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- PDB-3kvw: Crystal Structure of dual-specificity tyrosine phosphorylation re... -

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Basic information

Entry
Database: PDB / ID: 3kvw
TitleCrystal Structure of dual-specificity tyrosine phosphorylation regulated kinase 2 (DYRK2) in complex with an indirubin ligand
ComponentsDual specificity tyrosine-phosphorylation-regulated kinase 2
KeywordsTRANSFERASE / DYRK2 / dual-specificity tyrosine / ki-(Y)-phosphorylation regulated kinase 2 / PSK-H2 / kinase / Structural Genomics Consortium / SGC / Apoptosis / ATP-binding / Nucleotide-binding / Serine/threonine-protein kinase / Tyrosine-protein kinase
Function / homology
Function and homology information


dual-specificity kinase / negative regulation of calcineurin-NFAT signaling cascade / smoothened signaling pathway / positive regulation of glycogen biosynthetic process / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / ubiquitin ligase complex / protein serine/threonine/tyrosine kinase activity / regulation of signal transduction by p53 class mediator / manganese ion binding / protein tyrosine kinase activity ...dual-specificity kinase / negative regulation of calcineurin-NFAT signaling cascade / smoothened signaling pathway / positive regulation of glycogen biosynthetic process / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / ubiquitin ligase complex / protein serine/threonine/tyrosine kinase activity / regulation of signal transduction by p53 class mediator / manganese ion binding / protein tyrosine kinase activity / Regulation of TP53 Activity through Phosphorylation / cytoskeleton / ribonucleoprotein complex / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / DNA damage response / magnesium ion binding / nucleoplasm / ATP binding / nucleus / cytoplasm / cytosol
Similarity search - Function
DYRK / Dual specificity tyrosine-phosphorylation-regulated kinase / Trypsin Inhibitor V; Chain A / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain ...DYRK / Dual specificity tyrosine-phosphorylation-regulated kinase / Trypsin Inhibitor V; Chain A / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, 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 / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-IRB / Dual specificity tyrosine-phosphorylation-regulated kinase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.28 Å
AuthorsFilippakopoulos, P. / Myrianthopoulos, V. / Kritsanida, M. / Magiatis, P. / Skaltsounis, A.L. / Soundararajan, M. / Krojer, T. / Gileadi, O. / Hapka, E. / Fedorov, O. ...Filippakopoulos, P. / Myrianthopoulos, V. / Kritsanida, M. / Magiatis, P. / Skaltsounis, A.L. / Soundararajan, M. / Krojer, T. / Gileadi, O. / Hapka, E. / Fedorov, O. / Berridge, G. / Wang, J. / Shrestha, L. / Vollmar, M. / von Delft, F. / Arrowsmith, C.H. / Edwards, A. / Weigelt, J. / Bountra, C. / Mikros, E. / Knapp, S. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Crystal Structure of dual-specificity tyrosine phosphorylation regulated kinase 2 (DYRK2) in complex with an indirubin ligand
Authors: Filippakopoulos, P. / Myrianthopoulos, V. / Kritsanida, M. / Magiatis, P. / Skaltsounis, A.L. / Soundararajan, M. / Krojer, T. / Gileadi, O. / Hapka, E. / Fedorov, O. / Berridge, G. / Wang, ...Authors: Filippakopoulos, P. / Myrianthopoulos, V. / Kritsanida, M. / Magiatis, P. / Skaltsounis, A.L. / Soundararajan, M. / Krojer, T. / Gileadi, O. / Hapka, E. / Fedorov, O. / Berridge, G. / Wang, J. / Shrestha, L. / Vollmar, M. / von Delft, F. / Arrowsmith, C.H. / Edwards, A. / Weigelt, J. / Bountra, C. / Mikros, E. / Knapp, S.
History
DepositionNov 30, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 5, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 1, 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 22, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Dual specificity tyrosine-phosphorylation-regulated kinase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,1436
Polymers49,6011
Non-polymers5425
Water1,928107
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)84.280, 84.280, 149.120
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number94
Space group name H-MP42212

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Components

#1: Protein Dual specificity tyrosine-phosphorylation-regulated kinase 2 / DYRK2


Mass: 49600.906 Da / Num. of mol.: 1 / Fragment: UNP residues 146-552
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DYRK2 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-R3 / References: UniProt: Q92630, dual-specificity kinase
#2: Chemical ChemComp-IRB / (2Z,3E)-7'-bromo-3-(hydroxyimino)-2'-oxo-1,1',2',3-tetrahydro-2,3'-biindole-5-carboxylic acid / Indirubin-3'-monoxime derivative, (2Z,3E)-7'-bromo-3-(hydroxyimino)-2'-oxo-[2,3'-biindolinylidene]-5-carboxylic acid


Mass: 400.183 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H10BrN3O4
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 107 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHIS ENTRY USES SKIP NUMBERING TO CLARIFY THE EXPRESSION TAG REGION.

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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: 2.67 Å3/Da / Density % sol: 53.92 % / Mosaicity: 0.32 °
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2M Na(Acetate), 0.1M cacodylate pH 6.5, 30% PEG 8000, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9802 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 24, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9802 Å / Relative weight: 1
ReflectionResolution: 2.28→46.552 Å / Num. all: 25294 / Num. obs: 25294 / % possible obs: 100 % / Redundancy: 7.4 % / Biso Wilson estimate: 48.8 Å2 / Rmerge(I) obs: 0.105 / Rsym value: 0.105 / Net I/σ(I): 12.2
Reflection shellResolution: 2.28→2.4 Å / Redundancy: 7.6 % / Rmerge(I) obs: 0.885 / Mean I/σ(I) obs: 2.5 / Num. unique all: 3617 / Rsym value: 0.885 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 38.13 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å42.81 Å
Translation2.5 Å42.81 Å

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Processing

Software
NameVersionClassificationNB
SCALA3.3.9data scaling
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
GDAdata collection
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3K2L

3k2l


Resolution: 2.28→42.81 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.915 / WRfactor Rfree: 0.256 / WRfactor Rwork: 0.208 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.837 / SU B: 14.006 / SU ML: 0.159 / SU R Cruickshank DPI: 0.276 / SU Rfree: 0.227 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.276 / ESU R Free: 0.227 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.26 1292 5.1 %RANDOM
Rwork0.209 ---
all0.211 25362 --
obs0.211 25247 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 88.96 Å2 / Biso mean: 22.469 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-0.34 Å20 Å20 Å2
2--0.34 Å20 Å2
3----0.69 Å2
Refinement stepCycle: LAST / Resolution: 2.28→42.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3188 0 29 107 3324
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0213358
X-RAY DIFFRACTIONr_bond_other_d0.0020.022273
X-RAY DIFFRACTIONr_angle_refined_deg1.5481.9694554
X-RAY DIFFRACTIONr_angle_other_deg0.9393.0015507
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.5195412
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.29223.677155
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.52315.054560
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.5251520
X-RAY DIFFRACTIONr_chiral_restr0.0890.2482
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213749
X-RAY DIFFRACTIONr_gen_planes_other0.0070.02694
X-RAY DIFFRACTIONr_mcbond_it3.63332054
X-RAY DIFFRACTIONr_mcbond_other1.1463839
X-RAY DIFFRACTIONr_mcangle_it5.21753288
X-RAY DIFFRACTIONr_scbond_it8.39681304
X-RAY DIFFRACTIONr_scangle_it10.267111266
LS refinement shellResolution: 2.28→2.339 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.369 93 -
Rwork0.333 1721 -
all-1814 -
obs--100 %
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)
10.35520.50740.97975.6692-1.23049.98320.0655-0.24380.15290.52230.01660.1829-0.234-0.0098-0.08210.40770.02340.16470.421-0.05220.287427.4044-56.373639.2025
20.9403-0.6103-0.00027.01820.78372.15590.00850.23210.0099-0.2706-0.0741-0.0198-0.0890.05380.06550.11320.0010.03270.16980.05760.115328.1143-46.036521.556
32.3680.0548-0.06292.7143-0.89913.4385-0.03130.09520.17670.1096-0.1143-0.217-0.29580.22510.14560.1198-0.0412-0.02030.02670.01370.060129.8838-16.662212.7602
42.05120.20671.1371.30050.45764.322-0.1474-0.07460.5120.1823-0.090.024-0.8795-0.19230.23750.3867-0.036-0.03080.04130.00910.267427.4235-4.07429.6506
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-16 - 85
2X-RAY DIFFRACTION2A86 - 231
3X-RAY DIFFRACTION3A232 - 395
4X-RAY DIFFRACTION4A396 - 463

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