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- PDB-8bgc: Crystal structure of human Casein Kinase II subunit alpha (CK2a1)... -

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Basic information

Entry
Database: PDB / ID: 8bgc
TitleCrystal structure of human Casein Kinase II subunit alpha (CK2a1) in complex with compound 2 (AA-CS-9-003)
ComponentsCasein kinase II subunit alpha
KeywordsTRANSFERASE / CK2apha / 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 / 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
Similarity search - Domain/homology
Chem-QIA / Casein kinase II subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.8 Å
AuthorsKraemer, A. / Axtman, A.D. / Knapp, S. / Structural Genomics Consortium (SGC)
Funding support Canada, 1items
OrganizationGrant numberCountry
The Structural Genomics Consortium (SGC) Canada
CitationJournal: Acs Med.Chem.Lett. / Year: 2023
Title: Discovery of a Potent and Selective Naphthyridine-Based Chemical Probe for Casein Kinase 2.
Authors: Davis-Gilbert, Z.W. / Kramer, A. / Dunford, J.E. / Howell, S. / Senbabaoglu, F. / Wells, C.I. / Bashore, F.M. / Havener, T.M. / Smith, J.L. / Hossain, M.A. / Oppermann, U. / Drewry, D.H. / Axtman, A.D.
History
DepositionOct 27, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 23, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Structure summary
Category: audit_author / chem_comp_atom ...audit_author / chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _audit_author.name / _citation.country ..._audit_author.name / _citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 31, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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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)82,27714
Polymers80,6562
Non-polymers1,62112
Water34219
1
A: Casein kinase II subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,0436
Polymers40,3281
Non-polymers7155
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Casein kinase II subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,2358
Polymers40,3281
Non-polymers9077
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)127.340, 127.340, 125.731
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

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


Mass: 40327.977 Da / Num. of mol.: 2
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.: 10 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-QIA / 5-[(phenylmethyl)amino]pyrimido[4,5-c]quinoline-8-carboxylic acid


Mass: 330.340 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H14N4O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 19 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.16 Å3/Da / Density % sol: 61.07 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.2 M ammonia sulphate 0.1 M bis-tris pH 5.5 23-26% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.000009 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 29, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.000009 Å / Relative weight: 1
ReflectionResolution: 2.8→45.06 Å / Num. obs: 26114 / % possible obs: 100 % / Redundancy: 13.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.171 / Rpim(I) all: 0.048 / Rrim(I) all: 0.178 / Net I/σ(I): 13.6
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
2.8-2.9513.81.5195173337410.7490.4211.5772.1100
8.85-45.0211.70.0341104394510.010.03640.399.4

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Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.448
Highest resolutionLowest resolution
Rotation45.02 Å3.03 Å

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
Aimless0.7.9data scaling
MOLREPphasing
REFMAC5.8.0352refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6Z84

6z84


Resolution: 2.8→45.06 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.912 / SU B: 29.465 / SU ML: 0.264 / SU R Cruickshank DPI: 0.8866 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.887 / ESU R Free: 0.34 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2534 1364 5.2 %RANDOM
Rwork0.2225 ---
obs0.2241 24702 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 131.91 Å2 / Biso mean: 58.28 Å2 / Biso min: 28.22 Å2
Baniso -1Baniso -2Baniso -3
1-1 Å2-0 Å20 Å2
2--1 Å2-0 Å2
3----2.01 Å2
Refinement stepCycle: final / Resolution: 2.8→45.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5356 0 100 19 5475
Biso mean--75.16 40.15 -
Num. residues----653
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0125596
X-RAY DIFFRACTIONr_bond_other_d0.0010.0164893
X-RAY DIFFRACTIONr_angle_refined_deg0.7971.6567600
X-RAY DIFFRACTIONr_angle_other_deg0.2941.58111329
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8115649
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.022541
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.63610904
X-RAY DIFFRACTIONr_chiral_restr0.0380.2805
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.026616
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021200
LS refinement shellResolution: 2.8→2.872 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.377 93 -
Rwork0.317 1797 -
all-1890 -
obs--100 %
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)
13.73670.93750.25541.25640.18031.5814-0.20930.5826-0.0539-0.13960.18020.0148-0.03620.10680.0290.0966-0.04270.0340.1701-0.00440.07099.6085-41.48947.1464
21.82671.09880.2153.5754-0.3151.94740.1367-0.4454-0.06450.3115-0.1455-0.2154-0.0543-0.11050.00880.0411-0.0585-0.02120.22780.02060.09142.2278-8.6662-9.6552
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 405
2X-RAY DIFFRACTION2B3 - 407

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