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- PDB-6hop: Human protein kinase CK2 alpha in complex with curcumin degradati... -

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Basic information

Entry
Database: PDB / ID: 6hop
TitleHuman protein kinase CK2 alpha in complex with curcumin degradation products
ComponentsCasein kinase II subunit alpha
KeywordsTRANSFERASE / kinase domain
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 / Sin3-type complex / Synthesis of PC / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known ...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 / Sin3-type complex / Synthesis of PC / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / Maturation of hRSV A proteins / 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 ubiquitin-dependent protein catabolic process / Signal transduction by L1 / peptidyl-threonine phosphorylation / Hsp90 protein binding / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / 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 / double-strand break repair / rhythmic process / kinase activity / positive regulation of cell growth / peptidyl-serine phosphorylation / Regulation of TP53 Activity through Phosphorylation / protein stabilization / negative regulation of translation / non-specific serine/threonine protein kinase / regulation of cell cycle / cell cycle / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / apoptotic process / DNA damage response / positive regulation of cell population proliferation / 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
(2E)-3-(4-hydroxy-3-methoxyphenyl)prop-2-enal / 3-(4-HYDROXY-3-METHOXYPHENYL)-2-PROPENOIC ACID / Chem-GJK / 4-hydroxy-3-methoxybenzaldehyde / Casein kinase II subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.55 Å
AuthorsBattistutta, R. / Lolli, G.
CitationJournal: Febs J. / Year: 2020
Title: Biochemical and cellular mechanism of protein kinase CK2 inhibition by deceptive curcumin.
Authors: Cozza, G. / Zonta, F. / Dalle Vedove, A. / Venerando, A. / Dall'Acqua, S. / Battistutta, R. / Ruzzene, M. / Lolli, G.
History
DepositionSep 18, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 2, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2May 13, 2020Group: Database references / Structure summary / Category: chem_comp / citation
Item: _chem_comp.pdbx_synonyms / _citation.journal_volume ..._chem_comp.pdbx_synonyms / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year
Revision 1.3Jan 24, 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: Casein kinase II subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,2219
Polymers40,1541
Non-polymers1,0678
Water6,197344
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1210 Å2
ΔGint-36 kcal/mol
Surface area15300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.158, 46.303, 63.344
Angle α, β, γ (deg.)90.000, 111.900, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 40153.820 Da / Num. of mol.: 1 / Fragment: kinase domain (residues 1-337)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CSNK2A1, CK2A1 / Production host: Escherichia coli (E. coli)
References: UniProt: P68400, non-specific serine/threonine protein kinase

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Non-polymers , 7 types, 352 molecules

#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-FER / 3-(4-HYDROXY-3-METHOXYPHENYL)-2-PROPENOIC ACID / FERULIC ACID


Mass: 194.184 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H10O4
#5: Chemical ChemComp-V55 / 4-hydroxy-3-methoxybenzaldehyde / p-vanillin


Mass: 152.147 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H8O3
#6: Chemical ChemComp-GJK / (~{E})-4-(3-methoxy-4-oxidanyl-phenyl)but-3-en-2-one


Mass: 192.211 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H12O3
#7: Chemical ChemComp-CIY / (2E)-3-(4-hydroxy-3-methoxyphenyl)prop-2-enal / Coniferaldehyde


Mass: 178.185 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H10O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 344 / 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: 1.97 Å3/Da / Density % sol: 37.59 % / Mosaicity: 0.12 °
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 32% PEG4000, 0.2 M Lithium Sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Dec 11, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 1.55→46.3 Å / Num. obs: 45032 / % possible obs: 98.7 % / Redundancy: 5.3 % / Biso Wilson estimate: 18.47 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.06 / Rpim(I) all: 0.029 / Rrim(I) all: 0.067 / Net I/σ(I): 14.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.55-1.585.20.67321690.8360.3220.74997.8
8.49-46.34.90.043030.9960.020.04598.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHENIXrefinement
XDSdata reduction
Aimless0.3.11data scaling
PHASERphasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3Q04

3q04


Resolution: 1.55→36.371 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.53
RfactorNum. reflection% reflection
Rfree0.189 2255 5.01 %
Rwork0.1636 --
obs0.1649 45020 98.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 98.49 Å2 / Biso mean: 26.1456 Å2 / Biso min: 10.2 Å2
Refinement stepCycle: final / Resolution: 1.55→36.371 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2773 0 58 344 3175
Biso mean--34.62 35.24 -
Num. residues----328
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062940
X-RAY DIFFRACTIONf_angle_d1.0593978
X-RAY DIFFRACTIONf_chiral_restr0.043405
X-RAY DIFFRACTIONf_plane_restr0.005511
X-RAY DIFFRACTIONf_dihedral_angle_d15.5361107
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 16

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.55-1.58370.28841380.25472633277198
1.5837-1.62060.28891310.24852631276298
1.6206-1.66110.24861250.21752627275297
1.6611-1.7060.24951480.21082640278898
1.706-1.75620.24641380.19062638277699
1.7562-1.81290.19961360.18832658279498
1.8129-1.87770.20951400.1712639277998
1.8777-1.95280.18871390.18272676281599
1.9528-2.04170.20781230.17092657278099
2.0417-2.14930.18061590.16372666282599
2.1493-2.2840.20651290.1662708283799
2.284-2.46030.19571640.1652660282499
2.4603-2.70780.19471390.167127092848100
2.7078-3.09950.18631460.16382704285099
3.0995-3.90430.16141600.138927232883100
3.9043-36.38140.16311400.141427962936100
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)
11.3244-0.5319-0.23120.21840.21260.6859-0.1526-0.2215-0.40810.01820.08850.19630.1491-0.04180.03190.2167-0.0180.03520.18150.09730.3109-20.9901-1.408-11.0173
22.7424-0.81590.69991.0102-0.7620.74770.0239-0.0253-0.1097-0.1093-0.01940.11860.0484-0.05850.01050.16310.0069-0.01520.21660.04220.2104-28.2459.2812-13.5293
32.08331.0256-0.07871.11430.7941.1256-0.1356-0.14460.3836-0.18210.1870.2746-0.23740.2022-0.05760.1855-0.0246-0.0070.22510.03240.1804-11.633917.5918-8.306
42.09780.0421-0.86520.9243-0.11250.9279-0.0413-0.1193-0.0659-0.07690.03640.1290.02130.00180.01460.1297-0.005-0.01250.10570.02660.1202-9.3737.7064-16.5149
51.85910.2445-0.29521.47120.26151.5414-0.14120.165-0.009-0.27560.04510.04180.00310.05450.10210.2028-0.0211-0.00980.10480.00130.10524.66098.0714-29.3726
61.05040.3377-0.44271.4607-0.00521.63210.0377-0.32440.07350.0135-0.0224-0.04-0.08060.2454-0.02580.09830.002-0.0060.2206-0.02650.11634.46614.5597-10.0294
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 44 )A3 - 44
2X-RAY DIFFRACTION2chain 'A' and (resid 45 through 108 )A45 - 108
3X-RAY DIFFRACTION3chain 'A' and (resid 109 through 149 )A109 - 149
4X-RAY DIFFRACTION4chain 'A' and (resid 150 through 227 )A150 - 227
5X-RAY DIFFRACTION5chain 'A' and (resid 228 through 280 )A228 - 280
6X-RAY DIFFRACTION6chain 'A' and (resid 281 through 330 )A281 - 330

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