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- PDB-4ib5: Structure of human protein kinase CK2 catalytic subunit in comple... -

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Basic information

Entry
Database: PDB / ID: 4ib5
TitleStructure of human protein kinase CK2 catalytic subunit in complex with a CK2beta-competitive cyclic peptide
Components
  • CK2beta-derived cyclic peptide
  • Casein kinase II subunit alpha
KeywordsTRANSFERASE / protein kinase fold / protein phosphorylation / Binding of CK2beta / Phosphorylation / Nucleus
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
Casein kinase II subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsRaaf, J. / Guerra, B. / Neundorf, I. / Bopp, B. / Issinger, O.-G. / Jose, J. / Pietsch, M. / Niefind, K.
Citation
Journal: Acs Chem.Biol. / Year: 2013
Title: First structure of protein kinase CK2 catalytic subunit with an effective CK2 beta-competitive ligand
Authors: Raaf, J. / Guerra, B. / Neundorf, I. / Bopp, B. / Issinger, O.G. / Jose, J. / Pietsch, M. / Niefind, K.
#1: 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.
#2: Journal: Biochem.J. / Year: 2007
Title: Structure-based design of small peptide inhibitors of protein kinase CK2 subunit interaction.
Authors: Laudet, B. / Barette, C. / Dulery, V. / Renaudet, O. / Dumy, P. / Metz, A. / Prudent, R. / Deshiere, A. / Dideberg, O. / Filhol, O. / Cochet, C.
History
DepositionDec 8, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 20, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 5, 2013Group: Database references
Revision 1.2Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Casein kinase II subunit alpha
B: Casein kinase II subunit alpha
C: Casein kinase II subunit alpha
D: CK2beta-derived cyclic peptide
E: CK2beta-derived cyclic peptide
F: CK2beta-derived cyclic peptide
G: CK2beta-derived cyclic peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,79019
Polymers125,8557
Non-polymers93512
Water8,323462
1
A: Casein kinase II subunit alpha
D: CK2beta-derived cyclic peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,0129
Polymers41,4802
Non-polymers5317
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2460 Å2
ΔGint-28 kcal/mol
Surface area16000 Å2
MethodPISA
2
B: Casein kinase II subunit alpha
E: CK2beta-derived cyclic peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,5733
Polymers41,4802
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1470 Å2
ΔGint-10 kcal/mol
Surface area16460 Å2
MethodPISA
3
C: Casein kinase II subunit alpha
F: CK2beta-derived cyclic peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,7926
Polymers41,4802
Non-polymers3124
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1770 Å2
ΔGint-20 kcal/mol
Surface area16400 Å2
MethodPISA
4
G: CK2beta-derived cyclic peptide


  • defined by author&software
  • 1.41 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)1,4141
Polymers1,4141
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)77.380, 105.420, 152.110
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 40066.742 Da / Num. of mol.: 3 / Fragment: UNP residues 1-355
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
CK2beta-derived cyclic peptide


Mass: 1413.692 Da / Num. of mol.: 4 / Source method: obtained synthetically
Details: The molecule was synthesized by solid-phase peptide synthesis.
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 462 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.46 Å3/Da / Density % sol: 50.1 %

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→45.693 Å / Num. obs: 63979 / % possible obs: 99.6 % / Biso Wilson estimate: 39.1 Å2 / Rmerge(I) obs: 0.062 / Rsym value: 0.062

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Processing

Software
NameVersionClassification
PHASERphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→45.693 Å / Occupancy max: 1 / Occupancy min: 0.38 / SU ML: 0.21 / σ(F): 0 / Phase error: 21.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2183 3185 4.98 %
Rwork0.1768 --
obs0.1789 63972 99.57 %
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 187.36 Å2 / Biso mean: 66.8099 Å2 / Biso min: 23.01 Å2
Refinement stepCycle: LAST / Resolution: 2.2→45.693 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8767 0 57 462 9286
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0049153
X-RAY DIFFRACTIONf_angle_d0.97612336
X-RAY DIFFRACTIONf_dihedral_angle_d12.893458
X-RAY DIFFRACTIONf_chiral_restr0.0581262
X-RAY DIFFRACTIONf_plane_restr0.0031583
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 23

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.196-2.22880.26621160.25062446256293
2.2288-2.26360.27071370.228426022739100
2.2636-2.30070.22841380.217526162754100
2.3007-2.34040.30361400.223426552795100
2.3404-2.38290.26471340.209425752709100
2.3829-2.42870.2591370.208526182755100
2.4287-2.47830.24481380.200526282766100
2.4783-2.53220.27931380.199126052743100
2.5322-2.59110.22911380.198826312769100
2.5911-2.65590.25571390.197226202759100
2.6559-2.72770.22871380.191826262764100
2.7277-2.80790.25821390.190926532792100
2.8079-2.89860.22141370.188826212758100
2.8986-3.00210.22421400.192626502790100
3.0021-3.12230.24171400.190426502790100
3.1223-3.26440.24391380.18426392777100
3.2644-3.43640.18381410.164426552796100
3.4364-3.65160.19721400.162426712811100
3.6516-3.93350.23051400.158326652805100
3.9335-4.3290.15671410.144926742815100
4.329-4.95480.18671420.142226962838100
4.9548-6.240.21081430.175727332876100
6.24-45.70290.22271510.184128583009100
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)
12.88260.62420.76840.91990.37553.5255-0.0006-0.42070.35470.0871-0.02180.031-0.0546-0.36140.02640.2473-0.01680.01850.2674-0.03850.335814.2118-22.59573.7836
25.13020.7004-0.61882.46970.7962.3704-0.06121.31910.1282-0.38260.05780.1711-0.1078-0.32520.00830.2766-0.0233-0.01580.55980.0350.20410.6919-29.8522-17.2018
34.43223.67880.93613.85011.25161.71-0.2389-0.057-0.63550.04340.2882-0.61820.69060.0687-0.02080.9978-0.0147-0.05790.4173-0.03550.7797-28.0581-76.7628-24.219
43.3231.09270.63563.67080.47722.37070.071-0.2131-0.56040.39330.2315-0.60210.40510.298-0.28430.52120.017-0.13910.5606-0.13550.6001-16.0638-59.5366-15.5697
52.8803-1.10710.03962.9863-0.74413.37660.13190.6927-0.2234-1.0438-0.3796-0.17470.2712-0.0740.14180.73380.1180.10040.42940.13750.52061.0304-46.382414.0152
67.7219-1.53342.78242.58053.17577.16940.6711-0.8257-1.3521-1.0424-0.6307-1.19071.16930.82640.0271.03120.35110.35310.86990.38231.302417.5509-55.904910.4903
73.15970.0716-0.0012.4165-0.96722.6760.19290.4515-0.3533-0.6281-0.4617-0.61860.63341.38490.10370.69870.28690.18520.95850.2130.692613.2232-50.252715.3326
82.7492-0.62641.17563.1785-2.07345.9419-0.03070.14970.07350.0183-0.3347-0.3167-0.01320.70630.24780.32560.01790.02670.31110.1740.41616.2364-48.971335.892
96.5992-6.2734-3.3556.41271.97115.1032-0.8418-1.4315-0.8071.3651.17341.54540.2603-1.1534-0.22470.5803-0.02140.17521.1641-0.07630.66373.2883-22.930121.6293
108.8425.24070.81976.5264.25749.40660.48080.1740.3378-0.8178-0.83292.1236-0.7483-0.79070.31561.25-0.0738-0.26820.6108-0.07591.033-49.1234-80.8022-27.1285
114.0348-1.13320.91427.07633.95914.56390.19550.8308-1.0685-0.4952-0.0727-0.68491.10090.9523-0.0871.40340.52540.47711.16250.05471.621123.6846-61.05181.0095
122.5018-3.81643.55978.8655-3.71986.28940.0119-0.77750.94261.43240.2528-1.4156-0.92671.5805-0.32910.8415-0.1271-0.21140.85720.00780.78913.1226-38.213354.9635
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 129 )A2 - 129
2X-RAY DIFFRACTION2chain 'A' and (resid 130 through 332 )A130 - 332
3X-RAY DIFFRACTION3chain 'B' and (resid 3 through 129 )B3 - 129
4X-RAY DIFFRACTION4chain 'B' and (resid 130 through 331 )B130 - 331
5X-RAY DIFFRACTION5chain 'C' and (resid 2 through 44 )C2 - 44
6X-RAY DIFFRACTION6chain 'C' and (resid 45 through 74 )C45 - 74
7X-RAY DIFFRACTION7chain 'C' and (resid 75 through 129 )C75 - 129
8X-RAY DIFFRACTION8chain 'C' and (resid 130 through 333 )C130 - 333
9X-RAY DIFFRACTION9chain 'D' and (resid 184 through 196 )D184 - 196
10X-RAY DIFFRACTION10chain 'E' and (resid 184 through 196 )E184 - 196
11X-RAY DIFFRACTION11chain 'F' and (resid 184 through 196 )F184 - 196
12X-RAY DIFFRACTION12chain 'G' and (resid 184 through 196 )G184 - 196

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