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- PDB-6spw: Structure of protein kinase CK2 catalytic subunit with the CK2bet... -

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Basic information

Entry
Database: PDB / ID: 6spw
TitleStructure of protein kinase CK2 catalytic subunit with the CK2beta-competitive bisubstrate inhibitor ARC3140
Components
  • ARC3140
  • Casein kinase II subunit alphaCasein kinase 2
KeywordsTRANSFERASE / protein kinase CK2 casein kinase 2 bisubstrate inhibitor
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 / Sin3-type complex / Receptor Mediated Mitophagy / Synthesis of PC / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known ...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 / Sin3-type complex / Receptor Mediated Mitophagy / Synthesis of PC / 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 / chaperone-mediated protein folding / negative regulation of ubiquitin-dependent protein catabolic process / Signal transduction by L1 / peptidyl-threonine phosphorylation / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / Hsp90 protein binding / PML body / Wnt signaling pathway / Regulation of PTEN stability and activity / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / positive regulation of protein catabolic process / rhythmic process / KEAP1-NFE2L2 pathway / double-strand break repair / kinase activity / positive regulation of cell growth / peptidyl-serine phosphorylation / Regulation of TP53 Activity through Phosphorylation / negative regulation of translation / protein stabilization / non-specific serine/threonine protein kinase / regulation of cell cycle / cell cycle / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / apoptotic process / DNA damage response / positive regulation of cell population proliferation / signal transduction / nucleoplasm / ATP binding / nucleus / identical protein binding / plasma membrane / cytosol
Similarity search - Function
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 ...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
Chem-A0Z / Casein kinase II subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.599 Å
AuthorsNiefind, K. / Schnitzler, A.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationNI 643/4-2 Germany
Citation
Journal: Bioorg.Chem. / Year: 2020
Title: Unexpected CK2 beta-antagonistic functionality of bisubstrate inhibitors targeting protein kinase CK2.
Authors: Pietsch, M. / Viht, K. / Schnitzler, A. / Ekambaram, R. / Steinkruger, M. / Enkvist, E. / Nienberg, C. / Nickelsen, A. / Lauwers, M. / Jose, J. / Uri, A. / Niefind, K.
#1: Journal: Org. Biomol. Chem. / Year: 2012
Title: A subnanomolar fluorescent probe for protein kinase CK2 interaction studies.
Authors: Enkvist, E. / Viht, K. / Bischoff, N. / Vahter, J. / Saaver, S. / Raidaru, G. / Issinger, O.G. / Niefind, K. / Uri, A.
#2: 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.
History
DepositionSep 3, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 29, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 26, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 24, 2024Group: 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_conn_type
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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _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_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_conn_type.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: ARC3140
C: ARC3140
D: ARC3140
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,0368
Polymers47,7224
Non-polymers2,3154
Water5,278293
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3490 Å2
ΔGint-3 kcal/mol
Surface area17030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.503, 85.171, 90.432
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 II subunit alpha / Casein kinase 2 / CK II alpha


Mass: 45208.559 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 (E. coli)
References: UniProt: P68400, non-specific serine/threonine protein kinase
#2: Protein/peptide ARC3140


Mass: 837.722 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-A0Z / 8-[4,5,6,7-tetrakis(iodanyl)benzimidazol-1-yl]octanoic acid


Mass: 763.918 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C15H16I4N2O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 293 / 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: 2.02 Å3/Da / Density % sol: 39.21 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 1 MIKROLITER OF THE CK2ALPHA/ARC3140 MIXTURE (COMPOSITION: 7 MG/ML CK2ALPHA ENZYME, 1 MILLIMOLAR ARC3140, 10 % DIMETHYL SULFOXIDE, 450 MM NACL, 22.5 MM TRIS/HCL, PH 8.5) WAS MIXED WITH 2.5 ...Details: 1 MIKROLITER OF THE CK2ALPHA/ARC3140 MIXTURE (COMPOSITION: 7 MG/ML CK2ALPHA ENZYME, 1 MILLIMOLAR ARC3140, 10 % DIMETHYL SULFOXIDE, 450 MM NACL, 22.5 MM TRIS/HCL, PH 8.5) WAS MIXED WITH 2.5 MIKROLITER RESERVOIR SOLUTION (COMPOSITION: 30 % PEG4000, 0.2 M AMMONIUM ACETATE, 0.1 M SODIUM CITRATE, PH 5.6) FOLLOWED BY VAPOUR DIFFUSION EQUILIBRATION AGAINST MICROLITER OF THE RESERVOIR SOLUTION.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.12713 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jun 13, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.12713 Å / Relative weight: 1
ReflectionResolution: 1.599→42.59 Å / Num. obs: 49166 / % possible obs: 99.8 % / Redundancy: 6.1 % / Biso Wilson estimate: 16.41 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.1004 / Rsym value: 0.1004 / Net I/σ(I): 11.56
Reflection shellResolution: 1.599→1.656 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.7938 / Mean I/σ(I) obs: 1.98 / Num. unique obs: 4788 / CC1/2: 0.894 / Rsym value: 0.7938 / % possible all: 98.84

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2PVR
Resolution: 1.599→42.586 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.196 1960 3.99 %
Rwork0.1645 --
obs0.1658 49163 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.599→42.586 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3005 0 1 293 3299
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0173108
X-RAY DIFFRACTIONf_angle_d1.3774199
X-RAY DIFFRACTIONf_dihedral_angle_d12.1451851
X-RAY DIFFRACTIONf_chiral_restr0.098423
X-RAY DIFFRACTIONf_plane_restr0.011542
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5993-1.63930.31551340.25923288X-RAY DIFFRACTION98
1.6393-1.68360.29191340.23633325X-RAY DIFFRACTION100
1.6836-1.73310.25861470.21153301X-RAY DIFFRACTION100
1.7331-1.78910.28581320.20123344X-RAY DIFFRACTION100
1.7891-1.8530.23441470.18323344X-RAY DIFFRACTION100
1.853-1.92720.21281350.17433358X-RAY DIFFRACTION100
1.9272-2.01490.21131310.16653335X-RAY DIFFRACTION100
2.0149-2.12120.17051390.14993359X-RAY DIFFRACTION100
2.1212-2.2540.18761450.15223360X-RAY DIFFRACTION100
2.254-2.42810.20961450.15563356X-RAY DIFFRACTION100
2.4281-2.67240.18411410.15763392X-RAY DIFFRACTION100
2.6724-3.0590.18451360.15093411X-RAY DIFFRACTION100
3.059-3.85360.1741400.14393432X-RAY DIFFRACTION100
3.8536-42.5860.17081540.16453598X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
11.0415-0.5382-0.46260.61920.15430.4148-0.1181-0.25790.00520.12490.1075-0.04870.00080.103-0.05110.11650.0191-0.01020.1334-0.01310.11429.025462.249657.4641
20.4917-0.18310.34410.67380.12990.91940.0153-0.1965-0.29360.1245-0.09410.29870.144-0.38940.05870.1254-0.02130.04180.2263-0.03420.2582-8.287754.222554.1053
31.21010.19280.1181.1839-0.00560.5376-0.038-0.0442-0.0474-0.0037-0.01510.08480.07-0.0429-0.01570.0913-0.00780.03320.0792-0.00550.09144.808239.787247.5935
40.02190.0042-0.01040.0027-0.00060.0058-0.0305-0.01420.05940.0185-0.04010.0232-0.00860.0325-0.00011.0828-0.07-0.11450.7356-0.30240.79713.746746.904962.1911
50.01770.02050.00910.03820.02010.01090.0213-0.01350.0076-0.00280.01010.0611-0.00140.05370.00021.2458-0.02860.0791.2557-0.20461.4232-4.882149.253275.0337
60.02450.0067-0.04030.0098-0.01490.0683-0.00330.0217-0.02810.0308-0.0021-0.0074-0.0082-0.008201.40760.10460.28471.4743-0.06571.336328.163226.416763.9207
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 329 )
4X-RAY DIFFRACTION4chain 'B' and (resid 3 through 8 )
5X-RAY DIFFRACTION5chain 'C' and (resid 3 through 8 )
6X-RAY DIFFRACTION6chain 'D' and (resid 3 through 8 )

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