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- PDB-9fyf: Crystal structure of human Casein Kinase II subunit alpha (CK2a1)... -

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Basic information

Entry
Database: PDB / ID: 9fyf
TitleCrystal structure of human Casein Kinase II subunit alpha (CK2a1) in complex with TR06772818
ComponentsCasein kinase II subunit alpha
KeywordsTRANSFERASE / CK2 / Kinase / Inhibitor
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 / negative regulation of apoptotic signaling pathway / positive regulation of Wnt 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 / regulation of cell cycle / protein stabilization / non-specific serine/threonine protein kinase / 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 / 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: 2.7 Å
AuthorsKraemer, A. / Ong, H.W. / Yang, X. / Brown, J.W. / Chang, E. / Willson, T. / Knapp, S. / Structural Genomics Consortium (SGC)
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Innovative Medicines Initiative875510 Switzerland
CitationJournal: To Be Published
Title: Crystal structure of human Casein Kinase II subunit alpha (CK2a1) in complex with TR06772818
Authors: Kraemer, A. / Ong, H.W. / Yang, X. / Brown, J.W. / Chang, E. / Willson, T. / Knapp, S. / Structural Genomics Consortium (SGC)
History
DepositionJul 3, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 11, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)83,08019
Polymers80,6562
Non-polymers2,42417
Water79344
1
B: Casein kinase II subunit alpha
hetero molecules


  • defined by author
  • Evidence: gel filtration
  • 41.6 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)41,58810
Polymers40,3281
Non-polymers1,2609
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Casein kinase II subunit alpha
hetero molecules


  • defined by author
  • 41.5 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)41,4929
Polymers40,3281
Non-polymers1,1648
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)127.184, 127.184, 124.026
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 / CK II alpha


Mass: 40327.977 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: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-A1IG6 / ~{N}-[5-[[3-cyano-7-(cyclopropylamino)pyrazolo[1,5-a]pyrimidin-5-yl]amino]-4-fluoranyl-2-[(3~{S})-3-(methylamino)piperidin-1-yl]phenyl]propanamide / 7-[(1R,5S,6s)-6-amino-3-azabicyclo[3.1.0]hex-3-yl]-1-(2,4-difluorophenyl)-6-fluoro-4-oxo-1,4-dihydro-1,8-naphthyridine-3-carboxylic acid


Mass: 491.564 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C25H30FN9O / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 44 / 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: 3.11 Å3/Da / Density % sol: 60.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.1 M bis-tris pH 5.5 23-26% (v/v) PEG 3350 0.2 M ammonia sulphate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97626 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Dec 1, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97626 Å / Relative weight: 1
ReflectionResolution: 2.7→127.18 Å / Num. obs: 28599 / % possible obs: 100 % / Redundancy: 27.6 % / CC1/2: 0.998 / Net I/σ(I): 13.1
Reflection shellResolution: 2.7→2.83 Å / Num. unique obs: 3722 / CC1/2: 0.804

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
Aimlessdata scaling
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→88.95 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.92 / SU B: 25.861 / SU ML: 0.245 / Cross valid method: THROUGHOUT / ESU R: 0.625 / ESU R Free: 0.312 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24896 1335 4.7 %RANDOM
Rwork0.20199 ---
obs0.20421 27202 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 57.646 Å2
Baniso -1Baniso -2Baniso -3
1-2.32 Å2-0 Å20 Å2
2--2.32 Å2-0 Å2
3----4.64 Å2
Refinement stepCycle: 1 / Resolution: 2.7→88.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5482 0 147 44 5673
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0125782
X-RAY DIFFRACTIONr_bond_other_d0.0010.0165213
X-RAY DIFFRACTIONr_angle_refined_deg1.2561.6737859
X-RAY DIFFRACTIONr_angle_other_deg0.4551.60711965
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7975662
X-RAY DIFFRACTIONr_dihedral_angle_2_deg11.094541
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.78210936
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0610.2825
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026861
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021385
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_it2.6954.122654
X-RAY DIFFRACTIONr_mcbond_other2.6914.1212654
X-RAY DIFFRACTIONr_mcangle_it4.2897.4033314
X-RAY DIFFRACTIONr_mcangle_other4.2887.4043315
X-RAY DIFFRACTIONr_scbond_it3.3394.5013128
X-RAY DIFFRACTIONr_scbond_other3.3384.5023129
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.1988.154540
X-RAY DIFFRACTIONr_long_range_B_refined7.87241.586395
X-RAY DIFFRACTIONr_long_range_B_other7.87141.596394
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.329 93 -
Rwork0.327 1972 -
obs--100 %
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)
13.5755-0.72660.69111.4192-0.15061.7451-0.0275-0.19310.1260.278-0.0005-0.00260.0113-0.05180.0280.10910.01440.02620.02130.00040.02448.195742.189821.8164
21.074-0.8467-0.04673.42-0.61751.47310.03980.1733-0.0875-0.2484-0.0571-0.06720.0220.01230.01730.09810.0267-0.04270.0509-0.0120.105141.30119.624138.6397
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1B3 - 401
2X-RAY DIFFRACTION2A2 - 334

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