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- PDB-3u87: Structure of a chimeric construct of human CK2alpha and human CK2... -

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Basic information

Entry
Database: PDB / ID: 3u87
TitleStructure of a chimeric construct of human CK2alpha and human CK2alpha' in complex with a non-hydrolysable ATP-analogue
ComponentsCasein kinase II subunit alpha
KeywordsTRANSFERASE / protein kinase CK2 casein kinase 2 / protein kinase fold / eukaryotic protein kinase
Function / homology
Function and homology information


regulation of mitophagy / 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 / positive regulation of protein targeting to mitochondrion / Receptor Mediated Mitophagy / Synthesis of PC ...regulation of mitophagy / 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 / positive regulation of protein targeting to mitochondrion / 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 / 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 / liver regeneration / acrosomal vesicle / Signal transduction by L1 / Hsp90 protein binding / PML body / cerebral cortex development / Regulation of PTEN stability and activity / Wnt signaling pathway / positive regulation of protein catabolic process / KEAP1-NFE2L2 pathway / kinase activity / rhythmic process / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / double-strand break repair / positive regulation of cell growth / spermatogenesis / Regulation of TP53 Activity through Phosphorylation / non-specific serine/threonine protein kinase / regulation of cell cycle / negative regulation of translation / protein stabilization / protein serine kinase activity / protein serine/threonine kinase activity / positive regulation of cell population proliferation / apoptotic process / DNA damage response / chromatin / signal transduction / nucleoplasm / ATP binding / identical protein binding / nucleus / plasma membrane / cytosol
Similarity search - Function
Casein Kinase 2, subunit alpha / 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 ...Casein Kinase 2, subunit alpha / 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 Alpha / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Casein kinase II subunit alpha' / Casein kinase II subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsNiefind, K. / Raaf, J. / Issinger, O.-G. / Olsen, B.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2012
Title: Low-density crystal packing of human protein kinase CK2 catalytic subunit in complex with resorufin or other ligands: a tool to study the unique hinge-region plasticity of the enzyme without packing bias.
Authors: Klopffleisch, K. / Issinger, O.G. / Niefind, K.
#1: Journal: Mol.Cell.Biochem. / Year: 2011
Title: Enzymatic activity with an incomplete catalytic spine - insights from a comparative structural analysis of human CK2alpha and its paralogous isoform CK2alpha'
Authors: Bischoff, N. / Raaf, J. / Olsen, B. / Bretner, M. / Issinger, O.G. / Niefind, K.
#2: Journal: Nat.Struct.Biol. / Year: 1999
Title: GTP plus water mimic ATP in the active site of protein kinase CK2.
Authors: Niefind, K. / Putter, M. / Guerra, B. / Issinger, O.G. / Schomburg, D.
#3: Journal: J.Mol.Biol. / Year: 2011
Title: Structure of the human protein kinase CK2 catalytic subunit CK2alpha' and interaction thermodynamics with the regulatory subunit CK2beta
Authors: Bischoff, N. / Olsen, B. / Raaf, J. / Bretner, M. / Issinger, O.G. / Niefind, K.
#4: 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.
#5: Journal: J.Mol.Biol. / Year: 2003
Title: Crystal structure of a C-terminal deletion mutant of human protein kinase CK2 catalytic subunit.
Authors: Ermakova, I. / Boldyreff, B. / Issinger, O.G. / Niefind, K.
#6: Journal: J.Mol.Biol. / Year: 2005
Title: Inclining the purine base binding plane in protein kinase CK2 by exchanging the flanking side-chains generates a preference for ATP as a cosubstrate.
Authors: Yde, C.W. / Ermakova, I. / Issinger, O.G. / Niefind, K.
#7: Journal: J.Mol.Biol. / Year: 2007
Title: Evolved to be active: sulfate ions define substrate recognition sites of CK2alpha and emphasise its exceptional role within the CMGC family of eukaryotic protein kinases.
Authors: Niefind, K. / Yde, C.W. / Ermakova, I. / Issinger, O.G.
#8: Journal: Cell. Mol. Life Sci. / Year: 2009
Title: Protein kinase CK2: from structures to insights
Authors: Niefind, K. / Raaf, J. / Issinger, O.-G.
#9: Journal: J.Mol.Biol. / Year: 2009
Title: First inactive conformation of CK2alpha, the catalytic subunit of protein kinase CK2
Authors: Raaf, J. / Issinger, O.-G. / Niefind, K.
#10: Journal: Chem.Biol. / Year: 2008
Title: The CK2alpha/CK2beta interface of human protein kinase CK2 harbors a binding pocket for small molecules
Authors: Raaf, J. / Brunstein, E. / Issinger, O.-G. / Niefind, K.
#11: Journal: J.Mol.Biol. / Year: 2008
Title: The catalytic subunit of human protein kinase CK2 structurally deviates from its maize homologue in complex with the mucleotide competitive inhibitor emodin
Authors: Raaf, J. / Klopffleisch, K. / Issinger, O.-G. / Niefind, K.
History
DepositionOct 16, 2011Deposition site: RCSB / Processing site: RCSB
SupersessionMay 30, 2012ID: 3RP0
Revision 1.0May 30, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 23, 2013Group: Database references
Revision 1.2Aug 9, 2017Group: Source and taxonomy / Category: entity_src_gen
Revision 1.3Sep 13, 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_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_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_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_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,36514
Polymers82,8082
Non-polymers1,55712
Water91951
1
A: Casein kinase II subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,1837
Polymers41,4041
Non-polymers7786
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Casein kinase II subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,1837
Polymers41,4041
Non-polymers7786
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)127.821, 127.821, 125.333
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 41404.176 Da / Num. of mol.: 2
Fragment: KINASE II SUBUNIT ALPHA (UNP RESIDUES 1-325), KINASE II SUBUNIT ALPHA' (UNP RESIDUES 327-350)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CSNK2A1, CK2A1 / Plasmid: pT7-7 / Production host: Escherichia coli (E. coli)
References: UniProt: P68400, UniProt: P19784, non-specific serine/threonine protein kinase

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Non-polymers , 6 types, 63 molecules

#2: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 51 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsAN ADDITIONAL PEPTIDE WAS PRESENT IN THE CRYSTALLIZATION CONDITION, BUT THE WHOLE CHAIN IS ...AN ADDITIONAL PEPTIDE WAS PRESENT IN THE CRYSTALLIZATION CONDITION, BUT THE WHOLE CHAIN IS DISORDERED AND THUS NOT PRESENT IN THE MODEL: RRRADDSDDDDD
Sequence detailsTHE STRUCTURE IS REPRESENTATIVE OF A CHIMERIC PROTEIN BETWEEN CASEIN KINASE II SUBUNIT ALPHA AND ...THE STRUCTURE IS REPRESENTATIVE OF A CHIMERIC PROTEIN BETWEEN CASEIN KINASE II SUBUNIT ALPHA AND CASEIN KINASE II SUBUNIT ALPHA'

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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: 3.1 Å3/Da / Density % sol: 60.28 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.2
Details: reservoir: 15% polyethylene glycol 8000, 15% glycerol, 0.17 M ammonium sulfate, 0.1 M sodium cacodylate buffer; drop: 0.8 uL reservoir solution, 0.8 uL protein solution (12.6 mg/ml), 0.5 uL ...Details: reservoir: 15% polyethylene glycol 8000, 15% glycerol, 0.17 M ammonium sulfate, 0.1 M sodium cacodylate buffer; drop: 0.8 uL reservoir solution, 0.8 uL protein solution (12.6 mg/ml), 0.5 uL 10% anapoe 305 (detergent), 1.5 uL 5 mM AMPPNP, 1.5 uL 10 mM magnesium chloride, 1.5 uL CK2 substrate peptide (sequence RRRADDSDDDDD), pH 6.2, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 21, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 2.85→38 Å / Num. all: 24894 / Num. obs: 24724 / % possible obs: 99.3 % / Observed criterion σ(I): -3 / Redundancy: 8.03 % / Rmerge(I) obs: 0.097 / Rsym value: 0.097 / Net I/σ(I): 17.3
Reflection shellResolution: 2.85→2.92 Å / Redundancy: 8.26 % / Mean I/σ(I) obs: 2.43 / Rsym value: 0.953 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.7.2_869)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 3NGA

3nga


Resolution: 2.9→36.655 Å / SU ML: 0.3 / σ(F): 1.38 / Phase error: 20.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.218 1202 5.14 %
Rwork0.1857 --
obs0.1873 23394 99.16 %
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.991 Å2 / ksol: 0.334 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.5209 Å20 Å2-0 Å2
2--1.5209 Å2-0 Å2
3----3.0417 Å2
Refinement stepCycle: LAST / Resolution: 2.9→36.655 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5560 0 86 51 5697
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0065809
X-RAY DIFFRACTIONf_angle_d0.6417873
X-RAY DIFFRACTIONf_dihedral_angle_d11.8312173
X-RAY DIFFRACTIONf_chiral_restr0.045812
X-RAY DIFFRACTIONf_plane_restr0.003998
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-3.01610.27371380.27242408X-RAY DIFFRACTION100
3.0161-3.15330.30851220.26442440X-RAY DIFFRACTION100
3.1533-3.31940.24721430.23262435X-RAY DIFFRACTION100
3.3194-3.52730.25511510.21442421X-RAY DIFFRACTION100
3.5273-3.79930.19451190.192472X-RAY DIFFRACTION99
3.7993-4.18120.21631310.17542461X-RAY DIFFRACTION99
4.1812-4.78510.17381420.14832458X-RAY DIFFRACTION99
4.7851-6.02440.21821170.16652514X-RAY DIFFRACTION99
6.0244-36.65750.20511390.16892583X-RAY DIFFRACTION97
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)
11.6005-0.71610.13455.90773.37425.2569-0.1841-0.17980.09640.57340.1587-0.25630.49480.1119-0.02580.3121-0.02470.00040.37950.02520.299947.39741.89453.9696
22.3347-0.15563.17726.59653.51227.5413-0.07480.00870.3813-0.3308-0.2372-0.3548-0.43210.43020.41990.58960.05490.09610.4648-0.01810.507351.8425-9.820339.3988
38.0328-1.6027-0.05156.7440.27215.882-0.0238-0.04470.0294-0.0583-0.0071-0.39670.5236-0.15450.09560.28870.0804-0.05960.2216-0.04570.242849.9136-5.228749.5504
41.5467-1.82541.52522.1576-1.80341.50080.42270.898-0.1875-0.9901-0.65150.38580.14230.0074-0.13320.81240.3136-0.17360.8282-0.26740.503140.7295-3.045931.7777
53.629-0.69280.66534.38250.07654.53990.25110.4205-0.1205-0.6236-0.2555-0.0540.17420.2503-0.00690.4350.1795-0.00370.4565-0.0770.386939.75276.060541.5407
64.8821-0.62451.2594.7937-0.285.63110.01070.85410.5838-0.7377-0.2055-0.7892-0.61920.59380.18640.50270.14020.10040.51420.08560.475944.864223.693936.109
76.2771.00391.8912.4902-0.2045.27020.10360.45360.3243-0.5232-0.2350.3585-0.3826-0.24730.09630.52280.2612-0.08240.4833-0.08020.484728.951216.694434.508
81.9524-1.8417-0.56615.75022.96595.5809-0.0894-0.24940.0830.7852-0.0226-0.08970.64080.16760.06450.377-0.0879-0.0050.46910.13320.282447.42372.9901114.662
96.2905-1.29442.85832.83913.81948.8452-0.42590.64220.3877-1.41770.0106-0.0396-0.31530.70070.36410.65560.09080.11150.57250.06590.339850.7817-9.064799.8414
105.4917-0.32622.5746.5876-0.02926.50780.0599-0.3592-0.59730.226-0.00310.03710.5954-0.2606-0.05570.44020.01130.0060.38050.11660.242249.6455-4.2167110.1104
116.7863-7.05865.5737.49-5.65144.68790.85621.0347-0.1784-1.4412-0.98060.1941.29760.53710.29210.77370.1317-0.06580.8583-0.09610.562139.4067-2.255893.0012
123.2004-0.02450.1773.33380.02743.98820.04730.04510.1389-0.2049-0.1476-0.0285-0.28420.14880.13180.3510.04920.0350.34920.02480.291641.762916.560699.5467
135.6013-0.03751.98783.17560.57316.28410.1170.22920.0905-0.2785-0.14940.5326-0.4711-0.44140.01740.26990.1592-0.01620.3573-0.01670.389828.002917.722896.2595
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 2:44)
2X-RAY DIFFRACTION2chain 'A' and (resseq 45:74)
3X-RAY DIFFRACTION3chain 'A' and (resseq 75:108)
4X-RAY DIFFRACTION4chain 'A' and (resseq 109:129)
5X-RAY DIFFRACTION5chain 'A' and (resseq 130:197)
6X-RAY DIFFRACTION6chain 'A' and (resseq 198:280)
7X-RAY DIFFRACTION7chain 'A' and (resseq 281:330)
8X-RAY DIFFRACTION8chain 'B' and (resseq 2:44)
9X-RAY DIFFRACTION9chain 'B' and (resseq 45:74)
10X-RAY DIFFRACTION10chain 'B' and (resseq 75:108)
11X-RAY DIFFRACTION11chain 'B' and (resseq 109:129)
12X-RAY DIFFRACTION12chain 'B' and (resseq 130:280)
13X-RAY DIFFRACTION13chain 'B' and (resseq 281:330)

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