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- PDB-7pvs: Crystal structure of the Abl SH3 domain V73E-A74S-S75R-G76T-D77E-... -

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Basic information

Entry
Database: PDB / ID: 7pvs
TitleCrystal structure of the Abl SH3 domain V73E-A74S-S75R-G76T-D77E-G92N-Y93N-N94T-H95E mutant in presence of PEG 200
ComponentsTyrosine-protein kinase ABL1
KeywordsPROTEIN BINDING / beta barrel / SH3 domain
Function / homology
Function and homology information


: / positive regulation of actin filament binding / positive regulation of oxidoreductase activity / protein localization to cytoplasmic microtubule plus-end / DNA conformation change / podocyte apoptotic process / DN4 thymocyte differentiation / Role of ABL in ROBO-SLIT signaling / response to epinephrine / transitional one stage B cell differentiation ...: / positive regulation of actin filament binding / positive regulation of oxidoreductase activity / protein localization to cytoplasmic microtubule plus-end / DNA conformation change / podocyte apoptotic process / DN4 thymocyte differentiation / Role of ABL in ROBO-SLIT signaling / response to epinephrine / transitional one stage B cell differentiation / activation of protein kinase C activity / nicotinate-nucleotide adenylyltransferase activity / regulation of modification of synaptic structure / positive regulation of microtubule binding / delta-catenin binding / B cell proliferation involved in immune response / positive regulation of extracellular matrix organization / neuroepithelial cell differentiation / microspike assembly / positive regulation of Wnt signaling pathway, planar cell polarity pathway / cerebellum morphogenesis / positive regulation of blood vessel branching / B-1 B cell homeostasis / mitochondrial depolarization / negative regulation of ubiquitin-protein transferase activity / neuropilin signaling pathway / neuropilin binding / bubble DNA binding / negative regulation of protein serine/threonine kinase activity / activated T cell proliferation / cellular response to dopamine / regulation of cell motility / regulation of Cdc42 protein signal transduction / proline-rich region binding / positive regulation of dendrite development / mitogen-activated protein kinase binding / myoblast proliferation / alpha-beta T cell differentiation / regulation of hematopoietic stem cell differentiation / syntaxin binding / cardiac muscle cell proliferation / regulation of T cell differentiation / regulation of axon extension / HDR through Single Strand Annealing (SSA) / positive regulation of cell migration involved in sprouting angiogenesis / negative regulation of cell-cell adhesion / Fc-gamma receptor signaling pathway involved in phagocytosis / Myogenesis / regulation of microtubule polymerization / positive regulation of osteoblast proliferation / RUNX2 regulates osteoblast differentiation / platelet-derived growth factor receptor-beta signaling pathway / positive regulation of focal adhesion assembly / negative regulation of cellular senescence / Bergmann glial cell differentiation / associative learning / neuromuscular process controlling balance / regulation of endocytosis / negative regulation of BMP signaling pathway / negative regulation of mitotic cell cycle / actin monomer binding / negative regulation of long-term synaptic potentiation / endothelial cell migration / RHO GTPases Activate WASPs and WAVEs / positive regulation of T cell migration / canonical NF-kappaB signal transduction / signal transduction in response to DNA damage / negative regulation of double-strand break repair via homologous recombination / mismatch repair / BMP signaling pathway / regulation of cell adhesion / negative regulation of endothelial cell apoptotic process / four-way junction DNA binding / positive regulation of substrate adhesion-dependent cell spreading / peptidyl-tyrosine autophosphorylation / positive regulation of vasoconstriction / positive regulation of stress fiber assembly / spleen development / ruffle / cellular response to transforming growth factor beta stimulus / positive regulation of establishment of T cell polarity / ERK1 and ERK2 cascade / positive regulation of interleukin-2 production / actin filament polymerization / phosphotyrosine residue binding / SH2 domain binding / response to endoplasmic reticulum stress / ephrin receptor binding / positive regulation of endothelial cell migration / positive regulation of mitotic cell cycle / substrate adhesion-dependent cell spreading / positive regulation of release of sequestered calcium ion into cytosol / post-embryonic development / thymus development / regulation of autophagy / neural tube closure / establishment of localization in cell / integrin-mediated signaling pathway / regulation of actin cytoskeleton organization / protein kinase C binding
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 / Src homology 3 domains ...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 / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / 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
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: 1.05 Å
Model detailsChimera construction Abl-c-Src SH3 domain
AuthorsCamara-Artigas, A. / Salinas Garcia, M.C.
Funding support Spain, 1items
OrganizationGrant numberCountry
Ministry of Economy and Competitiveness (MINECO)BIO2006-78020-R Spain
CitationJournal: To be published
Title: The effect of the hinge loops composition in the domain swapping of the SH3 domain
Authors: Camara-Artigas, A. / Salinas Garcia, M.C.
History
DepositionOct 5, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 14, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)14,1509
Polymers13,3012
Non-polymers8507
Water2,540141
1
A: Tyrosine-protein kinase ABL1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,1126
Polymers6,6501
Non-polymers4615
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Tyrosine-protein kinase ABL1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,0393
Polymers6,6501
Non-polymers3882
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)27.125, 43.479, 94.580
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21221
Components on special symmetry positions
IDModelComponents
11A-331-

HOH

21A-342-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#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: 6650.293 Da / Num. of mol.: 2
Mutation: V73E, A74S, S75R, G76T, D77E, G92N, Y93N, N94T, H95E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ABL1, ABL, JTK7 / Plasmid: pHTP1 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P00519, non-specific protein-tyrosine kinase

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Non-polymers , 6 types, 148 molecules

#2: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400 / Polyethylene glycol


Mass: 282.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 141 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.1 Å3/Da / Density % sol: 41.33 % / Mosaicity: 0.09 °
Crystal growTemperature: 283 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 2.6 M ammonium sulfate, 5% PEG200, 10% Glicerol, 40mM LiCl, 0.1M MES

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97926 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 9, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 1.05→19.75 Å / Num. obs: 52808 / % possible obs: 99.3 % / Redundancy: 5.1 % / Biso Wilson estimate: 9.98 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.044 / Rpim(I) all: 0.021 / Rrim(I) all: 0.049 / Net I/σ(I): 14.8 / Num. measured all: 271721
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.05-1.073.50.638835723840.760.3740.7441.992.9
5.75-19.754.80.0218663880.9990.0110.02351.797.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.7.7data scaling
PHASERphasing
PHENIX1.19.1refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3EG3

3eg3


Resolution: 1.05→19.75 Å / SU ML: 0.08 / Cross valid method: THROUGHOUT / σ(F): 0.01 / Phase error: 18.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1843 5061 5.11 %
Rwork0.1688 93949 -
obs0.1695 99010 98.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 49.81 Å2 / Biso mean: 14.3649 Å2 / Biso min: 6.28 Å2
Refinement stepCycle: final / Resolution: 1.05→19.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms934 0 102 141 1177
Biso mean--30.18 23.37 -
Num. residues----117
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.05-1.060.27221380.2582629276783
1.06-1.070.25661420.23852959310191
1.07-1.090.22231590.22463102326196
1.09-1.10.20751920.19893051324399
1.1-1.120.18041550.18133187334298
1.12-1.130.19461440.18163160330498
1.13-1.150.19881600.1773108326898
1.15-1.160.18871740.16883156333099
1.16-1.180.1961760.1693200337699
1.18-1.20.17331750.17163099327499
1.2-1.220.18731770.16493209338699
1.22-1.240.18721890.16643107329699
1.24-1.270.18841850.1633112329798
1.27-1.290.17261380.1563189332798
1.29-1.320.1941770.16263124330199
1.32-1.350.17851830.15653199338299
1.35-1.390.16381660.14943093325999
1.39-1.420.17471550.14753231338699
1.43-1.470.17731900.15123119330999
1.47-1.510.15511810.143432133394100
1.51-1.570.17711770.13873114329199
1.57-1.630.18041560.14393155331199
1.63-1.710.18161840.147832073391100
1.71-1.80.18421520.15333164331699
1.8-1.910.1631840.14983132331699
1.91-2.050.15791760.145532183394100
2.05-2.260.1691740.14583164333899
2.26-2.590.18372060.181531433349100
2.59-3.260.19581630.191731773340100
3.26-19.750.2031330.190632283361100

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