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- PDB-3u9c: Structure of a C-terminal deletion mutant of human protein kinase... -

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Basic information

Entry
Database: PDB / ID: 3u9c
TitleStructure of a C-terminal deletion mutant of human protein kinase CK2 catalytic subunit with the ATP-competitive inhibitor resorufin
ComponentsCasein kinase II subunit alpha
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / protein kinase CK2 casein kinase 2 / eukaryotic protein kinase fold / ATP:protein phosphotransferase / protein kinase / ATP CK2beta / 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 / Sin3-type complex / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known ...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 / Sin3-type complex / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / Maturation of hRSV A proteins / positive regulation of Wnt signaling pathway / negative regulation of apoptotic signaling pathway / negative regulation of double-strand break repair via homologous recombination / chaperone-mediated protein folding / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / : / Signal transduction by L1 / peptidyl-threonine phosphorylation / Hsp90 protein binding / 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 / rhythmic process / double-strand break repair / kinase activity / peptidyl-serine phosphorylation / positive regulation of cell growth / Regulation of TP53 Activity through Phosphorylation / negative regulation of translation / non-specific serine/threonine protein kinase / regulation of cell cycle / protein stabilization / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / DNA damage response / positive regulation of cell population proliferation / apoptotic process / 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
7-hydroxy-3H-phenoxazin-3-one / Casein kinase II subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsKlopffleisch, K. / Issinger, O.-G. / Niefind, K.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2012
Title: Low-density crystal packing of human protein kinase CK2 catalytic subunit in complex with resorufin or other ligands: a tool to study the unique hinge-region plasticity of the enzyme without packing bias.
Authors: Klopffleisch, K. / Issinger, O.G. / Niefind, K.
#1: Journal: Biochim.Biophys.Acta / Year: 2010
Title: Conformational plasticity of the catalytic subunit of protein kinase CK2 and its consequences for regulation and drug design.
Authors: Niefind, K. / Issinger, O.G.
#2: 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.
#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.
#4: 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.
History
DepositionOct 18, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 30, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 23, 2013Group: Database references
Revision 1.2Sep 13, 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 / 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 / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,72817
Polymers80,1332
Non-polymers1,59515
Water99155
1
A: Casein kinase II subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,8809
Polymers40,0671
Non-polymers8138
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Casein kinase II subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,8488
Polymers40,0671
Non-polymers7827
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Casein kinase II subunit alpha
hetero molecules

B: Casein kinase II subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,72817
Polymers80,1332
Non-polymers1,59515
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area4400 Å2
ΔGint-108 kcal/mol
Surface area29530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.777, 127.777, 125.766
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 40066.742 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

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Non-polymers , 5 types, 70 molecules

#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-04G / 7-hydroxy-3H-phenoxazin-3-one / RESORUFIN


Mass: 213.189 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H7NO3
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 55 / 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: 3.2 Å3/Da / Density % sol: 61.6 %
Crystal growTemperature: 293 K / pH: 6.5
Details: reservoir: 30 % polyethylene glycol 8000, 0.2 M ammonium sulfate, 0.1 M sodium cacodylate buffer; drop: 2 microliters preincubated CK2alpha/resorufin mixture (5 mM resorufin, 5 mg/ml ...Details: reservoir: 30 % polyethylene glycol 8000, 0.2 M ammonium sulfate, 0.1 M sodium cacodylate buffer; drop: 2 microliters preincubated CK2alpha/resorufin mixture (5 mM resorufin, 5 mg/ml Ck2alpha), 1 reservoir solution , pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Feb 15, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 3.2→38.5 Å / Num. obs: 17653 / % possible obs: 99.6 % / Redundancy: 10.2 % / Rmerge(I) obs: 0.178 / Rsym value: 0.178 / Net I/σ(I): 14.6
Reflection shellResolution: 3.2→3.37 Å / Redundancy: 10.4 % / Rmerge(I) obs: 0.689 / Mean I/σ(I) obs: 3.9 / Rsym value: 0.689 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.7.2_869)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3NGA

3nga


Resolution: 3.2→19.948 Å / SU ML: 0.32 / σ(F): 1.36 / Phase error: 22.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2311 881 5 %
Rwork0.2008 --
obs0.2024 17632 99.89 %
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 28.111 Å2 / ksol: 0.343 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.871 Å20 Å2-0 Å2
2--0.871 Å2-0 Å2
3----1.7421 Å2
Refinement stepCycle: LAST / Resolution: 3.2→19.948 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5586 0 98 55 5739
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0025825
X-RAY DIFFRACTIONf_angle_d0.5747877
X-RAY DIFFRACTIONf_dihedral_angle_d10.8772178
X-RAY DIFFRACTIONf_chiral_restr0.044806
X-RAY DIFFRACTIONf_plane_restr0.0031002
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2001-3.39970.27831440.22882739X-RAY DIFFRACTION100
3.3997-3.66070.26421440.21252745X-RAY DIFFRACTION100
3.6607-4.02640.24581450.19732748X-RAY DIFFRACTION100
4.0264-4.60270.20861460.17532780X-RAY DIFFRACTION100
4.6027-5.77550.21081480.18332812X-RAY DIFFRACTION100
5.7755-19.9480.21721540.22342927X-RAY DIFFRACTION99
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)
11.0614-0.9242-0.0253.35371.31862.53860.06750.10310.01130.1579-0.0585-0.2980.1331-0.1473-0.03110.17270.0392-0.010.1999-0.01420.170949.3522-3.30648.5355
21.8026-2.11562.15193.1342-1.81024.08440.05670.69210.258-0.8493-0.74170.3024-0.4487-0.1608-0.95180.21170.2424-0.31820.1627-0.1018-0.170440.7087-2.654932.7746
32.0008-0.75950.20832.7012-0.24771.86680.11250.48180.0361-0.3731-0.1603-0.0385-0.12750.0940.05070.16050.1473-0.03830.1788-0.04980.115939.099716.057637.8322
41.3402-0.1392-0.57153.46611.23692.2609-0.025-0.0364-0.13970.41810.0817-0.16220.23760.1986-0.10060.23120.0445-0.0150.2510.0650.144249.0846-2.7478108.9854
53.8076-2.81613.74042.1237-2.57963.88180.24161.13580.3293-0.9384-0.6230.2025-0.2203-0.29120.10990.49780.3179-0.38120.5766-0.10450.258139.6873-2.202993.5492
62.445-0.28980.12092.402-0.41182.35590.04740.15950.0718-0.1313-0.01950.1115-0.3089-0.1431-0.01270.15870.09550.01470.136-0.010.08338.433116.781498.6517
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 2:108)
2X-RAY DIFFRACTION2chain 'A' and (resseq 109:129)
3X-RAY DIFFRACTION3chain 'A' and (resseq 130:332)
4X-RAY DIFFRACTION4chain 'B' and (resseq 2:108)
5X-RAY DIFFRACTION5chain 'B' and (resseq 109:129)
6X-RAY DIFFRACTION6chain 'B' and (resseq 130:332)

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