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- PDB-1ds5: DIMERIC CRYSTAL STRUCTURE OF THE ALPHA SUBUNIT IN COMPLEX WITH TW... -

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Basic information

Entry
Database: PDB / ID: 1ds5
TitleDIMERIC CRYSTAL STRUCTURE OF THE ALPHA SUBUNIT IN COMPLEX WITH TWO BETA PEPTIDES MIMICKING THE ARCHITECTURE OF THE TETRAMERIC PROTEIN KINASE CK2 HOLOENZYME.
Components
  • CASEIN KINASE, ALPHA CHAIN
  • CASEIN KINASE, BETA CHAIN
KeywordsTRANSFERASE / protein-complex / tetramer
Function / homology
Function and homology information


regulation of DNA binding / adiponectin-activated signaling pathway / positive regulation of activin receptor signaling pathway / endothelial tube morphogenesis / protein kinase regulator activity / negative regulation of viral life cycle / WNT mediated activation of DVL / Condensation of Prometaphase Chromosomes / protein kinase CK2 complex / symbiont-mediated disruption of host cell PML body ...regulation of DNA binding / adiponectin-activated signaling pathway / positive regulation of activin receptor signaling pathway / endothelial tube morphogenesis / protein kinase regulator activity / negative regulation of viral life cycle / 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 / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / positive regulation of SMAD protein signal transduction / negative regulation of blood vessel endothelial cell migration / Signal transduction by L1 / peptidyl-threonine phosphorylation / PML body / Wnt signaling pathway / Regulation of PTEN stability and activity / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / KEAP1-NFE2L2 pathway / protein-macromolecule adaptor activity / protein-containing complex assembly / secretory granule lumen / Regulation of TP53 Activity through Phosphorylation / ficolin-1-rich granule lumen / RNA polymerase II-specific DNA-binding transcription factor binding / regulation of cell cycle / non-specific serine/threonine protein kinase / protein domain specific binding / negative regulation of cell population proliferation / phosphorylation / signaling receptor binding / protein serine kinase activity / protein serine/threonine kinase activity / chromatin binding / chromatin / Neutrophil degranulation / signal transduction / extracellular exosome / extracellular region / nucleoplasm / ATP binding / identical protein binding / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Casein kinase II, regulatory subunit / Casein kinase II, regulatory subunit, N-terminal / Casein kinase II subunit beta-like / Casein kinase II regulatory subunit / Casein kinase II regulatory subunit signature. / Casein kinase II regulatory subunit / Casein Kinase 2, subunit alpha / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 ...Casein kinase II, regulatory subunit / Casein kinase II, regulatory subunit, N-terminal / Casein kinase II subunit beta-like / Casein kinase II regulatory subunit / Casein kinase II regulatory subunit signature. / Casein kinase II regulatory subunit / 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
ADENOSINE MONOPHOSPHATE / Casein kinase II subunit alpha / Casein kinase II subunit beta
Similarity search - Component
Biological speciesZea mays (maize)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.16 Å
AuthorsBattistutta, R. / Sarno, S. / De Moliner, E. / Marin, O. / Zanotti, G. / Pinna, L.A.
Citation
Journal: Eur.J.Biochem. / Year: 2000
Title: The crystal structure of the complex of Zea mays alpha subunit with a fragment of human beta subunit provides the clue to the architecture of protein kinase CK2 holoenzyme.
Authors: Battistutta, R. / Sarno, S. / De Moliner, E. / Marin, O. / Issinger, O.G. / Zanotti, G. / Pinna, L.A.
#1: Journal: Embo J. / Year: 1998
Title: Crystal Structure of the Catalytic Subunit of Protein Kinase CK2 from Zea mays at 2.1 A Resolution
Authors: Niefind, K. / Guerra, B. / Pinna, L.A. / Issinger, O.G. / Schomburg, D.
History
DepositionJan 7, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 7, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _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

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Assembly

Deposited unit
A: CASEIN KINASE, ALPHA CHAIN
B: CASEIN KINASE, ALPHA CHAIN
C: CASEIN KINASE, ALPHA CHAIN
D: CASEIN KINASE, ALPHA CHAIN
E: CASEIN KINASE, BETA CHAIN
F: CASEIN KINASE, BETA CHAIN
G: CASEIN KINASE, BETA CHAIN
H: CASEIN KINASE, BETA CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)169,71616
Polymers168,2308
Non-polymers1,4868
Water6,071337
1
A: CASEIN KINASE, ALPHA CHAIN
B: CASEIN KINASE, ALPHA CHAIN
E: CASEIN KINASE, BETA CHAIN
F: CASEIN KINASE, BETA CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,8588
Polymers84,1154
Non-polymers7434
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: CASEIN KINASE, ALPHA CHAIN
D: CASEIN KINASE, ALPHA CHAIN
G: CASEIN KINASE, BETA CHAIN
H: CASEIN KINASE, BETA CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,8588
Polymers84,1154
Non-polymers7434
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)87.681, 119.846, 145.560
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, ALPHA CHAIN / CK2


Mass: 39291.164 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zea mays (maize) / Production host: Escherichia coli (E. coli) / References: UniProt: P28523, EC: 2.7.1.37
#2: Protein/peptide
CASEIN KINASE, BETA CHAIN / CK2


Mass: 2766.244 Da / Num. of mol.: 4 / Fragment: RESIDUES 181-203 / Source method: obtained synthetically
Details: Synthetic peptide corresponding to the sequence 181-203 of the beta-subunit of human protein kinase CK2.
References: UniProt: P67870, EC: 2.7.1.37
#3: Chemical
ChemComp-AMP / ADENOSINE MONOPHOSPHATE / Adenosine monophosphate


Mass: 347.221 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 337 / 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: 2.27 Å3/Da / Density % sol: 45.87 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 8
Details: PEG 4000, sodium acetate, tris-HCl, magnesium chloride, ATP, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 292K
Crystal
*PLUS
Density % sol: 50 %
Crystal grow
*PLUS
pH: 8.5
Details: Guerra, B., (1998) Acta Crystallogr., Sect.D, 54, 143.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
13 mg/mlprotein1drop
2167 mM1dropNaCl
38.3 mMTris-HCl1drop
42 mM2-mercaptoethanol1drop
52 mMATP1drop
60.5 mM1dropMgCl2
725 %PEG40001reservoir
8200 mMsodium acetate1reservoir
9100 mMTris-HCl1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 18, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.16→50 Å / Num. all: 87314 / Num. obs: 25909 / % possible obs: 97.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Rmerge(I) obs: 0.16 / Net I/σ(I): 3.8
Reflection shellResolution: 3.16→3.35 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.43 / Num. unique all: 4164 / % possible all: 97.1
Reflection
*PLUS
Num. measured all: 87314
Reflection shell
*PLUS
% possible obs: 97.1 % / Mean I/σ(I) obs: 1.7

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Processing

Software
NameVersionClassification
AMoREphasing
CNS0.9refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementResolution: 3.16→45 Å / σ(F): 2 / Stereochemistry target values: Engh and Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.289 1799 -random
Rwork0.214 ---
all-25938 --
obs-25653 95.3 %-
Refinement stepCycle: LAST / Resolution: 3.16→45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11503 0 108 325 11936
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.029
X-RAY DIFFRACTIONc_angle_deg2.6
X-RAY DIFFRACTIONc_torsion_deg23.8
X-RAY DIFFRACTIONc_torsion_impr_deg1.66
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 45 Å / σ(F): 2 / Rfactor obs: 0.214
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: c_angle_deg / Dev ideal: 2.6
LS refinement shell
*PLUS
Rfactor Rfree: 0.366 / Rfactor obs: 0.289

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