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- PDB-3q9x: Crystal structure of human CK2 alpha in complex with emodin at pH 6.5 -

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Basic information

Entry
Database: PDB / ID: 3q9x
TitleCrystal structure of human CK2 alpha in complex with emodin at pH 6.5
ComponentsCasein kinase II subunit alpha
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / protein kinase / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


regulation of chromosome separation / positive regulation of aggrephagy / Condensation of Prometaphase Chromosomes / WNT mediated activation of DVL / protein kinase CK2 complex / symbiont-mediated disruption of host cell PML body / Receptor Mediated Mitophagy / Synthesis of PC / Maturation of hRSV A proteins / Sin3-type complex ...regulation of chromosome separation / positive regulation of aggrephagy / Condensation of Prometaphase Chromosomes / WNT mediated activation of DVL / protein kinase CK2 complex / symbiont-mediated disruption of host cell PML body / Receptor Mediated Mitophagy / Synthesis of PC / Maturation of hRSV A proteins / Sin3-type complex / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / 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 / kinase activity / KEAP1-NFE2L2 pathway / 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 / eukaryotic translation initiation factor 2alpha kinase activity / 3-phosphoinositide-dependent protein kinase activity / DNA-dependent protein kinase activity / ribosomal protein S6 kinase activity / histone H3S10 kinase activity / histone H2AXS139 kinase activity / histone H3S28 kinase activity / histone H4S1 kinase activity / histone H2BS14 kinase activity / histone H3T3 kinase activity / histone H2AS121 kinase activity / Rho-dependent protein serine/threonine kinase activity / histone H2BS36 kinase activity / histone H3S57 kinase activity / histone H2AT120 kinase activity / AMP-activated protein kinase activity / histone H2AS1 kinase activity / histone H3T6 kinase activity / histone H3T11 kinase activity / histone H3T45 kinase activity / non-specific serine/threonine protein kinase / regulation of cell cycle / negative regulation of translation / protein stabilization / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / apoptotic process / positive regulation of cell population proliferation / 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
Chem-7PE / 3-METHYL-1,6,8-TRIHYDROXYANTHRAQUINONE / DI(HYDROXYETHYL)ETHER / Casein kinase II subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsBattistutta, R. / Ranchio, A. / Papinutto, E.
CitationJournal: To be Published
Title: Structural and functional analysis of the flexible regions of the catalytic alpha-subunit of protein kinase CK2
Authors: Papinutto, E. / Ranchio, A. / Lolli, G. / Pinna, L.A. / Battistutta, R.
History
DepositionJan 10, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 11, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 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_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _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)82,06115
Polymers80,3082
Non-polymers1,75413
Water4,450247
1
A: Casein kinase II subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,0857
Polymers40,1541
Non-polymers9316
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)40,9768
Polymers40,1541
Non-polymers8237
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)128.010, 128.010, 124.597
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Ens-ID: 1 / Refine code: 2

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PROPROVALVALAA4 - 314 - 31
21PROPROVALVALBB4 - 314 - 31
12TRPTRPILEILEAA33 - 10033 - 100
22TRPTRPILEILEBB33 - 10033 - 100
13THRTHRPROPROAA129 - 159129 - 159
23THRTHRPROPROBB129 - 159129 - 159
14ASNASNILEILEAA161 - 174161 - 174
24ASNASNILEILEBB161 - 174161 - 174
15TRPTRPLYSLYSAA176 - 229176 - 229
25TRPTRPLYSLYSBB176 - 229176 - 229
16GLNGLNLYSLYSAA241 - 329241 - 329
26GLNGLNLYSLYSBB241 - 329241 - 329

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Casein kinase II subunit alpha / CK2alpha / CK II alpha


Mass: 40153.820 Da / Num. of mol.: 2 / Fragment: UNP residues 1-336
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CSNK2A1, CK2A1 / Plasmid: pT7-7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P68400, non-specific serine/threonine protein kinase

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Non-polymers , 6 types, 260 molecules

#2: Chemical ChemComp-EMO / 3-METHYL-1,6,8-TRIHYDROXYANTHRAQUINONE / EMODIN


Mass: 270.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H10O5
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-7PE / 2-(2-(2-(2-(2-(2-ETHOXYETHOXY)ETHOXY)ETHOXY)ETHOXY)ETHOXY)ETHANOL / POLYETHYLENE GLYCOL FRAGMENT


Mass: 310.384 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H30O7
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 247 / 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: 3.18 Å3/Da / Density % sol: 61.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 20% PEG 5000 MME, 0.2M ammonium sulfate, 0.1M Mes, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.972937 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 6, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.972937 Å / Relative weight: 1
ReflectionResolution: 2.2→73.32 Å / Num. all: 44592 / Num. obs: 44592 / % possible obs: 85.5 % / Redundancy: 2.3 % / Rmerge(I) obs: 0.086 / Rsym value: 0.086 / Net I/σ(I): 8.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) allRmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
2.2-2.3220.7570.5830.91286464990.4770.7570.5831.786.4
2.32-2.462.30.5090.4051.71462864570.3040.5090.4052.690.3
2.46-2.632.30.3550.2842.51371060130.210.3550.2843.789.4
2.63-2.842.30.2340.1873.31278255270.1380.2340.1875.488.1
2.84-3.112.30.1420.1146.21173050040.0830.1420.114886.4
3.11-3.482.40.0920.0748.81061344510.0530.0920.07411.484.9
3.48-4.022.40.0670.0549.7928738350.0380.0670.05415.482.4
4.02-4.922.50.0560.04611.8776831460.0320.0560.04618.579.6
4.92-6.962.40.050.04113.3564523400.0280.050.04119.275.9
6.96-73.3242.60.0460.03710.4341713200.0270.0460.03723.474.6

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Processing

Software
NameVersionClassificationNB
SCALA3.2.25data scaling
REFMACrefinement
PDB_EXTRACT3.1data extraction
ProDCdata collection
MOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2PVR

2pvr


Resolution: 2.2→73.32 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.924 / WRfactor Rfree: 0.2337 / WRfactor Rwork: 0.1941 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8518 / SU B: 11.24 / SU ML: 0.128 / SU R Cruickshank DPI: 0.2619 / SU Rfree: 0.2166 / Cross valid method: THROUGHOUT / ESU R Free: 0.217 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES
RfactorNum. reflection% reflectionSelection details
Rfree0.2431 2294 5.1 %RANDOM
Rwork0.1941 ---
obs0.1966 44560 84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 98 Å2 / Biso mean: 34.194 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-0.39 Å2-0 Å2-0 Å2
2--0.39 Å20 Å2
3----0.79 Å2
Refinement stepCycle: LAST / Resolution: 2.2→73.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5576 0 111 247 5934
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0215858
X-RAY DIFFRACTIONr_angle_refined_deg1.9591.9637925
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0895664
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.81923.089314
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.727151021
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.9581551
X-RAY DIFFRACTIONr_chiral_restr0.1410.2807
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0214503
X-RAY DIFFRACTIONr_mcbond_it0.8981.53313
X-RAY DIFFRACTIONr_mcangle_it1.64925391
X-RAY DIFFRACTIONr_scbond_it2.88532545
X-RAY DIFFRACTIONr_scangle_it4.5564.52533
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
1128TIGHT POSITIONAL0.080.05
1261MEDIUM POSITIONAL0.210.5
1128TIGHT THERMAL0.230.5
1261MEDIUM THERMAL0.282
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.343 163 -
Rwork0.291 2977 -
all-3140 -
obs--81.47 %
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)
11.2202-0.3281-0.02310.8718-0.00011.04460.03020.15060.1399-0.0289-0.0417-0.0282-0.08680.0190.01140.1167-0.017300.07470.00160.08386.364845.6284.451
22.0976-0.0674-1.34051.7275-0.94723.68470.008-0.12-0.01890.0242-0.0166-0.0199-0.04680.05610.00850.18120.037-0.00760.1224-0.01380.1654-10.720552.316222.2146
31.78620.1382-0.12090.1917-0.42951.7640.0251-0.01620.19960.00360.00390.0976-0.1968-0.1829-0.0290.1072-0.0042-0.02490.1247-0.01610.121-6.174249.100613.8651
40.6406-0.51661.06030.9087-1.35612.68550.0486-0.311-0.16820.15740.0851-0.01770.1565-0.2097-0.13360.2755-0.0221-0.03790.28790.05860.2286-3.654540.569831.3921
50.98430.20.14581.7879-0.75940.84930.0152-0.2356-0.05210.27650.02190.20080.004-0.1861-0.03710.1054-0.00740.00630.1042-0.01620.1094.224234.99924.7379
61.1528-0.34190.44620.63560.11811.7920.0103-0.15620.05960.1405-0.02060.0036-0.10290.05970.01040.10840.00860.00340.0876-0.00830.118813.517144.797623.1888
71.46180.2415-0.13441.4043-0.26622.01050.0399-0.07960.10660.102-0.0424-0.0346-0.11220.12270.00240.10750.0519-0.00060.1267-0.00840.133622.422536.361527.3169
88.8422-6.4562-2.11478.80812.73012.01430.19580.3836-0.0326-0.2822-0.2575-0.34990.29380.33620.06170.27220.03060.03050.28560.02670.2206-17.802936.0562-21.5614
90.9970.56050.25561.53710.95711.23690.0066-0.04760.0633-0.00070.0443-0.1605-0.10820.1613-0.05090.09610.01350.00030.09850.02890.0918-14.881868.2136-14.9317
100.2540.1124-0.10170.13640.05520.15660.0039-0.2497-0.25820.1836-0.1047-0.11550.20870.10770.10080.38190.0031-0.00170.3880.11660.395-26.483964.94192.4182
111.9407-0.2488-0.71790.7847-0.18130.85480.0222-0.25410.21990.19590.01820.0645-0.1964-0.0366-0.04050.10450.0027-0.01450.1037-0.0090.1061-30.0758.2095-6.6057
120.63460.51350.23021.5146-0.1911.9918-0.0185-0.09390.01180.10240.0198-0.06990.05350.0842-0.00130.0833-0.0143-0.00740.11180.00540.1073-19.684350.3292-10.7156
132.6173-0.8025-0.10140.9741-0.27930.7961-0.0408-0.1710.11510.1510.0848-0.17070.01120.1253-0.04410.1516-0.01160.00270.14440.01980.1291-21.617840.27591.6674
141.4772-0.1576-0.38421.33980.11742.011-0.0453-0.1145-0.02930.08870.0418-0.07170.08890.05550.00350.1289-0.0541-0.01080.0984-0.00640.1299-30.36941.4535-2.9725
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 36
2X-RAY DIFFRACTION2A37 - 77
3X-RAY DIFFRACTION3A78 - 112
4X-RAY DIFFRACTION4A113 - 125
5X-RAY DIFFRACTION5A126 - 167
6X-RAY DIFFRACTION6A168 - 243
7X-RAY DIFFRACTION7A244 - 331
8X-RAY DIFFRACTION8B2 - 9
9X-RAY DIFFRACTION9B10 - 113
10X-RAY DIFFRACTION10B114 - 127
11X-RAY DIFFRACTION11B128 - 167
12X-RAY DIFFRACTION12B168 - 221
13X-RAY DIFFRACTION13B222 - 258
14X-RAY DIFFRACTION14B259 - 331

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