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- PDB-6hor: Human protein kinase CK2 alpha in complex with feruloylmethane -

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Basic information

Entry
Database: PDB / ID: 6hor
TitleHuman protein kinase CK2 alpha in complex with feruloylmethane
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
Chem-GJK / Casein kinase II subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 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)40,6966
Polymers40,1541
Non-polymers5425
Water5,368298
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area830 Å2
ΔGint-42 kcal/mol
Surface area15340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.236, 46.346, 63.415
Angle α, β, γ (deg.)90.000, 112.030, 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-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
#3: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 298 / 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: 37.74 % / Mosaicity: 0.25 °
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: 1.8→46.35 Å / Num. obs: 29291 / % possible obs: 99.9 % / Redundancy: 5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.058 / Rpim(I) all: 0.028 / Rrim(I) all: 0.064 / Net I/σ(I): 19.1
Reflection shell

Diffraction-ID: 1 / Redundancy: 5 %

Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.8-1.840.64517170.8350.3190.72299.9
9-46.350.0225810.0090.02298.9

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Phasing

PhasingMethod: molecular replacement

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Processing

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

3q04


Resolution: 1.8→36.395 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.66
RfactorNum. reflection% reflection
Rfree0.1993 1511 5.17 %
Rwork0.1614 --
obs0.1635 29238 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 96.4 Å2 / Biso mean: 27.6238 Å2 / Biso min: 9.9 Å2
Refinement stepCycle: final / Resolution: 1.8→36.395 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2773 0 33 298 3104
Biso mean--35.92 34.97 -
Num. residues----328
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072893
X-RAY DIFFRACTIONf_angle_d1.0143916
X-RAY DIFFRACTIONf_chiral_restr0.043403
X-RAY DIFFRACTIONf_plane_restr0.005503
X-RAY DIFFRACTIONf_dihedral_angle_d14.4621093
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8-1.85810.33461120.234625362648100
1.8581-1.92450.25081360.207425032639100
1.9245-2.00160.2221220.19225192641100
2.0016-2.09260.2441520.179424772629100
2.0926-2.2030.21331380.172725192657100
2.203-2.3410.24271290.169325202649100
2.341-2.52170.22781360.17072490262699
2.5217-2.77530.22311450.17825032648100
2.7753-3.17670.2021490.162325192668100
3.1767-4.00160.15681520.136625252677100
4.0016-36.40260.16271400.138626162756100
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)
11.1062-0.3628-0.220.30980.05670.7229-0.165-0.271-0.4215-0.02310.11630.22110.1741-0.06390.01660.2229-0.01690.03430.1980.10710.3275-21.0689-1.9732-10.9712
22.4938-0.53780.29211.0427-0.68330.7472-0.022-0.1527-0.162-0.080.04450.14890.0301-0.1322-0.03210.14120.0034-0.01340.19770.05010.2101-27.45278.7737-12.7981
31.05840.12010.08090.01150.04270.1399-0.308-0.00460.2835-0.29170.16610.1588-0.45070.12060.10250.3094-0.0736-0.05980.28170.02390.3087-20.831318.6327-13.6755
42.0296-0.1909-0.74221.04360.09780.9217-0.0392-0.2906-0.0752-0.03970.05740.15170.00510.0949-0.00880.1184-0.0139-0.00390.13390.03740.1098-8.90148.2702-14.0139
51.6310.5542-0.24721.3770.42021.4378-0.17660.176-0.0059-0.27170.050.0471-0.01730.03120.110.1938-0.0232-0.00430.11150.00030.11764.57187.9942-29.0721
60.96230.0782-0.29971.59160.13511.11610.0402-0.38030.0986-0.0313-0.0285-0.0338-0.1020.2639-0.03420.127-0.00180.00040.2555-0.03040.13314.478214.0025-10.0356
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 103 )A45 - 103
3X-RAY DIFFRACTION3chain 'A' and (resid 104 through 129 )A104 - 129
4X-RAY DIFFRACTION4chain 'A' and (resid 130 through 226 )A130 - 226
5X-RAY DIFFRACTION5chain 'A' and (resid 227 through 280 )A227 - 280
6X-RAY DIFFRACTION6chain 'A' and (resid 281 through 330 )A281 - 330

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