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- PDB-4j9c: Crystal structure of the Abl-SH3 domain H59Q-N96T mutant complexe... -

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Basic information

Entry
Database: PDB / ID: 4j9c
TitleCrystal structure of the Abl-SH3 domain H59Q-N96T mutant complexed with the designed high-affinity peptide ligand P17
Components
  • P17
  • Tyrosine-protein kinase ABL1
KeywordsTransferase/unknown function / beta shandwich / SH3 domain / kinase / poly proline rich motifs / Transferase-unknown function complex
Function / homology
Function and homology information


positive regulation of actin filament binding / negative regulation of ubiquitin-protein transferase activity / positive regulation of oxidoreductase activity / protein localization to cytoplasmic microtubule plus-end / 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 ...positive regulation of actin filament binding / negative regulation of ubiquitin-protein transferase activity / positive regulation of oxidoreductase activity / protein localization to cytoplasmic microtubule plus-end / 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 / DNA conformation change / : / neuroepithelial cell differentiation / B cell proliferation involved in immune response / cerebellum morphogenesis / positive regulation of Wnt signaling pathway, planar cell polarity pathway / positive regulation of extracellular matrix organization / microspike assembly / B-1 B cell homeostasis / neuropilin signaling pathway / neuropilin binding / bubble DNA binding / mitochondrial depolarization / regulation of cell motility / activated T cell proliferation / positive regulation of establishment of T cell polarity / cellular response to dopamine / positive regulation of blood vessel branching / proline-rich region binding / regulation of Cdc42 protein signal transduction / syntaxin binding / mitogen-activated protein kinase binding / regulation of hematopoietic stem cell differentiation / myoblast proliferation / alpha-beta T cell differentiation / positive regulation of dendrite development / regulation of axon extension / regulation of T cell differentiation / cardiac muscle cell proliferation / positive regulation of cell migration involved in sprouting angiogenesis / HDR through Single Strand Annealing (SSA) / negative regulation of cell-cell adhesion / positive regulation of peptidyl-tyrosine phosphorylation / Myogenesis / platelet-derived growth factor receptor-beta signaling pathway / positive regulation of osteoblast proliferation / RUNX2 regulates osteoblast differentiation / regulation of microtubule polymerization / Fc-gamma receptor signaling pathway involved in phagocytosis / associative learning / vascular endothelial cell response to oscillatory fluid shear stress / Bergmann glial cell differentiation / regulation of endocytosis / neuromuscular process controlling balance / negative regulation of cellular senescence / negative regulation of long-term synaptic potentiation / negative regulation of mitotic cell cycle / negative regulation of BMP signaling pathway / actin monomer binding / canonical NF-kappaB signal transduction / signal transduction in response to DNA damage / positive regulation of focal adhesion assembly / RHO GTPases Activate WASPs and WAVEs / BMP signaling pathway / endothelial cell migration / positive regulation of T cell migration / negative regulation of double-strand break repair via homologous recombination / mismatch repair / negative regulation of endothelial cell apoptotic process / regulation of cell adhesion / peptidyl-tyrosine autophosphorylation / four-way junction DNA binding / cellular response to transforming growth factor beta stimulus / spleen development / positive regulation of stress fiber assembly / ruffle / positive regulation of vasoconstriction / ephrin receptor binding / actin filament polymerization / positive regulation of substrate adhesion-dependent cell spreading / phosphotyrosine residue binding / positive regulation of endothelial cell migration / ERK1 and ERK2 cascade / positive regulation of interleukin-2 production / positive regulation of mitotic cell cycle / substrate adhesion-dependent cell spreading / SH2 domain binding / response to endoplasmic reticulum stress / positive regulation of release of sequestered calcium ion into cytosol / thymus development / protein kinase C binding / Turbulent (oscillatory, disturbed) flow shear stress activates signaling by PIEZO1 and integrins in endothelial cells / post-embryonic development / integrin-mediated signaling pathway / establishment of localization in cell
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 / SH2 domain superfamily / Src homology 3 domains / SH3 type barrels. / 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
DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Tyrosine-protein kinase ABL1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.051 Å
AuthorsCamara-Artigas, A.
Citation
Journal: To be Published
Title: Crystal structure of the Abl-SH3 domain H59Q-N96T mutant complexed with the designed high-affinity peptide ligand P17
Authors: Camara-Artigas, A.
#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.
#2: 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.
History
DepositionFeb 16, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 29, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 15, 2014Group: Structure summary
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / 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_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 27, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tyrosine-protein kinase ABL1
B: P17
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,3084
Polymers8,0522
Non-polymers2562
Water1,44180
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.646, 49.646, 45.410
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number153
Space group name H-MP3212
Components on special symmetry positions
IDModelComponents
11A-303-

HOH

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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: 6986.677 Da / Num. of mol.: 1 / Fragment: SH3 domain (unp residues 60-121) / Mutation: H59Q, N96T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ABL, ABL1, JTK7 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P00519, non-specific protein-tyrosine kinase
#2: Protein/peptide P17


Mass: 1065.218 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 80 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.01 Å3/Da / Density % sol: 38.69 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 1.5 M AMS, 5% PEG 200, 20 mM LiCl, 0.1 M AcONa , pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.97 Å
DetectorDetector: CCD / Date: Apr 8, 2011
RadiationMonochromator: Channel cut ESRF monochromator and torodial focusing mirror
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.051→42.995 Å / Num. all: 29920 / Num. obs: 29561 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.3 % / Biso Wilson estimate: 8.3 Å2 / Rmerge(I) obs: 0.04 / Rsym value: 0.04 / Net I/σ(I): 28.7
Reflection shellResolution: 1.05→1.11 Å / Rmerge(I) obs: 0.472 / Mean I/σ(I) obs: 4.61 / Num. unique all: 4721 / % possible all: 99.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALA0.1.30data scaling
PHASERphasing
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.11data extraction
ADSCQuantumdata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2O88

2o88


Resolution: 1.051→16.754 Å / Occupancy max: 1 / Occupancy min: 0 / SU ML: 0.08 / σ(F): 0 / σ(I): 0 / Phase error: 13.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1622 1500 5.08 %RANDOM
Rwork0.146 ---
all0.1468 ---
obs0.1468 29561 98.64 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 40.03 Å2 / Biso mean: 14.95 Å2 / Biso min: 6.31 Å2
Refinement stepCycle: LAST / Resolution: 1.051→16.754 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms529 0 17 80 626
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008569
X-RAY DIFFRACTIONf_angle_d1.237772
X-RAY DIFFRACTIONf_chiral_restr0.0783
X-RAY DIFFRACTIONf_plane_restr0.00899
X-RAY DIFFRACTIONf_dihedral_angle_d14.422209
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 21

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.051-1.06830.26661250.22982575270098
1.0683-1.08670.24391300.1922612274299
1.0867-1.10650.18021520.17326322784100
1.1065-1.12770.15021400.156426142754100
1.1277-1.15070.21991190.141226332752100
1.1507-1.17580.18491760.131926162792100
1.1758-1.20310.13371470.130926232770100
1.2031-1.23320.15451270.133226062733100
1.2332-1.26650.19041700.131926352805100
1.2665-1.30380.18991520.128326012753100
1.3038-1.34580.15261340.126226932827100
1.3458-1.39390.14211330.116525842717100
1.3939-1.44970.1461580.11726242782100
1.4497-1.51560.14161330.116326552788100
1.5156-1.59550.17041800.123926212801100
1.5955-1.69530.12321540.117525922746100
1.6953-1.82610.17411230.121226802803100
1.8261-2.00960.13671360.12526112747100
2.0096-2.29970.12461360.13726432779100
2.2997-2.8950.15691280.163126472775100
2.895-16.75580.2325660.19482074214077

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