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- PDB-3q9z: Crystal structure of human CK2 alpha in complex with Quinalizarin... -

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Basic information

Entry
Database: PDB / ID: 3q9z
TitleCrystal structure of human CK2 alpha in complex with Quinalizarin 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 / Sin3-type complex / Maturation of hRSV A proteins ...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 / 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 apoptotic signaling pathway / positive regulation of Wnt signaling pathway / negative regulation of double-strand break repair via homologous recombination / chaperone-mediated protein folding / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / : / Signal transduction by L1 / peptidyl-threonine phosphorylation / Hsp90 protein binding / PML body / Wnt signaling pathway / Regulation of PTEN stability and activity / positive regulation of protein catabolic process / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / KEAP1-NFE2L2 pathway / rhythmic process / double-strand break repair / kinase activity / peptidyl-serine phosphorylation / positive regulation of cell growth / Regulation of TP53 Activity through Phosphorylation / negative regulation of translation / regulation of cell cycle / protein stabilization / non-specific serine/threonine protein kinase / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / DNA damage response / positive regulation of cell population proliferation / apoptotic process / signal transduction / nucleoplasm / ATP binding / identical protein binding / nucleus / plasma membrane / cytosol
Similarity search - Function
Casein Kinase 2, subunit alpha / 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 ...Casein Kinase 2, subunit alpha / 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
1,2,5,8-tetrahydroxyanthracene-9,10-dione / 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

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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)81,57613
Polymers80,3082
Non-polymers1,26811
Water4,972276
1
A: Casein kinase II subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,8387
Polymers40,1541
Non-polymers6856
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)40,7376
Polymers40,1541
Non-polymers5835
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)127.956, 127.956, 125.739
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

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PROPROGLUGLU2AA4 - 274 - 27
21PROPROGLUGLU2BB4 - 274 - 27
12LEULEULYSLYS6AA45 - 4945 - 49
22LEULEULYSLYS6BB45 - 4945 - 49
13SERSERILEILE2AA51 - 10051 - 100
23SERSERILEILE2BB51 - 10051 - 100
14THRTHRILEILE2AA129 - 226129 - 226
24THRTHRILEILE2BB129 - 226129 - 226
15ILEILEVALVAL2AA245 - 328245 - 328
25ILEILEVALVAL2BB245 - 328245 - 328

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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 , 5 types, 287 molecules

#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-TXQ / 1,2,5,8-tetrahydroxyanthracene-9,10-dione / 1,2,5,8-tetrahydroxy-anthraquinone


Mass: 272.210 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H8O6 / Comment: inhibitor*YM
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 276 / 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: 3.2 Å3/Da / Density % sol: 61.61 % / Mosaicity: 0.37 °
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: 0.976234 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 7, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976234 Å / Relative weight: 1
ReflectionResolution: 2.2→89.68 Å / Num. all: 50758 / Num. obs: 50758 / % possible obs: 95.6 % / Redundancy: 2.2 % / Rsym value: 0.08 / Net I/σ(I): 7.2
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
2.2-2.322.10.8150.6360.51385765210.4990.8150.6361.385
2.32-2.462.30.4870.3811.81636672230.2970.4870.3811.999.3
2.46-2.632.30.3270.2562.71540267920.1990.3270.2562.999.2
2.63-2.842.30.2550.1980.91434063300.1580.2550.1984.399
2.84-3.112.30.1280.1016.21312358100.0770.1280.1016.698.7
3.11-3.482.30.0890.074.71193252550.0530.0890.079.798.1
3.48-4.022.30.0750.0596.11039246030.0450.0750.05912.197.2
4.02-4.922.30.0750.068.7870738510.0440.0750.0613.595.8
4.92-6.962.20.0590.0479.9640728580.0350.0590.04718.890.9
6.96-57.2242.40.0550.0437.9363315150.0330.0550.04330.885

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Processing

Software
NameVersionClassificationNB
SCALA3.3.9data scaling
REFMAC5.5.0109refinement
PDB_EXTRACT3.1data extraction
ProDCdata collection
MOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2PVR

2pvr


Resolution: 2.2→57.22 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.92 / Occupancy max: 1 / Occupancy min: 0.5 / Cross valid method: THROUGHOUT / ESU R Free: 0.214 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES
RfactorNum. reflection% reflectionSelection details
Rfree0.2666 2564 5.1 %RANDOM
Rwork0.2126 ---
obs0.2153 50723 94.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 104.76 Å2 / Biso mean: 44.8147 Å2 / Biso min: 22.53 Å2
Baniso -1Baniso -2Baniso -3
1-1 Å2-0 Å2-0 Å2
2--1 Å20 Å2
3----2 Å2
Refinement stepCycle: LAST / Resolution: 2.2→57.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5608 0 79 276 5963
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0225853
X-RAY DIFFRACTIONr_angle_refined_deg1.8671.9597927
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4555668
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.12923.06317
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.896151027
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.5831553
X-RAY DIFFRACTIONr_chiral_restr0.1310.2811
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0214519
X-RAY DIFFRACTIONr_mcbond_it0.9421.53327
X-RAY DIFFRACTIONr_mcangle_it1.72725410
X-RAY DIFFRACTIONr_scbond_it2.90732526
X-RAY DIFFRACTIONr_scangle_it4.6254.52514
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
1024TIGHT POSITIONAL0.090.05
1137MEDIUM POSITIONAL0.190.5
36LOOSE POSITIONAL0.165
1024TIGHT THERMAL0.260.5
1137MEDIUM THERMAL0.292
36LOOSE THERMAL0.3710
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.38 152 -
Rwork0.335 2848 -
all-3000 -
obs--77.18 %
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)
10.8538-0.3604-0.59320.37560.05060.87660.07180.08010.1185-0.0351-0.0474-0.0007-0.0849-0.0697-0.02450.1981-0.023-0.01420.1618-0.00990.19731.266347.43179.3611
22.3667-1.0898-1.58611.19410.44263.02670.0202-0.09650.11360.14820.02360.067-0.08220.0119-0.04380.16890.0145-0.03040.13880.01880.1468-7.123350.871517.907
33.1867-1.4958-0.17644.4960.37382.18350.00050.01570.12280.0110.01220.3727-0.2221-0.2334-0.01260.1451-0.0275-0.00530.2079-0.00860.1312-10.2349.602216.5523
40.9301-0.13690.03351.6731-0.51381.75660.0422-0.2616-0.06550.2977-0.00650.21630.0039-0.1327-0.03560.15130.0033-0.01730.171-0.02030.18133.793238.64523.3081
50.96930.05210.35551.0433-0.06810.89130.0205-0.14030.08050.1199-0.0146-0.0569-0.10370.1103-0.00590.1660.004-0.00230.1567-0.00420.168820.131144.603526.1161
60.1832-0.1630.2472.3388-1.80172.0843-0.01360.06990.22140.2128-0.0614-0.1146-0.41840.17990.0750.24770.00950.02340.28310.00180.334330.352547.573729.2159
71.03890.1138-0.2281.6587-0.44742.53680.012-0.1083-0.14770.07-0.03870.12610.2418-0.16790.02670.16150.0340.00460.1735-0.00410.20415.080828.461528.107
80.40780.2735-0.02970.96040.74551.0183-0.04370.02450.0115-0.08210.078-0.1354-0.09080.0934-0.03420.12120.0224-0.01640.16190.01920.1551-16.719360.688-20.3933
91.16570.94320.18912.28511.70023.02630.0137-0.16010.05620.11240.0233-0.0990.02740.068-0.0370.1382-0.01630.01610.17040.02840.1508-13.917469.4489-11.2639
103.92071.12890.4552.91820.35852.22840.0661-0.38330.02980.2699-0.0817-0.0509-0.16770.16270.01550.2090.041-0.0180.13820.00230.162-17.100871.4205-10.2179
111.9996-0.3481-1.40451.2312-0.10351.57060.0146-0.35730.13760.36190.0252-0.007-0.12850.071-0.03980.1774-0.0079-0.01190.16150.00160.2003-32.191357.7127-5.429
120.66520.37740.0571.1617-0.40971.2373-0.03-0.1453-0.03810.18430.01080.00920.03250.01450.01930.1381-0.0054-0.00990.1782-0.00140.1645-21.098247.5918-5.8803
132.7190.1964-1.7730.1929-0.26331.7817-0.0632-0.2555-0.1209-0.0438-0.0181-0.22350.16580.39640.08140.2738-0.0071-0.00640.2395-0.02710.3221-18.030831.9384-0.1991
141.9189-0.0092-0.58591.09290.27592.9449-0.0458-0.03960.14840.09280.01420.1873-0.2013-0.28060.03160.1783-0.0369-0.00680.1623-0.00730.2092-37.077947.1999-3.1982
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 46
2X-RAY DIFFRACTION2A47 - 89
3X-RAY DIFFRACTION3A90 - 115
4X-RAY DIFFRACTION4A116 - 191
5X-RAY DIFFRACTION5A192 - 262
6X-RAY DIFFRACTION6A263 - 281
7X-RAY DIFFRACTION7A282 - 333
8X-RAY DIFFRACTION8B2 - 46
9X-RAY DIFFRACTION9B47 - 89
10X-RAY DIFFRACTION10B90 - 121
11X-RAY DIFFRACTION11B122 - 153
12X-RAY DIFFRACTION12B154 - 262
13X-RAY DIFFRACTION13B263 - 281
14X-RAY DIFFRACTION14B282 - 333

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