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- PDB-5nqc: CK2alpha in complex with NMR154 -

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Basic information

Entry
Database: PDB / ID: 5nqc
TitleCK2alpha in complex with NMR154
ComponentsCasein kinase II subunit alpha
KeywordsTRANSFERASE / protein kinase
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
Chem-1KP / Casein kinase II subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsSeetoh, W.-G. / Stubbs, C.J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust090340/Z/09/Z United Kingdom
CitationJournal: To Be Published
Title: Disrupting the CK2alpha-CK2beta protein-protein interaction within the protein kinase CK2 heterotetramer using a fragment-based approach
Authors: Seetoh, W.-G. / Stubbs, C.J. / Dickson, C. / Matak-Vinkovic, D. / Abell, C.
History
DepositionApr 19, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 7, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 30, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 16, 2019Group: Data collection / Category: reflns_shell
Revision 1.3Jan 17, 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

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Assembly

Deposited unit
A: Casein kinase II subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,4334
Polymers39,9361
Non-polymers4983
Water4,179232
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area160 Å2
ΔGint-11 kcal/mol
Surface area15640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.477, 71.477, 126.266
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-623-

HOH

21A-696-

HOH

31A-722-

HOH

41A-731-

HOH

51A-732-

HOH

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Components

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


Mass: 39935.547 Da / Num. of mol.: 1
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-1KP / (3E)-6,7-dichloro-3-(hydroxyimino)-1,3-dihydro-2H-indol-2-one


Mass: 231.036 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H4Cl2N2O2
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 232 / 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: 2.02 Å3/Da / Density % sol: 39.08 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop
Details: 0.1 M sodium tartrate pH 5.6, 2.2 M (NH4)2SO4, 0.2 M NaSCN, 5 mM TCEP, 5 mM NMR154, 5% (v/v) DMSO

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5406 Å
DetectorType: Bruker Platinum 135 / Detector: CCD / Date: Aug 28, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5406 Å / Relative weight: 1
ReflectionResolution: 2→28.88 Å / Num. obs: 22847 / % possible obs: 99.7 % / Redundancy: 7.61 % / Net I/σ(I): 11.91

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Processing

Software
NameVersionClassification
PHENIX1.7.3_928refinement
PROTEUM PLUSdata reduction
PROTEUM PLUSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3Q04

3q04


Resolution: 2→28.876 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.09
RfactorNum. reflection% reflection
Rfree0.2472 2000 8.78 %
Rwork0.1962 --
obs0.2007 22785 99.75 %
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Bsol: 40.284 Å2 / ksol: 0.4 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--2.4516 Å2-0 Å20 Å2
2---2.4516 Å2-0 Å2
3---4.9033 Å2
Refinement stepCycle: LAST / Resolution: 2→28.876 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2802 0 21 232 3055
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082913
X-RAY DIFFRACTIONf_angle_d1.1123939
X-RAY DIFFRACTIONf_dihedral_angle_d15.0791105
X-RAY DIFFRACTIONf_chiral_restr0.073406
X-RAY DIFFRACTIONf_plane_restr0.005506
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0001-2.05010.26581380.18831425X-RAY DIFFRACTION98
2.0501-2.10550.25291410.18591470X-RAY DIFFRACTION100
2.1055-2.16740.27491390.18411449X-RAY DIFFRACTION100
2.1674-2.23740.2441380.19891437X-RAY DIFFRACTION100
2.2374-2.31730.26331410.19181465X-RAY DIFFRACTION100
2.3173-2.410.31420.19941469X-RAY DIFFRACTION100
2.41-2.51970.27931390.20461456X-RAY DIFFRACTION100
2.5197-2.65240.29721440.20871492X-RAY DIFFRACTION100
2.6524-2.81850.24421400.21071455X-RAY DIFFRACTION100
2.8185-3.03590.2541430.20321488X-RAY DIFFRACTION100
3.0359-3.3410.24881440.19011496X-RAY DIFFRACTION100
3.341-3.82350.18681460.17791515X-RAY DIFFRACTION100
3.8235-4.81360.19631480.16721539X-RAY DIFFRACTION100
4.8136-28.87890.28821570.24171629X-RAY DIFFRACTION100

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