[English] 日本語
Yorodumi
- PDB-6tlu: HUMAN CK2 KINASE ALPHA SUBUNIT IN COMPLEX WITH THE ATP-COMPETITIV... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6tlu
TitleHUMAN CK2 KINASE ALPHA SUBUNIT IN COMPLEX WITH THE ATP-COMPETITIVE INHIBITOR 4,5-DIBROMOBENZOTRIAZOLE
ComponentsCasein kinase II subunit alpha
KeywordsTRANSFERASE / CK2 / CASEIN KINASE 2 / INHIBITOR / BROMO-BENZOTRIAZOLE / HALOGEN BOND / TRANSFERASE-TRANSFERASE INHIBITOR COMPLEX
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 / 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
Similarity search - Domain/homology
6,7-bis(bromanyl)-1~{H}-benzotriazole / Casein kinase II subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.81 Å
AuthorsCzapinska, H. / Piasecka, A. / Winiewska-Szajewska, M. / Bochtler, M. / Poznanski, J.
Funding support Poland, 3items
OrganizationGrant numberCountry
Polish National Science Centre2012/07/B/ST4/01334 Poland
Polish National Science Centre2017/25/B/ST4/01613 Poland
European Communitys Seventh Framework Programme283570
Citation
Journal: J.Phys.Chem.B / Year: 2021
Title: Halogen Atoms in the Protein-Ligand System. Structural and Thermodynamic Studies of the Binding of Bromobenzotriazoles by the Catalytic Subunit of Human Protein Kinase CK2.
Authors: Czapinska, H. / Winiewska-Szajewska, M. / Szymaniec-Rutkowska, A. / Piasecka, A. / Bochtler, M. / Poznanski, J.
#1: Journal: Biochim. Biophys. Acta / Year: 2015
Title: Thermodynamics parameters for binding of halogenated benzotriazole inhibitors of human protein kinase CK2 alpha.
Authors: Winiewska, M. / Kucinska, K. / Makowska, M. / Poznanski, J. / Shugar, D.
#2: Journal: Biochem. Biophys. Res. Commun. / Year: 2015
Title: Thermodynamic parameters for binding of some halogenated inhibitors of human protein kinase CK2.
Authors: Winiewska, M. / Makowska, M. / Maj, P. / Wielechowska, M. / Bretner, M. / Poznanski, J. / Shugar, D.
History
DepositionDec 3, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 16, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 7, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 24, 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
AAA: Casein kinase II subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,8574
Polymers46,2801
Non-polymers5773
Water7,404411
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area110 Å2
ΔGint-7 kcal/mol
Surface area15810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)129.320, 129.320, 60.696
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number94
Space group name H-MP42212
Components on special symmetry positions
IDModelComponents
11AAA-765-

HOH

-
Components

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


Mass: 46279.699 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CSNK2A1, CK2A1 / Plasmid: PET28 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P68400, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-NKT / 6,7-bis(bromanyl)-1~{H}-benzotriazole


Mass: 276.916 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C6H3Br2N3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 411 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.17 Å3/Da / Density % sol: 61.24 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M sodium HEPES/MOPS buffer pH 7.5, 20 mM sodium formate, 20 mM ammonium acetate, 20 mM sodium citrate tribasic dihydrate, 20 mM sodium potassium tartrate tetrahydrate, 20 mM sodium ...Details: 0.1 M sodium HEPES/MOPS buffer pH 7.5, 20 mM sodium formate, 20 mM ammonium acetate, 20 mM sodium citrate tribasic dihydrate, 20 mM sodium potassium tartrate tetrahydrate, 20 mM sodium oxamate, 20% polyethylene glycol 550 monomethyl ester, 10% polyethylene glycol 20000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.97935 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 25, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97935 Å / Relative weight: 1
ReflectionResolution: 1.81→36.52 Å / Num. obs: 46962 / % possible obs: 98.9 % / Redundancy: 24.7 % / Biso Wilson estimate: 45.45 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.078 / Rsym value: 0.077 / Net I/σ(I): 22.85
Reflection shellResolution: 1.81→1.92 Å / Redundancy: 23.7 % / Mean I/σ(I) obs: 2.12 / Num. unique obs: 7042 / CC1/2: 0.938 / Rpim(I) all: 1.022 / Rrim(I) all: 1.044 / % possible all: 93.6

-
Processing

Software
NameVersionClassification
REFMAC5.8.0257refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
ARP/wARPmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3WAR

3war


Resolution: 1.81→36.52 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.969 / SU B: 5.648 / SU ML: 0.074 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.106 / ESU R Free: 0.097
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED HAVE BEEN REPORTED. THE RELATIVE OCCUPANCIES OF THE LIGAND POSES AND STATICALLY DISORDERED RESIDUES HAVE BEEN ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED HAVE BEEN REPORTED. THE RELATIVE OCCUPANCIES OF THE LIGAND POSES AND STATICALLY DISORDERED RESIDUES HAVE BEEN ASSIGNED TENTATIVELY. THE DENSITY NEXT TO THE SIDE CHAIN OF TYR257 MAY CORRESPOND TO PARTIAL OXIDATION DUE TO XRAY RADIATION BUT SINCE THE EFFECT IS LIKELY TO BE AN ARTIFACT OF THE EXPERIMENTAL METHOD, IT WAS NOT MODELLED. THE ION IDENTITIES HAVE BEEN ASSIGNED TENTATIVELY. THERE ARE A FEW WATER CLUSTERS THAT MAY CORRESPOND TO SOLVENT MOLECULES BUT UNAMBIGUOUS DISTINCTION BETWEEN VARIOUS BUFFER COMPONENTS WAS NOT STRAIGHTFORWARD AND THUS THE WATER MOLECULES WERE RETAINED IN THE FINAL MODEL.
RfactorNum. reflection% reflectionSelection details
Rfree0.1845 2331 5 %RANDOM
Rwork0.1639 ---
obs0.1649 44583 98.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 132.68 Å2 / Biso mean: 45.287 Å2 / Biso min: 26.48 Å2
Baniso -1Baniso -2Baniso -3
1-0.79 Å2-0 Å2-0 Å2
2--0.79 Å2-0 Å2
3----1.59 Å2
Refinement stepCycle: final / Resolution: 1.81→36.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2812 0 34 413 3259
Biso mean--58.39 58.77 -
Num. residues----333
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0133344
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173027
X-RAY DIFFRACTIONr_angle_refined_deg1.3941.6534564
X-RAY DIFFRACTIONr_angle_other_deg1.2981.5897039
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2695409
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.65321.132212
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.18815610
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5281532
X-RAY DIFFRACTIONr_chiral_restr0.0680.2398
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023897
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02790
LS refinement shellResolution: 1.81→1.856 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.29 148 -
Rwork0.285 2807 -
all-2955 -
obs--85.98 %
Refinement TLS params.Method: refined / Origin x: 55.4625 Å / Origin y: 22.3491 Å / Origin z: 22.0515 Å
111213212223313233
T0.0803 Å20.0234 Å2-0.0104 Å2-0.0522 Å20.0033 Å2--0.0039 Å2
L1.9559 °2-0.4548 °2-0.4028 °2-0.8456 °20.1162 °2--1.5433 °2
S-0.0788 Å °-0.1099 Å °-0.0167 Å °0.0171 Å °0.1102 Å °-0.0003 Å °0.0003 Å °0.0414 Å °-0.0314 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1AAA2 - 334
2X-RAY DIFFRACTION1I1 - 10
3X-RAY DIFFRACTION1W1 - 800

+
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