: Overduin, M. / Rios, C.B. / Mayer, B.J. / Baltimore, D. / Cowburn, D.
#6: Journal: Nature / Year: 1992
Title: Crystal Structure of a Src-Homology 3 (SH3) Domain
Authors: Musacchio, A. / Noble, M. / Pauptit, R. / Wierenga, R. / Saraste, M.
History
DepositionOct 3, 1997Processing site: BNL
Revision 1.0Jan 28, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 16, 2022Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_ref_seq_dif.details
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ABL TYROSINE KINASE


Theoretical massNumber of molelcules
Total (without water)6,6371
Polymers6,6371
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100LOWEST TARGET FUNCTION
Representative

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Components

#1: Protein ABL TYROSINE KINASE


Mass: 6637.299 Da / Num. of mol.: 1 / Fragment: SRC-HOMOLOGY 3 (SH3) DOMAIN / Mutation: N64S, N120S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: EXPRESSED AS GST FUSIONS AND CLEAVED / Plasmid: PGEX / Production host: Escherichia coli (E. coli) / Strain (production host): NB42 / 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
111HMQX
121HTQC
131H/13C HSQC
1411H-13C HQQC
151NOESY
161NOESY-HMQC
171J-HMQC
181EXCHANGE
19115N{1H NOE

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Sample preparation

Sample conditionspH: 7.5 / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
GE GE OMEGA 400GEGE OMEGA 4005001
Bruker DMX 600BrukerDMX 6005002

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Processing

NMR software
NameVersionDeveloperClassification
DIANA2.1WUTHRICHrefinement
RUNMRstructure solution
UXNMRstructure solution
DIANA (REDAC)(REDAC)structure solution
RefinementMethod: VARIABLE TARGET FUNCTION TORSION ANGLE SIMULATED ANNEALING
Software ordinal: 1 / Details: USED REDAC STRATEGY
NMR ensembleConformer selection criteria: LOWEST TARGET FUNCTION / Conformers calculated total number: 100 / Conformers submitted total number: 20

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