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- PDB-3fwq: Inactive conformation of human protein kinase CK2 catalytic subunit -

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Basic information

Entry
Database: PDB / ID: 3fwq
TitleInactive conformation of human protein kinase CK2 catalytic subunit
ComponentsCasein kinase II subunit alphaCasein kinase 2
KeywordsTRANSFERASE / casein kinase 2 / protein kinase CK2 / eukaryotic protein kinases / inactive conformation / ATP-binding / Kinase / Nucleotide-binding / Phosphoprotein / Serine/threonine-protein kinase / Wnt signaling pathway
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 / negative regulation of apoptotic signaling pathway / positive regulation of Wnt signaling pathway / chaperone-mediated protein folding / negative regulation of ubiquitin-dependent protein catabolic process / Signal transduction by L1 / Hsp90 protein binding / peptidyl-threonine phosphorylation / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / PML body / Wnt signaling pathway / Regulation of PTEN stability and activity / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / positive regulation of protein catabolic process / rhythmic process / KEAP1-NFE2L2 pathway / double-strand break repair / kinase activity / positive regulation of cell growth / peptidyl-serine phosphorylation / Regulation of TP53 Activity through Phosphorylation / negative regulation of translation / protein stabilization / regulation of cell cycle / non-specific serine/threonine protein kinase / 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
Casein kinase II subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsNiefind, K. / Raaf, J. / Issinger, O.G.
Citation
Journal: J.Mol.Biol. / Year: 2009
Title: First inactive conformation of CK2 alpha, the catalytic subunit of protein kinase CK2
Authors: Raaf, J. / Issinger, O.G. / Niefind, K.
#1: Journal: Embo J. / Year: 1998
Title: Crystal structure of the catalytic subunit of protein kinase CK2 from Zea mays at 2.1 A resolution
Authors: Niefind, K. / Guerra, B. / Pinna, L.A. / Issinger, O.G. / Schomburg, D.
#2: Journal: Nat.Struct.Biol. / Year: 1999
Title: GTP plus water mimic ATP in the active site of protein kinase CK2
Authors: Niefind, K. / Putter, M. / Guerra, B. / Issinger, O.G. / Schomburg, D.
#3: Journal: Embo J. / Year: 2001
Title: Crystal structure of human protein kinase CK2: insights into basic properties of the CK2 holoenzyme
Authors: Niefind, K. / Guerra, B. / Ermakowa, I. / Issinger, O.G.
#4: 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.
#5: Journal: J.Mol.Biol. / Year: 2005
Title: Inclining the purine base binding plane in protein kinase CK2 by exchanging the flanking side-chains generates a preference for ATP as a cosubstrate
Authors: Yde, C.W. / Ermakova, I. / Issinger, O.G. / Niefind, K.
#6: Journal: Mol.Cell.Biochem. / Year: 2005
Title: Primary and secondary interactions between CK2alpha and CK2beta lead to ring-like structures in the crystals of the CK2 holoenzyme
Authors: Niefind, K. / Issinger, O.G.
#7: Journal: J.Mol.Biol. / Year: 2007
Title: Evolved to be active: sulfate ions define substrate recognition sites of CK2alpha and emphasise its exceptional role within the CMGC family of eukaryotic protein kinases
Authors: Niefind, K. / Yde, C.W. / Ermakova, I. / Issinger, O.G.
#8: 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.
#9: Journal: Chem.Biol. / Year: 2008
Title: The CK2 alpha/CK2 beta interface of human protein kinase CK2 harbors a binding pocket for small molecules
Authors: Raaf, J. / Brunstein, E. / Issinger, O.G. / Niefind, K.
History
DepositionJan 19, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 17, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Apr 4, 2012Group: Database references
Revision 1.3Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)80,68311
Polymers80,1332
Non-polymers5509
Water3,675204
1
A: Casein kinase II subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,4537
Polymers40,0671
Non-polymers3876
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Casein kinase II subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,2304
Polymers40,0671
Non-polymers1633
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)71.324, 71.324, 125.681
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

#1: Protein Casein kinase II subunit alpha / Casein kinase 2 / CK II


Mass: 40066.742 Da / Num. of mol.: 2 / Mutation: residues 1-335
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pT7-7 / Production host: Escherichia coli (E. coli)
References: UniProt: P68400, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


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


Mass: 18.015 Da / Num. of mol.: 204 / 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: 1.99 Å3/Da / Density % sol: 38.33 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Protein stock solution: 10mg/ml CK2alpha, 500mM sodium chloride, 25mM Tris/HCl, pH 8.5; Reservoir: 2M ammonium sulfate, 2M sodium chloride; Drop: 0.001mL reservoir solution, 0.001mL protein ...Details: Protein stock solution: 10mg/ml CK2alpha, 500mM sodium chloride, 25mM Tris/HCl, pH 8.5; Reservoir: 2M ammonium sulfate, 2M sodium chloride; Drop: 0.001mL reservoir solution, 0.001mL protein stock solution, 0.003mL 1mM AMPPNP, 0.0006mL 10mM magnesium chloride, 0.0001mL glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X12 / Wavelength: 0.9537 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 12, 2007
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11h,k,l10.501
11-h,k,-l20.499
ReflectionResolution: 2.3→34.5 Å / Num. all: 27863 / Num. obs: 26999 / % possible obs: 96.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.7 % / Biso Wilson estimate: 47.1 Å2 / Rmerge(I) obs: 0.1 / Rsym value: 0.1 / Net I/σ(I): 17.6
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.724 / Mean I/σ(I) obs: 2 / % possible all: 98.3

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Processing

Software
NameVersionClassification
HKL-2000data collection
AMoREphasing
REFMAC5.5.0063refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2PVR

2pvr


Resolution: 2.3→34.3 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.934 / SU B: 13.697 / SU ML: 0.144 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.136 / ESU R Free: 0.056 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23272 1253 4.6 %RANDOM
Rwork0.16969 ---
all0.17256 27046 --
obs0.17256 25746 96.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 41.145 Å2
Baniso -1Baniso -2Baniso -3
1-7.87 Å20 Å20 Å2
2--7.87 Å20 Å2
3----15.73 Å2
Refinement stepCycle: LAST / Resolution: 2.3→34.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5634 0 28 204 5866
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0225803
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.8851.9497841
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7345666
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.37723.057314
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.173151028
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.5621552
X-RAY DIFFRACTIONr_chiral_restr0.0640.2810
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0214478
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.61263338
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.55695422
X-RAY DIFFRACTIONr_scbond_it1.55862465
X-RAY DIFFRACTIONr_scangle_it2.17592419
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.324 105 -
Rwork0.205 1877 -
obs--97.59 %
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)
10.8730.0014-0.68261.3292-0.06730.98250.0039-0.07240.06940.12990.01780.11360.0329-0.0781-0.02160.0499-0.0070.00980.0518-0.01480.0196-15.8927.572.668
22.0347-0.28691.3250.319-0.50751.40530.0176-0.0594-0.2341-0.05410.0248-0.05530.17460.0641-0.04250.11850.03850.01990.10650.00620.05534.74613.896-5.066
31.2325-0.1043-0.01960.6973-0.62621.06520.0290.11190.141-0.0633-0.02010.0335-0.0950.0306-0.0090.05530.0028-0.01150.05250.00630.0238.12851.583-18.088
40.48-0.3717-0.44171.33361.2131.2440.0612-0.0351-0.0673-0.03620.0884-0.24340.05040.1833-0.14960.13620.03770.01710.14490.01850.102821.86130.971-10.332
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 12
2X-RAY DIFFRACTION1A117 - 335
3X-RAY DIFFRACTION2A13 - 116
4X-RAY DIFFRACTION3B2 - 12
5X-RAY DIFFRACTION3B117 - 335
6X-RAY DIFFRACTION4B13 - 116

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