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- PDB-4fbx: Complex structure of human protein kinase CK2 catalytic subunit c... -

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Basic information

Entry
Database: PDB / ID: 4fbx
TitleComplex structure of human protein kinase CK2 catalytic subunit crystallized in the presence of a bisubstrate inhibitor
Components
  • Casein kinase II subunit alpha
  • bisubstrate inhibitor
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / protein kinase fold / protein phosphorylation / Bisubstrate inhibitor / TRANSFERASE-TRANSFERASE INHIBITOR complex
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 / Maturation of hRSV A proteins / Sin3-type complex ...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 / Maturation of hRSV A proteins / Sin3-type complex / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / negative regulation of apoptotic signaling pathway / positive regulation of Wnt signaling pathway / negative regulation of double-strand break repair via homologous recombination / : / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / Signal transduction by L1 / Hsp90 protein binding / PML body / Wnt signaling pathway / Regulation of PTEN stability and activity / positive regulation of protein catabolic process / kinase activity / KEAP1-NFE2L2 pathway / rhythmic process / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / double-strand break repair / positive regulation of cell growth / Regulation of TP53 Activity through Phosphorylation / eukaryotic translation initiation factor 2alpha kinase activity / 3-phosphoinositide-dependent protein kinase activity / DNA-dependent protein kinase activity / ribosomal protein S6 kinase activity / histone H3S10 kinase activity / histone H2AXS139 kinase activity / histone H3S28 kinase activity / histone H4S1 kinase activity / histone H2BS14 kinase activity / histone H3T3 kinase activity / histone H2AS121 kinase activity / Rho-dependent protein serine/threonine kinase activity / histone H2BS36 kinase activity / histone H3S57 kinase activity / histone H2AT120 kinase activity / AMP-activated protein kinase activity / histone H2AS1 kinase activity / histone H3T6 kinase activity / histone H3T11 kinase activity / histone H3T45 kinase activity / non-specific serine/threonine protein kinase / regulation of cell cycle / negative regulation of translation / protein stabilization / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / apoptotic process / positive regulation of cell population proliferation / DNA damage response / signal transduction / nucleoplasm / ATP binding / identical protein binding / nucleus / plasma membrane / cytosol
Similarity search - Function
Casein Kinase 2, subunit alpha / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); 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 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); 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
bisubstrate inhibitor / Casein kinase II subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.33 Å
AuthorsEnkvist, E. / Viht, K. / Bischoff, N. / Vahter, J. / Saaver, S. / Raidaru, G. / Issinger, O.-G. / Niefind, K. / Uri, A.
Citation
Journal: Org.Biomol.Chem. / Year: 2012
Title: A subnanomolar fluorescent probe for protein kinase CK2 interaction studies.
Authors: Enkvist, E. / Viht, K. / Bischoff, N. / Vahter, J. / Saaver, S. / Raidaru, G. / Issinger, O.G. / Niefind, K. / Uri, A.
#1: Journal: J.Mol.Biol. / Year: 2003
Title: Crystal structure of a C-terminal deletion mutant of human protein kinase CK2 catalytic subunit.
Authors: Ermakova, I. / Boldyreff, B. / Issinger, O.G. / Niefind, K.
#2: Journal: J.Mol.Biol. / Year: 2008
Title: The catalytic subunit of human protein kinase CK2 structurally deviates from its maize homologue in complex with the nucleotide competitive inhibitor emodin.
Authors: Raaf, J. / Klopffleisch, K. / Issinger, O.G. / Niefind, K.
#3: Journal: Cell.Mol.Life Sci. / Year: 2009
Title: Protein kinase CK2 in health and disease: Protein kinase CK2: from structures to insights.
Authors: Niefind, K. / Raaf, J. / Issinger, O.G.
History
DepositionMay 23, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 17, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 31, 2012Group: Database references
Revision 1.2Dec 12, 2012Group: Other
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.0Jul 10, 2024Group: Data collection / Non-polymer description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / entity
Item: _chem_comp.formula / _chem_comp.formula_weight / _entity.formula_weight
Revision 2.1Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Casein kinase II subunit alpha
B: bisubstrate inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,4817
Polymers41,3042
Non-polymers1775
Water2,198122
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)72.114, 72.114, 135.056
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

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


Mass: 40066.742 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: Protein/peptide bisubstrate inhibitor


Type: Polypeptide / Class: Enzyme inhibitor / Mass: 1237.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / References: bisubstrate inhibitor
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 122 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCHAIN B IS A BISUBSTRATE INHIBITOR, I.E. A MODIFIED CK2 SUBSTRATE PEPTIDE TO WHICH AN ATP- ...CHAIN B IS A BISUBSTRATE INHIBITOR, I.E. A MODIFIED CK2 SUBSTRATE PEPTIDE TO WHICH AN ATP-COMPETITIVE INHIBITOR MOIETY IS LINKED. ONLY THE LATTER IS DEFINED IN THE ELECTRON DENSITY WHILE THE PEPTIDIC PART IS COMPLETELY FLEXIBLE PROBABLY DUE TO ITS HIGH NEGATIVE CHARGE DENSITY.
Has protein modificationN

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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: 2.16 Å3/Da / Density % sol: 42.98 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: The concentrated enzyme solution contained 6.2 mg/ml protein dissolved in 500 mM NaCl, 25 mM Tris/HCl, pH 8.5. Nine volume parts of this protein stock solution were mixed with one part 12 mM ...Details: The concentrated enzyme solution contained 6.2 mg/ml protein dissolved in 500 mM NaCl, 25 mM Tris/HCl, pH 8.5. Nine volume parts of this protein stock solution were mixed with one part 12 mM ARC-1154 dissolved in 100% dimethyl sulfoxide. The CK2alpha1-335/ARC-1154 mixture was incubated for 30 min at room temperature. The best crystals grew with a reservoir solution composed of 4.4 M NaCl, 100 mM citric acid, pH 5.25 and mixing 2 microliter of this reservoir solution with microliter CK2alpha1-335/ARC-1154 mixture, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SEALED TUBE / Type: OTHER / Wavelength: 1.5418 Å
DetectorType: AGILENT ATLAS CCD / Detector: CCD / Date: Dec 14, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.33→32.25 Å / Num. all: 15941 / Num. obs: 15925 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8 % / Biso Wilson estimate: 38.8 Å2 / Rmerge(I) obs: 0.095 / Rsym value: 0.095 / Net I/σ(I): 18.8

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Processing

Software
NameVersionClassification
PHENIXmodel building
PHENIX(phenix.refine: 1.7.3_928)refinement
XDSdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.33→31.807 Å / SU ML: 0.37 / σ(F): 1.35 / Phase error: 23.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2492 924 5.82 %Random
Rwork0.1988 ---
obs0.2018 15868 99.9 %-
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 36.043 Å2 / ksol: 0.361 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.0349 Å20 Å20 Å2
2---0.0349 Å20 Å2
3---0.0698 Å2
Refinement stepCycle: LAST / Resolution: 2.33→31.807 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2829 0 5 122 2956
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032905
X-RAY DIFFRACTIONf_angle_d0.6773930
X-RAY DIFFRACTIONf_dihedral_angle_d13.761098
X-RAY DIFFRACTIONf_chiral_restr0.054405
X-RAY DIFFRACTIONf_plane_restr0.003505
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.33-2.45290.37341100.27752093X-RAY DIFFRACTION100
2.4529-2.60650.32361410.26042071X-RAY DIFFRACTION100
2.6065-2.80760.28991200.23092095X-RAY DIFFRACTION100
2.8076-3.08990.27571420.21772115X-RAY DIFFRACTION100
3.0899-3.53650.25321520.19572104X-RAY DIFFRACTION100
3.5365-4.45370.1971250.15942168X-RAY DIFFRACTION100
4.4537-31.80970.21711340.18222298X-RAY DIFFRACTION100
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)
10.5073-0.1326-0.46660.54890.20421.15510.0063-0.0496-0.02970.1075-0.0083-0.17310.31670.028800.26370.0886-0.0320.2229-0.03090.190921.4813-2.422128.1565
21.4434-0.0124-0.31210.7826-0.65911.4880.01880.19310.25320.13740.0246-0.0625-0.0232-0.13070.02070.02630.0241-0.02030.1690.01690.17779.909716.266622.6869
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ 2:129)
2X-RAY DIFFRACTION2CHAIN A AND (RESSEQ 130:334)

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