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- PDB-3juh: Crystal structure of a mutant of human protein kinase CK2alpha wi... -

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Basic information

Entry
Database: PDB / ID: 3juh
TitleCrystal structure of a mutant of human protein kinase CK2alpha with altered cosubstrate specificity
ComponentsCasein kinase II subunit alpha
KeywordsTRANSFERASE / eukaryotic protein kinase / ATP-binding / Kinase / Nucleotide-binding / Phosphoprotein / Serine/threonine-protein kinase / Wnt signaling pathway
Function / homology
Function and homology information


regulation of chromosome separation / positive regulation of aggrephagy / WNT mediated activation of DVL / Condensation of Prometaphase Chromosomes / protein kinase CK2 complex / symbiont-mediated disruption of host cell PML body / Receptor Mediated Mitophagy / Synthesis of PC / Sin3-type complex / Maturation of hRSV A proteins ...regulation of chromosome separation / positive regulation of aggrephagy / WNT mediated activation of DVL / Condensation of Prometaphase Chromosomes / protein kinase CK2 complex / symbiont-mediated disruption of host cell PML body / Receptor Mediated Mitophagy / Synthesis of PC / Sin3-type complex / Maturation of hRSV A proteins / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / negative regulation of signal transduction by p53 class mediator / negative regulation of apoptotic signaling pathway / positive regulation of Wnt signaling pathway / negative regulation of double-strand break repair via homologous recombination / : / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / Signal transduction by L1 / Hsp90 protein binding / PML body / Wnt signaling pathway / Regulation of PTEN stability and activity / positive regulation of protein catabolic process / KEAP1-NFE2L2 pathway / kinase activity / rhythmic process / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / double-strand break repair / positive regulation of cell growth / Regulation of TP53 Activity through Phosphorylation / non-specific serine/threonine protein kinase / regulation of cell cycle / negative regulation of translation / protein stabilization / protein serine kinase activity / protein serine/threonine kinase activity / positive regulation of cell population proliferation / apoptotic process / DNA damage response / signal transduction / nucleoplasm / ATP binding / identical protein binding / nucleus / plasma membrane / cytosol
Similarity search - Function
Casein Kinase 2, subunit alpha / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); 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 ...Casein Kinase 2, subunit alpha / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); 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
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Casein kinase II subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.66 Å
AuthorsNiefind, K. / Issinger, O.-G.
Citation
Journal: J.Mol.Biol. / Year: 2005
Title: Inclining the purine base binding plane in protein kinase CK2 by exchanging the flanking side-chains generates a preference for ATP as a cosubstrate
Authors: Yde, C.W. / Ermakova, I. / Issinger, O.-G. / Niefind, K.
#1: Journal: Chem.Biol. / Year: 2008
Title: The CK2 alpha/CK2 beta interface of human protein kinase CK2 harbors a binding pocket for small molecules
Authors: Raaf, J. / Brunstein, E. / Issinger, O.-G. / Niefind, K.
#2: Journal: Biochim.Biophys.Acta / Year: 2010
Title: Conformational plasticity of the catalytic subunit of protein kinase CK2 and its consequences for regulation and drug design
Authors: Niefind, K. / Issinger, O.-G.
#3: Journal: Cell.Mol.Life Sci. / Year: 2009
Title: Protein kinase CK2 in health and disease: Protein kinase CK2: from structures to insights
Authors: Niefind, K. / Raaf, J. / Issinger, O.-G.
History
DepositionSep 15, 2009Deposition site: RCSB / Processing site: PDBJ
SupersessionOct 20, 2009ID: 3BW5
Revision 1.0Oct 20, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Oct 26, 2011Group: Database references
Revision 1.3Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / 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 / _diffrn_source.pdbx_synchrotron_site / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Casein kinase II subunit alpha
B: Casein kinase II subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,45112
Polymers80,0412
Non-polymers1,40910
Water9,332518
1
A: Casein kinase II subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,7256
Polymers40,0211
Non-polymers7055
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Casein kinase II subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,7256
Polymers40,0211
Non-polymers7055
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)71.368, 71.368, 126.467
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

#1: Protein Casein kinase II subunit alpha / CK II


Mass: 40020.652 Da / Num. of mol.: 2 / Fragment: residues 1-335 / Mutation: V66A, M163L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: csnk2a1 / Plasmid: PT7-7 / Production host: Escherichia coli (E. coli) / Strain (production host): bl21(de3)
References: UniProt: P68400, non-specific serine/threonine protein kinase
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 518 / 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: 2.01 Å3/Da / Density % sol: 38.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 2.2M sodium citrate, 2mM AMPPNP, 4mM magnesium chloride, 0.62mM peptide RRRADDSDDDDD, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.811 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jan 19, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.811 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.5
11-H, K, -L20.5
ReflectionResolution: 1.66→39.5 Å / Num. all: 74683 / Num. obs: 72782 / % possible obs: 97.5 % / Observed criterion σ(I): -3 / Redundancy: 5.1 % / Biso Wilson estimate: 30.398 Å2 / Rmerge(I) obs: 0.058 / Net I/σ(I): 17.51
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.66-1.70.522.412313453782.4
1.7-1.750.443.517539526598.4
1.75-1.80.3624.217243515298.7
1.8-1.850.2765.316707500798.8
1.85-1.910.2146.716154485798.8
1.91-1.980.1668.215681472298.7
1.98-2.060.12110.515018453298.5
2.06-2.140.09512.814263434798.3
2.14-2.240.07714.413740417398.4
2.24-2.340.0671613117396997.7
2.34-2.470.05717.512493379198.4
2.47-2.620.0521911789356697.8
2.62-2.80.04520.811024335097.3
2.8-3.030.10526.424625314298.4
3.03-3.320.08337386702947100
3.32-3.710.05745.4349342672100
3.71-4.280.04652.5305812342100
4.28-5.240.04258.3262762004100
5.24-7.420.04654.5201181549100
7.420.04466.81074685899.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.66→39.45 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.956 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.825 / SU B: 4.569 / SU ML: 0.065 / SU R Cruickshank DPI: 0.021 / SU Rfree: 0.023 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.021 / ESU R Free: 0.024 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES: RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2184 2239 3.1 %RANDOM
Rwork0.15628 ---
obs0.15821 70535 97.34 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 57.09 Å2 / Biso mean: 25.858 Å2 / Biso min: 6.35 Å2
Baniso -1Baniso -2Baniso -3
1--3.32 Å20 Å20 Å2
2---3.32 Å20 Å2
3---6.64 Å2
Refinement stepCycle: LAST / Resolution: 1.66→39.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5630 0 80 518 6228
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0225946
X-RAY DIFFRACTIONr_bond_other_d0.0030.024143
X-RAY DIFFRACTIONr_angle_refined_deg2.1481.9628063
X-RAY DIFFRACTIONr_angle_other_deg1.1239992
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3695686
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.97123.06317
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.439151049
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.421553
X-RAY DIFFRACTIONr_chiral_restr0.130.2831
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0216570
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021311
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.0180.234038
X-RAY DIFFRACTIONr_mcbond_other0.0150.265374
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.658→1.701 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.345 144 -
Rwork0.216 4314 -
all-4458 -
obs--80.76 %
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)
10.08060.81660.03338.78680.39460.03360.0702-0.021-0.10430.3315-0.0693-1.1114-0.00540.0285-0.00090.3491-0.0333-0.02530.37420.08280.3063-38.35489.43313.866
212.271-0.262910.75650.0065-0.22979.4312-0.019-0.27910.02480.0006-0.00930.00850.0091-0.25860.02830.40870.00370.05390.291-0.06910.3725-53.54973.489-14.525
30.86930.51540.64361.29740.24461.12210.0035-0.0237-0.0710.10.0715-0.1569-0.06950.1346-0.07510.0593-0.00840.00090.0619-0.01870.0346-19.66579.38110.573
42.3638-0.6924-1.51090.53640.84551.81410.029-0.09340.2649-0.06530.02480.0369-0.2813-0.1119-0.05390.18960.0318-0.00670.13010.00820.0839-40.26893.2242.807
51.29790.45030.08780.92690.62620.72170.05480.1273-0.142-0.03030.005-0.05710.0814-0.0505-0.05990.0615-0.0064-0.02550.06810.00230.0256-43.71155.138-10.427
60.3439-0.62970.8282.6017-2.00992.47610.0108-0.11560.0337-0.02360.05750.2816-0.1619-0.4406-0.06840.15530.07840.00330.2581-0.00620.0948-57.90175.706-2.769
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A339
2X-RAY DIFFRACTION2B339
3X-RAY DIFFRACTION3A2 - 12
4X-RAY DIFFRACTION3A117 - 335
5X-RAY DIFFRACTION4A13 - 116
6X-RAY DIFFRACTION5B2 - 12
7X-RAY DIFFRACTION5B117 - 335
8X-RAY DIFFRACTION6B13 - 116

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