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- PDB-3eg3: Crystal structure of the N114A mutant of ABL-SH3 domain -

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Basic information

Entry
Database: PDB / ID: 3eg3
TitleCrystal structure of the N114A mutant of ABL-SH3 domain
ComponentsProto-oncogene tyrosine-protein kinase ABL1
KeywordsTRANSFERASE / beta / ATP-binding / Cell adhesion / Cytoskeleton / Kinase / Lipoprotein / Magnesium / Manganese / Metal-binding / Myristate / Nucleotide-binding / Nucleus / Phosphoprotein / Proto-oncogene / SH2 domain / SH3 domain / Tyrosine-protein kinase
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 / myoblast proliferation / negative regulation of long-term synaptic potentiation / 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 / mismatch repair / regulation of cell adhesion / 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 / response to endoplasmic reticulum stress / peptidyl-tyrosine phosphorylation / positive regulation of release of sequestered calcium ion into cytosol / thymus development / 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)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.4 Å
AuthorsCamara-Artigas, A.
Citation
Journal: J.Biol.Chem. / Year: 2010
Title: Role of interfacial water molecules in proline-rich ligand recognition by the Src homology 3 domain of Abl.
Authors: Palencia, A. / Camara-Artigas, A. / Pisabarro, M.T. / Martinez, J.C. / Luque, I.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2007
Title: Crystallization by capillary counter-diffusion and structure determination of the N114A mutant of the SH3 domain of Abl tyrosine kinase complexed with a high-affinity peptide ligand
Authors: Camara-Artigas, A. / Palencia, A. / Martinez, J.C. / Luque, I. / Gavira, J.A. / Garcia-Ruiz, J.M.
History
DepositionSep 10, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 15, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Oct 20, 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 1.3Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)7,0592
Polymers6,9671
Non-polymers921
Water64936
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.819, 53.096, 41.296
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number21
Space group name H-MC222
Components on special symmetry positions
IDModelComponents
11A-36-

HOH

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Components

#1: Protein Proto-oncogene tyrosine-protein kinase ABL1 / p150 / c- ABL / Abelson murine leukemia viral oncogene homolog 1


Mass: 6966.669 Da / Num. of mol.: 1 / Fragment: SH3 DOMAIN, RESIDUES 60-121 / Mutation: N114A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Strain: PBAT4 / Gene: ABL1, ABL, JTK7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P00519, non-specific protein-tyrosine kinase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 36 / 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: 1.76 Å3/Da / Density % sol: 30.24 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 3
Details: 2M ammonium sulphate, 5% PEG300, 10% glycerol, and 0.1 M of buffer solution, vapor diffusion, hanging drop, temperature 288K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.54 Å
DetectorType: BRUKER SMART 6000 / Detector: CCD / Date: Jan 19, 2006 / Details: Montel Optics
RadiationMonochromator: BRUKER MICROSTAR MICRO-FOCUS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.35→41.31 Å / Num. all: 11162 / Num. obs: 10303 / % possible obs: 92.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.79 % / Biso Wilson estimate: 12.829 Å2 / Rmerge(I) obs: 0.0328 / Rsym value: 0.0328
Reflection shellResolution: 1.35→1.45 Å / Redundancy: 3 % / Rmerge(I) obs: 0.1326 / Mean I/σ(I) obs: 7.3 / Num. unique all: 1734 / Rsym value: 0.1326 / % possible all: 82.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SAINTdata scaling
SCALAdata scaling
MOLREPphasing
REFMAC5.2.0019refinement
PDB_EXTRACT3.006data extraction
PROTEUM PLUSdata collection
SAINTdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1ABQ

1abq


Resolution: 1.4→13.77 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.937 / Occupancy max: 1 / Occupancy min: 0.2 / SU B: 1.22 / SU ML: 0.051 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.087 / ESU R Free: 0.087 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24 442 4.7 %RANDOM
Rwork0.208 ---
obs0.21 9380 93.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 40.23 Å2 / Biso mean: 15.844 Å2 / Biso min: 2.77 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20 Å20 Å2
2--0.07 Å20 Å2
3----0.05 Å2
Refinement stepCycle: LAST / Resolution: 1.4→13.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms491 0 6 36 533
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.021524
X-RAY DIFFRACTIONr_angle_refined_deg2.0971.931716
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.659566
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.06125.76926
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.1851578
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.097151
X-RAY DIFFRACTIONr_chiral_restr0.120.276
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.02415
X-RAY DIFFRACTIONr_nbd_refined0.2360.2184
X-RAY DIFFRACTIONr_nbtor_refined0.3170.2341
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2410.235
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2730.275
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2280.223
X-RAY DIFFRACTIONr_mcbond_it1.4321.5332
X-RAY DIFFRACTIONr_mcangle_it2.1742518
X-RAY DIFFRACTIONr_scbond_it3.3353228
X-RAY DIFFRACTIONr_scangle_it3.784.5197
LS refinement shellResolution: 1.4→1.436 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.342 30 -
Rwork0.235 578 -
all-608 -
obs--85.88 %

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