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- PDB-5np5: Abl2 SH3 pTyr116/161 -

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Basic information

Entry
Database: PDB / ID: 5np5
TitleAbl2 SH3 pTyr116/161
ComponentsAbelson tyrosine-protein kinase 2
KeywordsTRANSFERASE / signaling / tyrosine phosphorylation / SH3 domain / kinase
Function / homology
Function and homology information


positive regulation of oxidoreductase activity / Role of ABL in ROBO-SLIT signaling / regulation of cell motility / exploration behavior / negative regulation of Rho protein signal transduction / regulation of endocytosis / actin monomer binding / RAC3 GTPase cycle / positive regulation of T cell migration / regulation of cell adhesion ...positive regulation of oxidoreductase activity / Role of ABL in ROBO-SLIT signaling / regulation of cell motility / exploration behavior / negative regulation of Rho protein signal transduction / regulation of endocytosis / actin monomer binding / RAC3 GTPase cycle / positive regulation of T cell migration / regulation of cell adhesion / cellular response to retinoic acid / positive regulation of establishment of T cell polarity / RAC1 GTPase cycle / Negative regulation of FLT3 / phosphotyrosine residue binding / regulation of autophagy / regulation of actin cytoskeleton organization / non-specific protein-tyrosine kinase / non-membrane spanning protein tyrosine kinase activity / epidermal growth factor receptor signaling pathway / protein modification process / positive regulation of neuron projection development / peptidyl-tyrosine phosphorylation / actin filament binding / actin cytoskeleton / manganese ion binding / phospholipase C-activating G protein-coupled receptor signaling pathway / positive regulation of cytosolic calcium ion concentration / protein tyrosine kinase activity / cell adhesion / protein kinase activity / magnesium ion binding / signal transduction / ATP binding / plasma membrane / cytosol
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 / SH3 type barrels. / 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 / 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 ABL2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsMero, B. / Radnai, L. / Gogl, G. / Leveles, I. / Buday, L.
CitationJournal: J.Biol.Chem. / Year: 2019
Title: Structural insights into the tyrosine phosphorylation-mediated inhibition of SH3 domain-ligand interactions.
Authors: Mero, B. / Radnai, L. / Gogl, G. / Toke, O. / Leveles, I. / Koprivanacz, K. / Szeder, B. / Dulk, M. / Kudlik, G. / Vas, V. / Cserkaszky, A. / Sipeki, S. / Nyitray, L. / Vertessy, B.G. / Buday, L.
History
DepositionApr 13, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 16, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 30, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Apr 3, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Oct 23, 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: Abelson tyrosine-protein kinase 2
B: Abelson tyrosine-protein kinase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,9493
Polymers13,8532
Non-polymers961
Water1,69394
1
A: Abelson tyrosine-protein kinase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,0232
Polymers6,9261
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Abelson tyrosine-protein kinase 2


Theoretical massNumber of molelcules
Total (without water)6,9261
Polymers6,9261
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)22.510, 45.910, 45.770
Angle α, β, γ (deg.)90.00, 89.74, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Abelson tyrosine-protein kinase 2 / Abelson murine leukemia viral oncogene homolog 2 / Abelson-related gene protein / Tyrosine-protein kinase ARG


Mass: 6926.440 Da / Num. of mol.: 2 / Fragment: SH3 domain, UNP Residues 110-166
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ABL2, ABLL, ARG / Production host: Escherichia coli (E. coli)
References: UniProt: P42684, non-specific protein-tyrosine kinase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 94 / 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: 1.71 Å3/Da / Density % sol: 27.95 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6 / Details: 1.8 M (NH4)2SO4, 0.1 M sodium acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 7, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.4→32.413 Å / Num. obs: 18354 / % possible obs: 99.4 % / Redundancy: 3.35 % / CC1/2: 1 / Rmerge(I) obs: 0.031 / Net I/σ(I): 18.34
Reflection shellResolution: 1.4→1.44 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 1.93 / CC1/2: 0.686 / % possible all: 99

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Processing

Software
NameVersionClassification
PHENIXdev_1750refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ABO

1abo


Resolution: 1.4→32.413 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.66
RfactorNum. reflection% reflection
Rfree0.1985 962 5.25 %
Rwork0.1719 --
obs0.1733 18336 99.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.4→32.413 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms935 0 5 94 1034
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0161016
X-RAY DIFFRACTIONf_angle_d1.611400
X-RAY DIFFRACTIONf_dihedral_angle_d14.299359
X-RAY DIFFRACTIONf_chiral_restr0.088146
X-RAY DIFFRACTIONf_plane_restr0.009183
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.47380.31391410.27812427X-RAY DIFFRACTION99
1.4738-1.56620.26461100.23812502X-RAY DIFFRACTION100
1.5662-1.68710.24351380.21532479X-RAY DIFFRACTION99
1.6871-1.85680.22311670.19342456X-RAY DIFFRACTION100
1.8568-2.12550.21261010.17262503X-RAY DIFFRACTION99
2.1255-2.67770.21161590.17472490X-RAY DIFFRACTION100
2.6777-32.42220.16261460.14462517X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.2579-2.69360.35215.81531.15731.671-0.00210.27020.15930.0375-0.17090.0567-0.35610.18940.19430.1022-0.03140.00230.17660.03310.11431.670412.2227-12.8803
26.9823-1.8721-1.2495.21961.91343.402-0.00970.2291-0.49260.05320.1794-0.4370.1570.0686-0.02670.0722-0.0189-0.01510.1527-0.03680.201716.2456.6729-15.3674
32.35731.07790.95912.76511.92354.140.0013-0.02680.0271-0.1705-0.0543-0.0559-0.0552-0.09950.10860.09590.0005-0.01730.15860.00280.12466.34618.9782-18.5621
45.57782.71941.08493.18980.70822.454-0.1481-0.03720.0588-0.3152-0.0488-0.2134-0.16060.07770.03490.1134-0.0135-0.0150.15510.01830.132612.053211.4205-18.0888
52.39580.887-1.28967.81533.04942.5409-0.239-0.3173-0.19530.478-0.0590.02730.36960.01030.14530.1364-0.0144-0.00110.22060.02560.10524.19894.8896-10.6778
63.21350.84532.02966.6447-0.89711.57510.196-0.2706-0.486-0.20960.40750.4301-0.16260.1045-0.19130.2946-0.08490.01180.24830.01260.19781.63063.17474.9136
71.0512-0.10071.22431.3563-0.17491.4482-0.2024-0.02880.18740.76310.32190.1586-1.29260.05170.66990.5228-0.0733-0.00470.12580.01720.18981.11977.9794.633
83.56412.1441-1.06951.79780.33222.15790.0798-0.3895-0.0704-0.22280.0837-0.1761-0.99510.22740.0430.34630.010.04590.1453-0.05630.12316.31685.442213.3277
95.1027-2.91120.32993.3594-0.73620.2002-0.29280.17890.06060.6250.33410.3374-0.5665-0.4742-0.17570.30460.1450.11810.31710.0620.2361-2.19617.40428.7128
104.2434-1.8585-1.087.7796-4.58717.1018-0.06750.3988-0.0002-0.8537-0.25940.18870.31290.81270.44380.3062-0.10990.00190.49-0.0090.14088.45715.72831.9152
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 60 through 69 )
2X-RAY DIFFRACTION2chain 'A' and (resid 71 through 85 )
3X-RAY DIFFRACTION3chain 'A' and (resid 86 through 104 )
4X-RAY DIFFRACTION4chain 'A' and (resid 105 through 112 )
5X-RAY DIFFRACTION5chain 'A' and (resid 113 through 120 )
6X-RAY DIFFRACTION6chain 'B' and (resid 64 through 79 )
7X-RAY DIFFRACTION7chain 'B' and (resid 80 through 93 )
8X-RAY DIFFRACTION8chain 'B' and (resid 94 through 103 )
9X-RAY DIFFRACTION9chain 'B' and (resid 104 through 112 )
10X-RAY DIFFRACTION10chain 'B' and (resid 113 through 120 )

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