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- PDB-7qux: Crystal structure of P7C8 bound to CK2alpha -

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Basic information

Entry
Database: PDB / ID: 7qux
TitleCrystal structure of P7C8 bound to CK2alpha
Components
  • Casein kinase II subunit alpha
  • P7C8
KeywordsTRANSFERASE / Stapled peptide / CK2alpha
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 / Synthesis of PC / Sin3-type complex / Maturation of hRSV A proteins ...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 / Synthesis of PC / Sin3-type complex / Maturation of hRSV A proteins / 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 / chaperone-mediated protein folding / Signal transduction by L1 / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / peptidyl-threonine phosphorylation / Hsp90 protein binding / PML body / Wnt signaling pathway / Regulation of PTEN stability and activity / positive regulation of protein catabolic process / rhythmic process / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / KEAP1-NFE2L2 pathway / double-strand break repair / kinase activity / peptidyl-serine phosphorylation / positive regulation of cell growth / Regulation of TP53 Activity through Phosphorylation / protein stabilization / regulation of cell cycle / non-specific serine/threonine protein kinase / negative regulation of translation / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / positive regulation of cell population proliferation / DNA damage response / 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. / Serine/Threonine protein kinases, catalytic domain / Protein kinase 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
ADENOSINE-5'-DIPHOSPHATE / CARBAMIC ACID / Casein kinase II subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.48 Å
AuthorsAtkinson, E. / Iegre, J. / Brear, P. / Baker, D. / Sore, H. / Hyvonen, M. / Spring, D.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Chem.Commun.(Camb.) / Year: 2022
Title: Development of small cyclic peptides targeting the CK2 alpha / beta interface.
Authors: Atkinson, E.L. / Iegre, J. / D'Amore, C. / Brear, P. / Salvi, M. / Hyvonen, M. / Spring, D.R.
History
DepositionJan 19, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 28, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Casein kinase II subunit alpha
D: P7C8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,5899
Polymers42,7722
Non-polymers8177
Water5,206289
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2690 Å2
ΔGint-47 kcal/mol
Surface area15750 Å2
Unit cell
Length a, b, c (Å)57.461, 63.250, 58.672
Angle α, β, γ (deg.)90.000, 108.440, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AD

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


Mass: 41697.867 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CSNK2A1, CK2A1 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P68400, non-specific serine/threonine protein kinase
#2: Protein/peptide P7C8


Mass: 1074.299 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: synthetic construct (others)

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Non-polymers , 6 types, 296 molecules

#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#7: Chemical ChemComp-OUT / CARBAMIC ACID


Mass: 61.040 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH3NO2 / Feature type: SUBJECT OF INVESTIGATION
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 289 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.36 Å3/Da / Density % sol: 47.99 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 0.2 M Ammonium sulfate, 30 % w/v PEG 4000

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Data collection

DiffractionMean temperature: 88 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Dec 9, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.48→55.66 Å / Num. obs: 66333 / % possible obs: 99.8 % / Redundancy: 17.1 % / CC1/2: 1 / Rmerge(I) obs: 0.077 / Rpim(I) all: 0.019 / Rrim(I) all: 0.079 / Net I/σ(I): 18 / Num. measured all: 1135548 / Scaling rejects: 1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.48-1.5616.64.02715907196000.4091.014.1540.799.3
4.68-55.6617.60.02738484218710.0070.02888.299.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
Aimless0.7.7data scaling
PHASERphasing
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5CVH

5cvh


Resolution: 1.48→55.66 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.968 / SU B: 1.903 / SU ML: 0.066 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.069 / ESU R Free: 0.07 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2037 3442 5.2 %RANDOM
Rwork0.1797 ---
obs0.1809 62522 99.18 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 124.49 Å2 / Biso mean: 33.211 Å2 / Biso min: 16.21 Å2
Baniso -1Baniso -2Baniso -3
1-1.2 Å2-0 Å20.04 Å2
2--0.06 Å2-0 Å2
3----1.05 Å2
Refinement stepCycle: final / Resolution: 1.48→55.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2865 0 49 289 3203
Biso mean--33.04 41 -
Num. residues----338
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0133020
X-RAY DIFFRACTIONr_bond_other_d0.0010.0152785
X-RAY DIFFRACTIONr_angle_refined_deg1.6721.6494086
X-RAY DIFFRACTIONr_angle_other_deg1.3781.5886404
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.945343
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.30221.087184
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.29815525
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2531526
X-RAY DIFFRACTIONr_chiral_restr0.0870.2361
X-RAY DIFFRACTIONr_gen_planes_refined0.010.023349
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02746
LS refinement shellResolution: 1.48→1.518 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.359 262 -
Rwork0.398 4296 -
all-4558 -
obs--92.83 %

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