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- PDB-5np3: Abl2 SH3 -

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Basic information

Entry
Database: PDB / ID: 5np3
TitleAbl2 SH3
ComponentsAbelson tyrosine-protein kinase 2
KeywordsTRANSFERASE / signaling / tyrosine phosphorylation / SH3 domain / kinase
Function / homology
Function and homology information


Role of ABL in ROBO-SLIT signaling / regulation of cell motility / positive regulation of establishment of T cell polarity / negative regulation of Rho protein signal transduction / exploration behavior / regulation of endocytosis / actin monomer binding / RAC3 GTPase cycle / positive regulation of T cell migration / regulation of cell adhesion ...Role of ABL in ROBO-SLIT signaling / regulation of cell motility / positive regulation of establishment of T cell polarity / negative regulation of Rho protein signal transduction / exploration behavior / regulation of endocytosis / actin monomer binding / RAC3 GTPase cycle / positive regulation of T cell migration / regulation of cell adhesion / cellular response to retinoic acid / phosphotyrosine residue binding / RAC1 GTPase cycle / Negative regulation of FLT3 / regulation of actin cytoskeleton organization / non-membrane spanning protein tyrosine kinase activity / non-specific protein-tyrosine kinase / enzyme activator activity / peptidyl-tyrosine phosphorylation / protein modification process / positive regulation of neuron projection development / epidermal growth factor receptor signaling pathway / actin filament binding / actin cytoskeleton / manganese ion binding / positive regulation of cytosolic calcium ion concentration / cellular response to oxidative stress / protein tyrosine kinase activity / phospholipase C-activating G protein-coupled receptor signaling pathway / protein kinase activity / cell adhesion / regulation of autophagy / enzyme binding / 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 / SH2 domain / Src homology 3 domains / SH3 type barrels. / 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: 2 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

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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
C: Abelson tyrosine-protein kinase 2
D: Abelson tyrosine-protein kinase 2


Theoretical massNumber of molelcules
Total (without water)27,0664
Polymers27,0664
Non-polymers00
Water66737
1
A: Abelson tyrosine-protein kinase 2


Theoretical massNumber of molelcules
Total (without water)6,7661
Polymers6,7661
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Abelson tyrosine-protein kinase 2


Theoretical massNumber of molelcules
Total (without water)6,7661
Polymers6,7661
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Abelson tyrosine-protein kinase 2


Theoretical massNumber of molelcules
Total (without water)6,7661
Polymers6,7661
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Abelson tyrosine-protein kinase 2


Theoretical massNumber of molelcules
Total (without water)6,7661
Polymers6,7661
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.780, 44.780, 173.910
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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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: 6766.482 Da / Num. of mol.: 4 / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 37 / 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: 1.86 Å3/Da / Density % sol: 33.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 1.8 M di-sodium-DL-malate

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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: 2→38.8 Å / Num. obs: 13363 / % possible obs: 99.9 % / Redundancy: 10.1 % / CC1/2: 1 / Rmerge(I) obs: 0.089 / Net I/σ(I): 15.46
Reflection shellResolution: 2→2.05 Å / Redundancy: 8.3 % / Rmerge(I) obs: 1.05 / Mean I/σ(I) obs: 1.94 / Num. unique obs: 1002 / CC1/2: 0.53 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ABO

1abo


Resolution: 2→38.781 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 30.45
RfactorNum. reflection% reflection
Rfree0.2344 690 5.19 %
Rwork0.2006 --
obs0.2024 13289 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2→38.781 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1803 0 0 37 1840
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051856
X-RAY DIFFRACTIONf_angle_d0.9522532
X-RAY DIFFRACTIONf_dihedral_angle_d13.307646
X-RAY DIFFRACTIONf_chiral_restr0.029273
X-RAY DIFFRACTIONf_plane_restr0.004333
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0003-2.15480.35321420.3262539X-RAY DIFFRACTION100
2.1548-2.37160.26551370.26422508X-RAY DIFFRACTION100
2.3716-2.71470.30661320.26112505X-RAY DIFFRACTION100
2.7147-3.41990.26611380.19872531X-RAY DIFFRACTION100
3.4199-38.78790.1811410.15872516X-RAY DIFFRACTION100
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)
10.04590.0106-0.17180.23870.16210.14890.0490.17710.3407-0.0927-0.0595-0.0889-0.0401-0.1519-00.2382-0.01160.01450.39560.04360.44326.263657.687-10.3516
20.2022-0.0065-0.24910.232-0.02550.0739-0.18180.03130.16870.16850.1105-0.10.1147-0.0165-00.20970.0340.02950.4246-0.01120.270129.39851.4549-7.9962
3-0.0407-0.0308-0.01130.26920.0349-0.0648-0.09660.1580.18120.1869-0.01860.0890.20140.1877-00.1972-0.0050.05960.41580.0120.332327.910153.0327-10.1738
4-0.0267-0.0206-0.0155-0.101-0.013-0.00370.03790.245-0.48250.24150.26880.17510.28110.137600.29640.02230.00580.35190.06110.460532.521767.318613.0207
5-0.0574-0.06670.1245-0.07260.07810.23750.20590.03490.5746-0.2870.1123-0.2722-0.06340.006400.24530.0288-0.02520.52660.06480.408227.370767.1356-2.7516
60.2275-0.1618-0.12180.05460.2062-0.11050.20530.06060.28040.032-0.18-0.06130.0155-0.391300.29730.00910.01020.4081-0.04820.296326.516566.45045.6399
70.0462-0.0023-0.08990.02750.06310.00510.38650.1070.096-0.1186-0.318-0.4317-0.0522-0.7677-00.24950.09430.02690.3427-0.03090.372125.192671.08015.5351
80.04890.0165-0.0312-0.0835-0.04860.130.2311-0.14670.1828-0.0149-0.0654-0.36370.0788-0.108200.2730.0043-0.02770.3446-0.00850.308829.097764.38176.4107
90.1899-0.0470.01280.02360.0150.30310.0183-0.14470.0332-0.46160.04920.3638-0.0722-0.0049-00.2939-0.0108-0.0630.514-0.0260.3145-0.047162.00338.3233
100.00650.0085-0.0056-0.01030.00290.0332-0.4569-0.24220.2987-0.2976-0.4714-0.46640.7305-0.1167-00.37330.0759-0.23860.47610.13030.672913.361652.959610.1462
110.0377-0.09910.01560.10190.12840.0621-0.114-0.61380.0944-0.19740.02690.1867-0.03710.027700.257-0.009-0.010.4313-0.01890.26483.76162.417311.365
120.02110.0033-0.01340.0132-0.00820.01180.06260.3875-0.2955-0.40780.0003-0.07880.3258-0.0131-00.2879-0.2038-0.02020.5841-0.02430.22814.042763.9497-0.2688
13-0.00150.0170.01260.02630.1640.02340.0034-0.42730.1966-0.16320.4863-0.11380.12110.3297-00.16940.0111-0.04160.5045-0.06010.21317.971662.77113.364
14-0.01960.02380.0410.152-0.0423-0.02070.12490.0042-0.25030.02-0.0340.0865-0.032-0.0239-00.2136-0.0034-0.04630.39350.00810.19814.101464.02277.0597
150.0017-0.15870.05110.03180.25450.21570.1774-0.0446-0.0076-0.07810.0813-0.23930.18580.026500.2429-0.0399-0.00940.3737-0.01520.36617.918248.5574-4.7592
160.12560.00230.40250.25580.41870.08030.1457-0.00970.01210.1108-0.2-0.1622-0.0056-0.188300.2295-0.01570.01250.3361-0.02130.31953.702250.3509-7.7932
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 64 through 83 )
2X-RAY DIFFRACTION2chain 'A' and (resid 84 through 98 )
3X-RAY DIFFRACTION3chain 'A' and (resid 99 through 120 )
4X-RAY DIFFRACTION4chain 'B' and (resid 63 through 68 )
5X-RAY DIFFRACTION5chain 'B' and (resid 69 through 78 )
6X-RAY DIFFRACTION6chain 'B' and (resid 79 through 98 )
7X-RAY DIFFRACTION7chain 'B' and (resid 99 through 107 )
8X-RAY DIFFRACTION8chain 'B' and (resid 108 through 120 )
9X-RAY DIFFRACTION9chain 'C' and (resid 64 through 73 )
10X-RAY DIFFRACTION10chain 'C' and (resid 74 through 78 )
11X-RAY DIFFRACTION11chain 'C' and (resid 79 through 93 )
12X-RAY DIFFRACTION12chain 'C' and (resid 94 through 98 )
13X-RAY DIFFRACTION13chain 'C' and (resid 99 through 106 )
14X-RAY DIFFRACTION14chain 'C' and (resid 107 through 120 )
15X-RAY DIFFRACTION15chain 'D' and (resid 61 through 86 )
16X-RAY DIFFRACTION16chain 'D' and (resid 87 through 120 )

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