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- PDB-6hot: Human protein kinase CK2 alpha in complex with ferulic aldehyde -

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Basic information

Entry
Database: PDB / ID: 6hot
TitleHuman protein kinase CK2 alpha in complex with ferulic aldehyde
ComponentsCasein kinase II subunit alpha
KeywordsTRANSFERASE / kinase domain
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 / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known ...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 / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / Maturation of hRSV A proteins / positive regulation of Wnt signaling pathway / negative regulation of apoptotic 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 / non-specific serine/threonine protein kinase / regulation of cell cycle / protein stabilization / 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
(2E)-3-(4-hydroxy-3-methoxyphenyl)prop-2-enal / Casein kinase II subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.5 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 / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._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)40,7447
Polymers40,1541
Non-polymers5916
Water6,900383
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1070 Å2
ΔGint-41 kcal/mol
Surface area15450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.443, 46.331, 63.338
Angle α, β, γ (deg.)90.000, 112.080, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#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
#2: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 383 / 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: 1.98 Å3/Da / Density % sol: 37.85 % / Mosaicity: 0.22 °
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: ELETTRA / Beamline: 5.2R / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: May 5, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→46.33 Å / Num. obs: 49911 / % possible obs: 99 % / Redundancy: 3.7 % / CC1/2: 0.997 / Rmerge(I) obs: 0.069 / Rpim(I) all: 0.04 / Rrim(I) all: 0.081 / Net I/σ(I): 16.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.5-1.5330.532726224530.850.3420.6372.599.2
8.22-46.333.90.04212573260.9970.0240.0483796.2

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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: 1.5→35.206 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.26
RfactorNum. reflection% reflection
Rfree0.1964 2654 5.32 %
Rwork0.1701 --
obs0.1715 49864 98.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 77.74 Å2 / Biso mean: 23.101 Å2 / Biso min: 7.76 Å2
Refinement stepCycle: final / Resolution: 1.5→35.206 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2773 0 36 383 3192
Biso mean--28.12 32.94 -
Num. residues----328
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062909
X-RAY DIFFRACTIONf_angle_d1.0443937
X-RAY DIFFRACTIONf_chiral_restr0.045405
X-RAY DIFFRACTIONf_plane_restr0.005505
X-RAY DIFFRACTIONf_dihedral_angle_d14.7351105
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 19

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5-1.52730.31551330.29382452258599
1.5273-1.55670.29191460.25912484263099
1.5567-1.58850.24811130.24462527264099
1.5885-1.6230.2761360.2352491262799
1.623-1.66070.25751410.22182463260499
1.6607-1.70230.25721580.21452447260599
1.7023-1.74830.26211340.20932475260999
1.7483-1.79970.2281500.2032451260198
1.7997-1.85780.20251410.19342466260798
1.8578-1.92420.20641390.18312483262299
1.9242-2.00130.22521370.171725062643100
2.0013-2.09230.20621290.16292502263199
2.0923-2.20260.20611370.156825232660100
2.2026-2.34060.17321200.16282513263399
2.3406-2.52130.2011350.16392462259798
2.5213-2.77490.20371480.17322468261698
2.7749-3.17620.18841640.15992481264599
3.1762-4.00080.15951590.13722492265198
4.0008-35.21590.14431340.1422524265896
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)
10.6529-0.1833-0.2890.15410.12730.5168-0.1423-0.1556-0.30710.00110.05630.170.1607-0.0330.05630.1813-0.01530.0370.14730.08580.2958-20.88-2.4689-11.0817
22.0378-0.50110.31160.6619-0.33720.7033-0.0065-0.0392-0.0977-0.0907-0.00980.10470.034-0.08930.03210.11140.002-0.00880.16180.04130.1909-28.37578.5381-13.4333
31.60080.6657-0.06770.2746-0.02470.0029-0.22030.13260.4314-0.19230.1680.2037-0.32530.00830.0650.2694-0.0508-0.03980.20570.05860.3048-17.515221.0076-11.4022
41.85150.0019-0.75110.71090.02450.7585-0.0552-0.102-0.0624-0.11240.05190.0920.01450.04550.00040.094-0.0117-0.01910.06310.020.0683-4.06738.0258-19.4204
50.86860.0898-0.2271.38410.16551.07550.0203-0.31510.061-0.01010.0154-0.0408-0.09080.2186-0.0470.0834-0.009-0.00010.1897-0.02420.09914.453313.8053-9.9975
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 129 )A109 - 129
4X-RAY DIFFRACTION4chain 'A' and (resid 130 through 280 )A130 - 280
5X-RAY DIFFRACTION5chain 'A' and (resid 281 through 330 )A281 - 330

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