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- PDB-4nh1: Crystal structure of a heterotetrameric CK2 holoenzyme complex ca... -

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Basic information

Entry
Database: PDB / ID: 4nh1
TitleCrystal structure of a heterotetrameric CK2 holoenzyme complex carrying the Andante-mutation in CK2beta and consistent with proposed models of autoinhibition and trans-autophosphorylation
Components(Casein kinase II subunit ...) x 2
KeywordsTRANSFERASE / eukaryotic protein kinase fold / phosphotransferase (kinase) / phosphorylation
Function / homology
Function and homology information


regulation of DNA binding / adiponectin-activated signaling pathway / positive regulation of activin receptor signaling pathway / endothelial tube morphogenesis / negative regulation of viral life cycle / protein kinase regulator activity / regulation of chromosome separation / positive regulation of aggrephagy / WNT mediated activation of DVL / Condensation of Prometaphase Chromosomes ...regulation of DNA binding / adiponectin-activated signaling pathway / positive regulation of activin receptor signaling pathway / endothelial tube morphogenesis / negative regulation of viral life cycle / protein kinase regulator activity / 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 signal transduction by p53 class mediator / negative regulation of apoptotic signaling pathway / negative regulation of blood vessel endothelial cell migration / positive regulation of SMAD protein signal transduction / peptidyl-threonine phosphorylation / positive regulation of Wnt signaling pathway / negative regulation of double-strand break repair via homologous recombination / : / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / Signal transduction by L1 / Hsp90 protein binding / PML body / Regulation of PTEN stability and activity / Wnt signaling pathway / fibrillar center / positive regulation of protein catabolic process / kinase activity / KEAP1-NFE2L2 pathway / rhythmic process / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / double-strand break repair / positive regulation of cell growth / protein-containing complex assembly / secretory granule lumen / protein-macromolecule adaptor activity / Regulation of TP53 Activity through Phosphorylation / ficolin-1-rich granule lumen / RNA polymerase II-specific DNA-binding transcription factor binding / non-specific serine/threonine protein kinase / regulation of cell cycle / negative regulation of translation / protein stabilization / signaling receptor binding / protein domain specific binding / negative regulation of cell population proliferation / protein serine kinase activity / protein serine/threonine kinase activity / positive regulation of cell population proliferation / apoptotic process / DNA damage response / Neutrophil degranulation / chromatin binding / chromatin / signal transduction / extracellular exosome / extracellular region / nucleoplasm / ATP binding / metal ion binding / identical protein binding / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
protein kinase ck2 holoenzyme, chain C, domain 1 / protein kinase ck2 holoenzyme, chain C, 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 / N-terminal domain of TfIIb - #20 / Casein Kinase 2, subunit alpha ...protein kinase ck2 holoenzyme, chain C, domain 1 / protein kinase ck2 holoenzyme, chain C, 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 / N-terminal domain of TfIIb - #20 / Casein Kinase 2, subunit alpha / N-terminal domain of TfIIb / Single Sheet / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); 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 Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / Casein kinase II subunit beta / Casein kinase II subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsSchnitzler, A. / Issinger, O.-G. / Niefind, K.
Citation
Journal: J.Mol.Biol. / Year: 2014
Title: The Protein Kinase CK2(Andante) Holoenzyme Structure Supports Proposed Models of Autoregulation and Trans-Autophosphorylation
Authors: Schnitzler, A. / Olsen, B.B. / Issinger, O.-G. / Niefind, K.
#1: Journal: Mol.Cell.Biochem. / Year: 2005
Title: Biochemical characterization of the recombinant human Drosophila homologues Timekeeper and Andante involved in the Drosophila circadian oscillator.
Authors: Rasmussen, T. / Skjth, I.H. / Jensen, H.H. / Niefind, K. / Boldyreff, B. / Issinger, O.G.
#2: Journal: Embo J. / Year: 2001
Title: Crystal structure of human protein kinase CK2: insights into basic properties of the CK2 holoenzyme.
Authors: Niefind, K. / Guerra, B. / Ermakowa, I. / Issinger, O.G.
#3: Journal: Mol.Cell.Biochem. / Year: 2005
Title: Primary and secondary interactions between CK2alpha and CK2beta lead to ring-like structures in the crystals of the CK2 holoenzyme.
Authors: Niefind, K. / Issinger, O.G.
History
DepositionNov 4, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 12, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 16, 2014Group: Database references
Revision 1.2Nov 8, 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 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _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
C: Casein kinase II subunit beta
D: Casein kinase II subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,36713
Polymers130,0364
Non-polymers1,3319
Water36020
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10290 Å2
ΔGint-104 kcal/mol
Surface area48630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)210.537, 57.441, 139.394
Angle α, β, γ (deg.)90.00, 118.54, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Casein kinase II subunit ... , 2 types, 4 molecules ABCD

#1: Protein Casein kinase II subunit alpha / protein kinase CK2 catalytic subunit / CK2alpha / CK II alpha


Mass: 40066.742 Da / Num. of mol.: 2 / Fragment: UNP residues 1-335
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CSNK2A1 / Plasmid: pT7-7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3)
References: UniProt: P68400, non-specific serine/threonine protein kinase
#2: Protein Casein kinase II subunit beta / protein kinase CK2 non-catalytic subunit / CK2beta / CK II beta / Phosvitin / Protein G5a


Mass: 24951.375 Da / Num. of mol.: 2 / Mutation: Met166Ile
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CSNK2B / Plasmid: pT7-7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P67870

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Non-polymers , 5 types, 29 molecules

#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-ACP / PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / ADENOSINE-5'-[BETA, GAMMA-METHYLENE]TRIPHOSPHATE


Mass: 505.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H18N5O12P3 / Comment: AMP-PCP, energy-carrying molecule analogue*YM
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 20 / 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: 2.85 Å3/Da / Density % sol: 56.8 %

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorDate: Jun 12, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.3→46.24 Å / Num. obs: 21878 / Redundancy: 2.4 % / Biso Wilson estimate: 106.58 Å2 / Rmerge(I) obs: 0.05 / Rsym value: 0.05 / Net I/σ(I): 13.85

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Processing

Software
NameVersionClassification
PHASERphasing
PHENIX(phenix.refine: 1.8.4_1496)refinement
XDSdata reduction
XSCALEfrom XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1JWH

1jwh


Resolution: 3.3→46.237 Å / Occupancy max: 1 / Occupancy min: 0.29 / SU ML: 0.46 / σ(F): 1.35 / Phase error: 29.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2514 1117 5.11 %
Rwork0.213 --
obs0.215 21873 97.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 308.81 Å2 / Biso mean: 130.8526 Å2 / Biso min: 27.82 Å2
Refinement stepCycle: LAST / Resolution: 3.3→46.237 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8877 0 74 20 8971
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0039225
X-RAY DIFFRACTIONf_angle_d0.63212514
X-RAY DIFFRACTIONf_chiral_restr0.0251282
X-RAY DIFFRACTIONf_plane_restr0.0021615
X-RAY DIFFRACTIONf_dihedral_angle_d11.7453464
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.3001-3.45020.34611450.30472551269698
3.4502-3.6320.3761210.28012637275898
3.632-3.85950.33411520.25122572272498
3.8595-4.15730.26051040.23292567267197
4.1573-4.57530.2451640.19772587275197
4.5753-5.23660.24531340.18872595272997
5.2366-6.59450.27191550.22092572272797
6.5945-46.24150.19011420.18492675281796
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)
12.29810.9763-1.65053.1227-1.77216.4079-0.13660.18620.77930.7676-0.512-0.4272-1.6398-0.0815-0.2062.0324-0.3419-0.340.88940.48361.072143.04752.270679.9347
20.1907-0.52570.44576.4875-5.60764.7873-0.52180.45010.4414-0.57960.0091-0.7056-0.46690.67570.56091.6898-0.2818-0.06040.96260.27330.73749.7577-15.410677.6284
34.9816-0.97330.66653.6351.80782.9601-0.29670.0337-0.1023-0.00250.0207-0.2211-0.45510.13670.25421.3781-0.1891-0.03780.77170.29080.720736.5584-17.896392.384
44.63630.8338-3.42881.5344-2.02186.5132-0.1664-0.2058-2.6726-0.2495-0.3547-0.10680.7165-0.2670.24081.1155-0.125-0.00650.96480.67041.762381.0043-2.596310.9186
57.5315.8561-3.45835.5821-3.80423.04490.7775-1.7804-0.3051.0139-0.19320.5506-0.84750.2431-0.45551.1515-0.08870.05721.38810.08570.829781.731715.248317.5765
67.505-0.54531.65324.58130.31687.223-0.152-0.1153-0.5239-0.36180.26760.2147-0.3422-0.4876-0.12050.8908-0.04560.06380.56960.13110.65587.349417.3881-1.3283
76.7777-2.2969-0.42328.7404-1.18846.3558-0.2407-1.18930.00930.66650.61181.79350.2721-0.4548-0.54580.7389-0.04540.15771.2844-0.2961.187921.46720.240356.1624
87.020.22785.85743.39272.60138.3872-2.20381.5185-0.37151.01860.90110.5241-1.00580.42160.39441.7726-0.03110.38112.7194-0.72531.20858.57938.656653.3148
92.94041.2302-1.44541.7125-0.05262.9334-0.10820.4016-0.20430.1911-0.58820.5279-0.33490.22610.12751.2259-0.2781-0.13720.92420.43230.963943.5885-1.892644.8868
108.5397-3.2026-3.98198.15133.25492.95520.23911.23011.0942-0.90610.0894-0.54010.40850.6293-0.13371.22570.143-0.08921.7816-0.05420.835949.4719-0.68097.0471
115.92681.47762.87252.37222.66763.2728-1.6986-0.1296-0.0524-1.64280.821-0.4291-2.1170.933-0.11792.16470.16340.4771.94930.03840.763245.602-7.1283-5.0292
124.216-0.3299-0.48656.90441.38524.9095-0.35922.28070.1347-1.2304-0.22380.3927-0.97280.94680.63381.13530.2066-0.06891.92110.25860.692248.6323-0.649510.6278
131.7872-0.29780.37631.20050.63713.9337-0.07870.1291-0.1236-0.098-0.30650.3915-0.50030.26330.19021.0476-0.2019-0.09440.98560.51751.022651.51950.354235.3768
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 3 THROUGH 108 )
2X-RAY DIFFRACTION2CHAIN A AND (RESID 109 THROUGH 129 )
3X-RAY DIFFRACTION3CHAIN A AND (RESID 130 THROUGH 332 )
4X-RAY DIFFRACTION4CHAIN B AND (RESID 2 THROUGH 108 )
5X-RAY DIFFRACTION5CHAIN B AND (RESID 109 THROUGH 129 )
6X-RAY DIFFRACTION6CHAIN B AND (RESID 130 THROUGH 333 )
7X-RAY DIFFRACTION7CHAIN C AND (RESID 7 THROUGH 53 )
8X-RAY DIFFRACTION8CHAIN C AND (RESID 54 THROUGH 72 )
9X-RAY DIFFRACTION9CHAIN C AND (RESID 73 THROUGH 207 )
10X-RAY DIFFRACTION10CHAIN D AND (RESID 7 THROUGH 45 )
11X-RAY DIFFRACTION11CHAIN D AND (RESID 46 THROUGH 63 )
12X-RAY DIFFRACTION12CHAIN D AND (RESID 64 THROUGH 103 )
13X-RAY DIFFRACTION13CHAIN D AND (RESID 104 THROUGH 207 )

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