[English] 日本語
Yorodumi
- PDB-5oni: LOW-SALT STRUCTURE OF PROTEIN KINASE CK2 CATALYTIC SUBUNIT (ISOFO... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5oni
TitleLOW-SALT STRUCTURE OF PROTEIN KINASE CK2 CATALYTIC SUBUNIT (ISOFORM CK2ALPHA) IN COMPLEX WITH THE INDENOINDOLE-TYPE INHIBITOR 4P
ComponentsCasein kinase II subunit alpha
KeywordsTRANSFERASE / protein kinase CK2 / casein kinase 2 / indenoindole-type inhibitors
Function / homology
Function and homology information


regulation of chromosome separation / positive regulation of aggrephagy / Condensation of Prometaphase Chromosomes / WNT mediated activation of DVL / protein kinase CK2 complex / symbiont-mediated disruption of host cell PML body / Receptor Mediated Mitophagy / Synthesis of PC / Maturation of hRSV A proteins / Sin3-type complex ...regulation of chromosome separation / positive regulation of aggrephagy / Condensation of Prometaphase Chromosomes / WNT mediated activation of DVL / protein kinase CK2 complex / symbiont-mediated disruption of host cell PML body / Receptor Mediated Mitophagy / Synthesis of PC / Maturation of hRSV A proteins / Sin3-type complex / 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 / : / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / Signal transduction by L1 / Hsp90 protein binding / PML body / Wnt signaling pathway / Regulation of PTEN stability and activity / 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 / Regulation of TP53 Activity through Phosphorylation / eukaryotic translation initiation factor 2alpha kinase activity / 3-phosphoinositide-dependent protein kinase activity / DNA-dependent protein kinase activity / ribosomal protein S6 kinase activity / histone H3S10 kinase activity / histone H2AXS139 kinase activity / histone H3S28 kinase activity / histone H4S1 kinase activity / histone H2BS14 kinase activity / histone H3T3 kinase activity / histone H2AS121 kinase activity / Rho-dependent protein serine/threonine kinase activity / histone H2BS36 kinase activity / histone H3S57 kinase activity / histone H2AT120 kinase activity / AMP-activated protein kinase activity / histone H2AS1 kinase activity / histone H3T6 kinase activity / histone H3T11 kinase activity / histone H3T45 kinase activity / non-specific serine/threonine protein kinase / regulation of cell cycle / negative regulation of translation / protein stabilization / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / apoptotic process / positive regulation of cell population proliferation / DNA damage response / 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
Chem-9YE / 1,4-BUTANEDIOL / Casein kinase II subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsHochscherf, J. / Lindenblatt, D. / Witulski, B. / Birus, R. / Aichele, D. / Marminon, C. / Bouaziz, Z. / Le Borgne, M. / Jose, J. / Niefind, K.
Citation
Journal: Pharmaceuticals (Basel) / Year: 2017
Title: Unexpected Binding Mode of a Potent Indeno[1,2-b]indole-Type Inhibitor of Protein Kinase CK2 Revealed by Complex Structures with the Catalytic Subunit CK2 alpha and Its Paralog CK2 alpha '.
Authors: Hochscherf, J. / Lindenblatt, D. / Witulski, B. / Birus, R. / Aichele, D. / Marminon, C. / Bouaziz, Z. / Le Borgne, M. / Jose, J. / Niefind, K.
#1: Journal: Pharmaceuticals (Basel) / Year: 2017
Title: Development of Pharmacophore Model for Indeno[1,2-b]indoles as Human Protein Kinase CK2 Inhibitors and Database Mining.
Authors: Haidar, S. / Bouaziz, Z. / Marminon, C. / Laitinen, T. / Poso, A. / Le Borgne, M. / Jose, J.
#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.
#3: Journal: Bioorg. Med. Chem. / Year: 2012
Title: Indeno[1,2-b]indole derivatives as a novel class of potent human protein kinase CK2 inhibitors.
Authors: Hundsdoerfer, C. / Hemmerling, H.J. / Goetz, C. / Totzke, F. / Bednarski, P. / Le Borgne, M. / Jose, J.
#4: Journal: Biochem. Biophys. Res. Commun. / Year: 2012
Title: Novel indeno[1,2-b]indoloquinones as inhibitors of the human protein kinase CK2 with antiproliferative activity towards a broad panel of cancer cell lines.
Authors: Hundsdoerfer, C. / Hemmerling, H.J. / Hamberger, J. / Le Borgne, M. / Bednarski, P. / Goetz, C. / Totzke, F. / Jose, J.
History
DepositionAug 3, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 27, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Casein kinase II subunit alpha
B: Casein kinase II subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,28918
Polymers90,4172
Non-polymers1,87216
Water5,350297
1
A: Casein kinase II subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,0758
Polymers45,2091
Non-polymers8677
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)46,21310
Polymers45,2091
Non-polymers1,0059
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)128.453, 128.453, 124.106
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

-
Components

-
Protein , 1 types, 2 molecules AB

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


Mass: 45208.559 Da / Num. of mol.: 2 / Mutation: C-terminal deletion from Ser336 to Gln391
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

-
Non-polymers , 6 types, 313 molecules

#2: Chemical ChemComp-9YE / 4-(3-methylbut-2-enoxy)-5-propan-2-yl-7,8-dihydro-6~{H}-indeno[1,2-b]indole-9,10-dione


Mass: 363.450 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H25NO3
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-BU1 / 1,4-BUTANEDIOL


Mass: 90.121 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 297 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.2 Å3/Da / Density % sol: 61.62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 90 MICROLITER ENZYME STOCK SOLUTION (6 MG/ML IN 500 MM NACL, 25 MM TRIS/HCL, PH 8.5) WAS MIXED WITH 10 MIKROLITER 4P STOCK SOLUTION (10 MM 4P IN DMSO). THIS MIXTURE WAS INCUBATED FOR 30 MIN ...Details: 90 MICROLITER ENZYME STOCK SOLUTION (6 MG/ML IN 500 MM NACL, 25 MM TRIS/HCL, PH 8.5) WAS MIXED WITH 10 MIKROLITER 4P STOCK SOLUTION (10 MM 4P IN DMSO). THIS MIXTURE WAS INCUBATED FOR 30 MIN AT ROOM TEMPERATURE. THE RESERVOIR SOLUTION OF THE CRYSTALLIZATION EXPERIMENT WAS 25 % (W/V) PEG5000, 0.2 M AMMONIUM SULPHATE, 0.1 M MES BUFFER, PH 6.5. PRIOR TO EQUILIBRATION THE CRYSTALLIZATION DROP WAS COMPOSED OF 1 MICROLITER RESERVOIR SOLUTION PLUS 1 MICROLITER ENZYME/4P MIXTURE., VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.966 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Dec 15, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.966 Å / Relative weight: 1
ReflectionResolution: 2→57.041 Å / Num. obs: 70221 / % possible obs: 99.51 % / Redundancy: 6.2 % / Biso Wilson estimate: 44.4 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.06473 / Rsym value: 0.06473 / Net I/σ(I): 14.2
Reflection shellResolution: 2→2.072 Å / Redundancy: 6.3 % / Rmerge(I) obs: 1.909 / Mean I/σ(I) obs: 0.93 / Num. unique obs: 6881 / CC1/2: 0.437 / Rsym value: 1.909 / % possible all: 98.84

-
Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2PVR

2pvr


Resolution: 2→57.041 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 22.44
RfactorNum. reflection% reflection
Rfree0.2042 1388 1.98 %
Rwork0.1751 --
obs0.1757 70115 99.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2→57.041 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5634 0 113 297 6044
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075901
X-RAY DIFFRACTIONf_angle_d0.8077991
X-RAY DIFFRACTIONf_dihedral_angle_d13.1953612
X-RAY DIFFRACTIONf_chiral_restr0.054811
X-RAY DIFFRACTIONf_plane_restr0.0051023
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0001-2.07160.30321330.30596748X-RAY DIFFRACTION99
2.0716-2.15450.35021090.26166804X-RAY DIFFRACTION100
2.1545-2.25260.27171390.24766808X-RAY DIFFRACTION100
2.2526-2.37140.23181490.20956801X-RAY DIFFRACTION100
2.3714-2.51990.21921450.19476835X-RAY DIFFRACTION100
2.5199-2.71450.24131610.19696825X-RAY DIFFRACTION100
2.7145-2.98770.22211480.19636889X-RAY DIFFRACTION100
2.9877-3.41990.22521170.18996902X-RAY DIFFRACTION99
3.4199-4.30850.18541410.1496928X-RAY DIFFRACTION99
4.3085-57.0640.16551460.14517187X-RAY DIFFRACTION99
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)
10.2495-0.0585-0.07060.1415-0.14360.115-0.047-0.4861-0.17230.3349-0.0986-0.2633-0.05260.39840.00010.4638-0.047-0.10140.46420.05320.458714.1943-42.563327.1368
21.34711.10121.34341.13820.68011.4109-0.04390.0291-0.40950.0373-0.0272-0.01520.3928-0.089-0.00010.4305-0.0106-0.03810.563-0.01870.4515-10.0085-52.360711.8677
30.4337-0.0919-0.3890.34130.380.5159-0.11120.0994-0.25990.2586-0.0812-0.07910.1011-0.2665-0.00010.4199-0.0554-0.03470.36880.04760.5054-4.9853-49.865717.9087
40.58810.1417-0.73540.03420.06261.1008-0.55160.88070.0366-0.51810.2517-0.0349-0.0578-0.0566-0.70710.6928-0.2144-0.15360.76750.1150.4737-2.5797-41.23410.2991
52.25511.139-0.81730.787-0.17370.7506-0.0570.274-0.124-0.1380.1830.09550.1741-0.264-0.00010.4084-0.0641-0.08810.38880.03690.42766.4972-40.17159.7803
61.68310.5565-0.61551.9548-0.57631.3465-0.1220.1407-0.4798-0.32180.0635-0.27360.29410.151600.4838-0.0253-0.02560.4254-0.04580.539824.0039-45.40314.3958
70.87980.404-0.14551.7228-0.08630.8889-0.0110.32920.1723-0.27220.0310.0633-0.34610.1581-00.4576-0.0787-0.05390.43040.04310.429115.568-28.54913.1838
80.7883-0.8052-0.67662.83211.17641.8251-0.0388-0.1337-0.06280.03660.006-0.03730.29480.1267-0.00010.39610.02360.01820.43220.00490.3592-16.5682-66.046144.2176
91.952-0.38770.1751.6424-0.45832.32350.15660.06590.0922-0.1146-0.07180.0967-0.13650.0368-00.35570.04430.02770.3456-0.02860.3419-25.8993-47.394336.1775
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 24 )
2X-RAY DIFFRACTION2chain 'A' and (resid 25 through 74 )
3X-RAY DIFFRACTION3chain 'A' and (resid 75 through 108 )
4X-RAY DIFFRACTION4chain 'A' and (resid 109 through 129 )
5X-RAY DIFFRACTION5chain 'A' and (resid 130 through 197 )
6X-RAY DIFFRACTION6chain 'A' and (resid 198 through 280 )
7X-RAY DIFFRACTION7chain 'A' and (resid 281 through 335 )
8X-RAY DIFFRACTION8chain 'B' and (resid 2 through 129 )
9X-RAY DIFFRACTION9chain 'B' and (resid 130 through 335 )

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more