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- PDB-7b8i: Tetragonal structure of human protein kinase CK2 catalytic subuni... -

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Basic information

Entry
Database: PDB / ID: 7b8i
TitleTetragonal structure of human protein kinase CK2 catalytic subunit in complex with a heparin oligo saccharide
ComponentsCasein kinase II subunit alphaCasein kinase 2
KeywordsTRANSFERASE / protein kinase CK2 / casein kinase 2 / catalytic subunit CK2alpha / heparin
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 / 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
Similarity search - Domain/homology
Casein kinase II subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsNiefind, K. / Schnitzler, A.
Funding support Germany, 2items
OrganizationGrant numberCountry
German Research Foundation (DFG)NI 643/4-1 Germany
German Research Foundation (DFG)NI 643/4-2 Germany
CitationJournal: Eur.J.Med.Chem. / Year: 2021
Title: Structural basis for the design of bisubstrate inhibitors of protein kinase CK2 provided by complex structures with the substrate-competitive inhibitor heparin.
Authors: Schnitzler, A. / Niefind, K.
History
DepositionDec 12, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 3, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 17, 2021Group: Database references / Category: citation / Item: _citation.title
Revision 1.2Feb 24, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.3Jan 31, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entity_branch_descriptor / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)82,8427
Polymers80,1332
Non-polymers2,7085
Water2,576143
1
A: Casein kinase II subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,6795
Polymers40,0671
Non-polymers2,6124
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Casein kinase II subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,1632
Polymers40,0671
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)128.401, 128.401, 124.154
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 / Casein kinase 2 / 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
#2: Polysaccharide 2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid- ...2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid


Type: oligosaccharide / Mass: 2327.897 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
WURCS=2.0/2,8,7/[a2121A-1a_1-5_2*OSO/3=O/3=O][a2122h-1a_1-5_2*NSO/3=O/3=O_6*OSO/3=O/3=O]/1-2-1-2-1-2-1-2/a4-b1_b4-c1_c4-d1_d4-e1_e4-f1_f4-g1_g4-h1WURCSPDB2Glycan 1.1.0
[][a-L-IdopA2SO3]{[(4+1)][a-D-GlcpNSO36SO3]{[(4+1)][a-L-IdopA2SO3]{[(4+1)][a-D-GlcpNSO36SO3]{[(4+1)][a-L-IdopA2SO3]{[(4+1)][a-D-GlcpNSO36SO3]{[(4+1)][a-L-IdopA2SO3]{[(4+1)][a-D-GlcpNSO36SO3]{}}}}}}}}LINUCSPDB-CARE
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 143 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.22 Å3/Da / Density % sol: 61.78 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: Prior to crystallization, the enzyme was incubated with heparin decasaccharide; the composition of this preincubation solution was 5 mg/ml CK2alpha1-335, 1.4 mM Heparin decasaccharide, 340 ...Details: Prior to crystallization, the enzyme was incubated with heparin decasaccharide; the composition of this preincubation solution was 5 mg/ml CK2alpha1-335, 1.4 mM Heparin decasaccharide, 340 mM NaCl, 25 mM Tris/HCl, pH 8.5. 4 microliter of this enzyme/heparin mixture was mixed with 1 microliter reservoir solution. The composition of the reservoir solution was 32 % (w/v) PEG4000, 0.2 M Lithium sulfate, 0.1 M Tris/HCl, pH 7.5. As a preparation of X-ray diffraction data collection, the crystals were transferred to a cryo solution composed of 32 % (w/v) PEG4000, 10 % (v/v) glycerol, 0.2 M lithium sulfate, 0.5 mM Heparin decasaccharide, 0.1 M Tris/HCl, pH 7.5.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.97795 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Jun 5, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97795 Å / Relative weight: 1
ReflectionResolution: 2.55→45.4 Å / Num. obs: 33919 / % possible obs: 98.43 % / Redundancy: 6.7 % / Biso Wilson estimate: 48.47 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.08534 / Rpim(I) all: 0.03554 / Rrim(I) all: 0.09263 / Rsym value: 0.08534 / Net I/σ(I): 16.16
Reflection shellResolution: 2.55→2.642 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.7234 / Mean I/σ(I) obs: 2.57 / Num. unique obs: 3259 / CC1/2: 0.802 / Rpim(I) all: 0.3073 / Rrim(I) all: 0.7877 / Rsym value: 0.7234 / % possible all: 96.19

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2PVR

2pvr


Resolution: 2.55→45.397 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.94
RfactorNum. reflection% reflection
Rfree0.2396 1695 5 %
Rwork0.204 --
obs0.2057 33889 98.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.55→45.397 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5608 0 162 143 5913
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0025935
X-RAY DIFFRACTIONf_angle_d0.5348061
X-RAY DIFFRACTIONf_dihedral_angle_d16.8563543
X-RAY DIFFRACTIONf_chiral_restr0.044861
X-RAY DIFFRACTIONf_plane_restr0.0041011
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5504-2.62550.29781350.26612571X-RAY DIFFRACTION96
2.6255-2.71020.28811390.25212641X-RAY DIFFRACTION98
2.7102-2.8070.25781370.24772605X-RAY DIFFRACTION98
2.807-2.91940.29111410.24732672X-RAY DIFFRACTION99
2.9194-3.05230.32071390.23582635X-RAY DIFFRACTION98
3.0523-3.21310.33541390.23532660X-RAY DIFFRACTION99
3.2131-3.41440.25571410.22272661X-RAY DIFFRACTION99
3.4144-3.67790.25321410.2092693X-RAY DIFFRACTION99
3.6779-4.04780.19051420.1772694X-RAY DIFFRACTION99
4.0478-4.6330.18761430.16292708X-RAY DIFFRACTION99
4.633-5.83520.23641450.17852771X-RAY DIFFRACTION99
5.8352-45.3970.21051530.20632883X-RAY DIFFRACTION98
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)
14.8190.9877-0.29391.814-0.07952.86370.2249-0.53550.04910.3888-0.1838-0.0169-0.19920.15790.00630.42880.05230.02010.30140.0240.3498-2.308847.3906-39.762
27.08222.0111-1.94263.5926-0.22456.38980.0010.09960.30010.0039-0.1763-0.0548-0.35770.01390.11980.23750.0145-0.04260.24380.00340.3097.378350.4163-48.8058
32.01871.08872.37371.42721.9293.2818-0.40530.7868-0.2412-0.45440.3058-0.17240.13850.2897-0.43240.6634-0.23710.27250.7067-0.25680.47712.992340.3235-61.6748
42.33070.59050.35472.4720.67242.3789-0.07180.2360.0029-0.31380.17740.0753-0.1282-0.064-0.09760.3687-0.05780.05040.38910.01980.4214-15.858138.7012-56.0229
55.08781.2393.33461.66230.82433.97960.1591-0.52290.00940.2449-0.18220.12020.3766-0.6134-0.01810.4016-0.0140.07790.38680.00470.3374-1.289280.4306-46.2013
62.92320.48370.06190.9329-1.20082.934-0.74220.2279-0.5293-0.45970.1639-0.38970.556-0.67270.51080.5153-0.13730.01760.3866-0.02880.4935-5.652682.9939-57.0023
72.42040.3261-0.12352.2723-0.20592.5843-0.03140.05560.1147-0.15060.1228-0.02990.08720.1-0.08970.3399-0.0602-0.01760.36590.00290.422216.490390.3161-57.0326
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 44 )
2X-RAY DIFFRACTION2chain 'A' and (resid 45 through 108 )
3X-RAY DIFFRACTION3chain 'A' and (resid 109 through 129 )
4X-RAY DIFFRACTION4chain 'A' and (resid 130 through 333 )
5X-RAY DIFFRACTION5chain 'B' and (resid 2 through 96 )
6X-RAY DIFFRACTION6chain 'B' and (resid 97 through 129 )
7X-RAY DIFFRACTION7chain 'B' and (resid 130 through 333 )

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