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- PDB-4dgl: Crystal Structure of the CK2 Tetrameric Holoenzyme -

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Basic information

Entry
Database: PDB / ID: 4dgl
TitleCrystal Structure of the CK2 Tetrameric Holoenzyme
Components
  • Casein kinase II subunit alphaCasein kinase 2
  • Casein kinase II subunit betaCasein kinase 2
KeywordsTRANSFERASE / protein kinase
Function / homology
Function and homology information


regulation of DNA binding / adiponectin-activated signaling pathway / positive regulation of activin receptor signaling pathway / UTP-C complex / endothelial tube morphogenesis / negative regulation of viral life cycle / regulation of transcription by RNA polymerase III / protein kinase regulator activity / regulation of chromosome separation / positive regulation of aggrephagy ...regulation of DNA binding / adiponectin-activated signaling pathway / positive regulation of activin receptor signaling pathway / UTP-C complex / endothelial tube morphogenesis / negative regulation of viral life cycle / regulation of transcription by RNA polymerase III / protein kinase regulator activity / 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 / Maturation of hRSV A proteins / Receptor Mediated Mitophagy / Sin3-type complex / Synthesis of PC / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / positive regulation of SMAD protein signal transduction / negative regulation of apoptotic signaling pathway / negative regulation of blood vessel endothelial cell migration / 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 / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / positive regulation of protein catabolic process / KEAP1-NFE2L2 pathway / double-strand break repair / rhythmic process / protein-macromolecule adaptor activity / kinase activity / positive regulation of cell growth / peptidyl-serine phosphorylation / protein-containing complex assembly / secretory granule lumen / Regulation of TP53 Activity through Phosphorylation / RNA polymerase II-specific DNA-binding transcription factor binding / ficolin-1-rich granule lumen / negative regulation of translation / protein stabilization / non-specific serine/threonine protein kinase / regulation of cell cycle / cell cycle / protein domain specific binding / negative regulation of cell population proliferation / protein phosphorylation / signaling receptor binding / protein serine kinase activity / protein serine/threonine kinase activity / apoptotic process / DNA damage response / chromatin binding / chromatin / Neutrophil degranulation / positive regulation of cell population proliferation / signal transduction / extracellular exosome / extracellular region / nucleoplasm / ATP binding / identical protein binding / metal ion binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
protein kinase ck2 holoenzyme, chain C, domain 1 / protein kinase ck2 holoenzyme, chain C, domain 1 / Casein kinase II, regulatory subunit / Casein kinase II, regulatory subunit, N-terminal / Casein kinase II subunit beta-like / Casein kinase II regulatory subunit / Casein kinase II regulatory subunit signature. / Casein kinase II regulatory subunit / N-terminal domain of TfIIb - #20 / Casein Kinase 2, subunit alpha ...protein kinase ck2 holoenzyme, chain C, domain 1 / protein kinase ck2 holoenzyme, chain C, domain 1 / Casein kinase II, regulatory subunit / Casein kinase II, regulatory subunit, N-terminal / Casein kinase II subunit beta-like / Casein kinase II regulatory subunit / Casein kinase II regulatory subunit signature. / Casein kinase II regulatory subunit / N-terminal domain of TfIIb - #20 / Casein Kinase 2, subunit alpha / N-terminal domain of TfIIb / Single Sheet / 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 Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Casein kinase II subunit beta / Casein kinase II subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3 Å
AuthorsLolli, G. / Battistutta, R.
CitationJournal: Acs Chem.Biol. / Year: 2012
Title: Structural determinants of protein kinase CK2 regulation by autoinhibitory polymerization.
Authors: Lolli, G. / Pinna, L.A. / Battistutta, R.
History
DepositionJan 26, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 2, 2012Provider: repository / Type: Initial release
Revision 1.1May 16, 2012Group: Database references
Revision 1.2Jan 2, 2013Group: Database references
Revision 1.3Feb 28, 2024Group: 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 / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref_seq_dif.details / _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

Downloads & links

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Assembly

Deposited unit
A: Casein kinase II subunit beta
B: Casein kinase II subunit beta
C: Casein kinase II subunit alpha
D: Casein kinase II subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,1916
Polymers130,0604
Non-polymers1312
Water21612
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7850 Å2
ΔGint-59 kcal/mol
Surface area50900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)175.652, 175.652, 96.260
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12C
22D

NCS domain segments:

Refine code: 5

Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111SERSERLEULEUAA8 - 568 - 56
211SERSERLEULEUBB8 - 568 - 56
121GLNGLNGLYGLYAA68 - 18968 - 189
221GLNGLNGLYGLYBB68 - 18968 - 189
131LYSLYSALAALAAA191 - 203191 - 203
231LYSLYSALAALABB191 - 203191 - 203
112GLYGLYASPASPCC3 - 373 - 37
212GLYGLYASPASPDD3 - 373 - 37
122LYSLYSLYSLYSCC74 - 10274 - 102
222LYSLYSLYSLYSDD74 - 10274 - 102
132LEULEUTYRTYRCC128 - 325128 - 325
232LEULEUTYRTYRDD128 - 325128 - 325

NCS ensembles :
ID
1
2

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Components

#1: Protein Casein kinase II subunit beta / Casein kinase 2 / CK II beta / Phosvitin / Protein G5a


Mass: 24969.412 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CSNK2B, CK2N, G5A / Production host: Escherichia coli (E. coli) / References: UniProt: P67870
#2: Protein Casein kinase II subunit alpha / Casein kinase 2 / CK II alpha


Mass: 40060.762 Da / Num. of mol.: 2 / Mutation: R125Y
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
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 12 / 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: 3.29 Å3/Da / Density % sol: 62.65 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7
Details: PEG 3350 18%, 0.2 M sodium malonate, pH 7, vapor diffusion, temperature 293K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 9, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 3→152.119 Å / Num. all: 34036 / Num. obs: 34036 / % possible obs: 100 % / Redundancy: 19.1 % / Rsym value: 0.122 / Net I/σ(I): 23.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
3-3.1619.20.993.19466149280.99100
3.16-3.3519.20.5925.18987646720.592100
3.35-3.5919.10.3558.78445544140.355100
3.59-3.8719.20.20914.37824240780.209100
3.87-4.2419.10.12722.67246237900.127100
4.24-4.7419.10.08134.36583634390.081100
4.74-5.4819.10.07139.65770930190.071100
5.48-6.71190.06543.44884025680.065100
6.71-9.4918.70.03867.73746220010.038100
9.49-44.86317.80.02794.62003711270.02799.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALA3.3.20data scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→152.119 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.937 / WRfactor Rfree: 0.185 / WRfactor Rwork: 0.1683 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8299 / SU B: 45.944 / SU ML: 0.324 / SU R Cruickshank DPI: 0.0816 / SU Rfree: 0.0751 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.075 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.2217 1726 5.1 %RANDOM
Rwork0.1953 ---
obs0.1966 34021 99.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 206.53 Å2 / Biso mean: 92.1847 Å2 / Biso min: 46.79 Å2
Baniso -1Baniso -2Baniso -3
1--26.57 Å2-0 Å2-0 Å2
2---26.57 Å2-0 Å2
3---53.14 Å2
Refinement stepCycle: LAST / Resolution: 3→152.119 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8863 0 2 12 8877
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.029109
X-RAY DIFFRACTIONr_angle_refined_deg1.5971.94812325
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.04551058
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.0223.374489
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.177151574
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9031572
X-RAY DIFFRACTIONr_chiral_restr0.1190.21265
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0217100
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A736MEDIUM POSITIONAL0.190.5
1A768LOOSE POSITIONAL0.455
1A736MEDIUM THERMAL5.922
1A768LOOSE THERMAL6.1110
2C1048MEDIUM POSITIONAL0.30.5
2C1188LOOSE POSITIONAL0.525
2C1048MEDIUM THERMAL4.182
2C1188LOOSE THERMAL5.1710
LS refinement shellResolution: 2.998→3.076 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.374 116 -
Rwork0.361 2334 -
all-2450 -
obs--96.99 %
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)
12.5774-0.4464-1.53491.66880.89641.2849-0.0959-0.2126-0.18190.3806-0.16750.38370.1825-0.26250.26340.6819-0.112-0.06920.83470.01721.009621.3811-16.4396-2.0463
20.49940.48220.6361.07590.84420.8997-0.12190.2661-0.23790.27190.22880.65310.12870.3265-0.1070.9829-0.0690.23271.08790.13421.425515.503-22.37453.0627
31.691-0.4023-0.51871.31340.72791.1613-0.1468-0.0806-0.1407-0.05190.11850.36940.0723-0.57920.02830.5787-0.0509-0.13440.6290.05020.955226.5826-7.4183-5.9363
40.99050.34380.14192.39450.48680.7522-0.0395-0.2216-0.0785-0.08980.10590.1097-0.1051-0.1107-0.06640.50350.0081-0.01440.2599-0.02120.80141.1716.715-2.4245
53.2529-0.91890.12471.9785-0.421.1916-0.10450.10780.1782-0.06010.25580.2184-0.0126-0.0992-0.15130.6043-0.0095-0.04080.270.00850.867228.896540.0641-9.1776
66.0469-1.49526.15193.28891.53929.53430.6302-0.07550.0467-0.037-0.5759-0.03661.03-0.7811-0.05430.9296-0.19730.00270.6090.18730.986716.773147.071-19.436
72.8953-1.88450.88432.2534-0.65420.3326-0.0321-0.06480.0941-0.17490.16140.29290.0721-0.1025-0.12930.5466-0.0561-0.01240.2219-0.02670.856134.170927.3028-5.5503
81.7097-0.37420.04643.60170.12280.0373-0.03250.1019-0.06-0.16530.11710.1122-0.0360.0704-0.08460.5363-0.01780.00180.1749-0.04480.762642.146510.8154-6.2818
90.5129-0.3553-0.06664.10730.86350.2638-0.1242-0.4921-0.03620.29630.01530.24070.0994-0.02840.1090.64130.05550.00490.509-0.02620.757250.4502-33.3173-1.9621
103.0476-1.4793-2.4552.69332.97983.69070.11450.12080.1386-0.1359-0.0227-0.0452-0.391-0.1144-0.09170.55220.0935-0.02390.1765-0.00760.78157.189-31.6826-14.1937
111.97050.84050.11732.02870.14943.3575-0.1568-0.1184-0.10290.36480.15720.29920.0697-0.4692-0.00040.17320.10580.07980.1563-0.02320.881346.7025-48.5296-19.1859
123.28131.9746-2.10074.3096-0.41722.7912-0.1617-0.0316-0.40260.2460.1301-0.20730.10860.05470.03160.05290.02120.01310.012-0.0370.841361.6829-48.697-26.5089
130.64660.43020.09853.1970.10630.9368-0.06760.4783-0.0314-0.6035-0.12620.10890.10340.09040.19370.5169-0.0348-0.02160.4375-0.06440.79858.63646.4875-14.1593
140.0760.1720.29671.31770.71031.36350.01940.0496-0.0478-0.41360.0193-0.18730.2945-0.0504-0.03870.4111-0.08310.03860.3573-0.08840.932565.786846.1438-2.7686
151.3491-0.2362-0.34131.89390.41492.7856-0.17410.24120.0453-0.33760.03290.3699-0.0236-0.45230.14110.1967-0.0542-0.09530.2054-0.06060.917355.256562.40451.6494
164.3553-0.01532.2065.2039-1.50986.5607-0.2084-0.01040.0024-0.2155-0.0528-0.09810.0180.45450.26120.06790.0086-0.07610.0543-0.07730.82768.959964.26099.2747
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A8 - 45
2X-RAY DIFFRACTION2A46 - 56
3X-RAY DIFFRACTION3A65 - 122
4X-RAY DIFFRACTION4A123 - 215
5X-RAY DIFFRACTION5B7 - 53
6X-RAY DIFFRACTION6B54 - 68
7X-RAY DIFFRACTION7B69 - 133
8X-RAY DIFFRACTION8B134 - 207
9X-RAY DIFFRACTION9C2 - 88
10X-RAY DIFFRACTION10C89 - 149
11X-RAY DIFFRACTION11C150 - 280
12X-RAY DIFFRACTION12C281 - 335
13X-RAY DIFFRACTION13D3 - 88
14X-RAY DIFFRACTION14D89 - 149
15X-RAY DIFFRACTION15D150 - 280
16X-RAY DIFFRACTION16D281 - 330

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