[English] 日本語
Yorodumi
- PDB-2r7i: Crystal structure of catalytic subunit of protein kinase CK2 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2r7i
TitleCrystal structure of catalytic subunit of protein kinase CK2
ComponentsCasein kinase II subunit alpha
KeywordsTRANSFERASE / catalytic subunit / kinase / ATP-binding / Nucleotide-binding / Serine/threonine-protein kinase / Wnt signaling pathway
Function / homology
Function and homology information


WNT mediated activation of DVL / Condensation of Prometaphase Chromosomes / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / Regulation of CDH1 posttranslational processing and trafficking to plasma membrane / Receptor Mediated Mitophagy / Synthesis of PC / Regulation of PTEN stability and activity / Regulation of TP53 Activity through Phosphorylation / protein targeting to vacuole involved in autophagy / Signal transduction by L1 ...WNT mediated activation of DVL / Condensation of Prometaphase Chromosomes / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / Regulation of CDH1 posttranslational processing and trafficking to plasma membrane / Receptor Mediated Mitophagy / Synthesis of PC / Regulation of PTEN stability and activity / Regulation of TP53 Activity through Phosphorylation / protein targeting to vacuole involved in autophagy / Signal transduction by L1 / aggrephagy / deadenylation-dependent decapping of nuclear-transcribed mRNA / PcG protein complex / protein phosphatase regulator activity / membraneless organelle assembly / double-strand break repair via classical nonhomologous end joining / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / protein localization to site of double-strand break / positive regulation of aggrephagy / regulation of chromosome separation / protein kinase CK2 complex / symbiont-mediated disruption of host cell PML body / execution phase of apoptosis / response to testosterone / Sin3-type complex / negative regulation of signal transduction by p53 class mediator / negative regulation of apoptotic signaling pathway / ribonucleoprotein complex binding / negative regulation of double-strand break repair via homologous recombination / positive regulation of Wnt signaling pathway / regulation of protein localization to plasma membrane / negative regulation of translational initiation / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / liver regeneration / DNA damage checkpoint signaling / protein catabolic process / double-strand break repair via homologous recombination / cerebral cortex development / PML body / beta-catenin binding / Wnt signaling pathway / positive regulation of protein catabolic process / kinase activity / rhythmic process / double-strand break repair / positive regulation of cell growth / 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 / DNA damage response / regulation of transcription by RNA polymerase II / chromatin / nucleoplasm / ATP binding / identical protein binding / nucleus / 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
Casein kinase II subunit alpha
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.003 Å
AuthorsShen, Y.
CitationJournal: CHIN.SCI.BULL. / Year: 2009
Title: Crystal structures of catalytic and regulatory subunits of rat protein kinase CK2
Authors: Zhou, W. / Qin, X. / Yan, X. / Xie, X. / Li, L. / Fang, S. / Long, J. / Adelman, J. / Tang, W.-J. / Shen, Y.
History
DepositionSep 8, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 23, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)161,15612
Polymers160,3874
Non-polymers7698
Water55831
1
A: Casein kinase II subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,2893
Polymers40,0971
Non-polymers1922
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)40,2893
Polymers40,0971
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Casein kinase II subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,2893
Polymers40,0971
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Casein kinase II subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,2893
Polymers40,0971
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)127.517, 127.517, 126.406
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111CHAIN A AND (RESSEQ 2:44 OR RESSEQ 53:103 OR RESSEQ 108:330 )A2 - 44
121CHAIN A AND (RESSEQ 2:44 OR RESSEQ 53:103 OR RESSEQ 108:330 )A53 - 103
131CHAIN A AND (RESSEQ 2:44 OR RESSEQ 53:103 OR RESSEQ 108:330 )A108 - 330
211CHAIN B AND (RESSEQ 2:44 OR RESSEQ 53:103 OR RESSEQ 108:330 )B2 - 44
221CHAIN B AND (RESSEQ 2:44 OR RESSEQ 53:103 OR RESSEQ 108:330 )B53 - 103
231CHAIN B AND (RESSEQ 2:44 OR RESSEQ 53:103 OR RESSEQ 108:330 )B108 - 330
311CHAIN C AND (RESSEQ 2:44 OR RESSEQ 53:103 OR RESSEQ 108:330 )C2 - 44
321CHAIN C AND (RESSEQ 2:44 OR RESSEQ 53:103 OR RESSEQ 108:330 )C53 - 103
331CHAIN C AND (RESSEQ 2:44 OR RESSEQ 53:103 OR RESSEQ 108:330 )C108 - 330
411CHAIN D AND (RESSEQ 2:44 OR RESSEQ 53:103 OR RESSEQ 108:330 )D2 - 44
421CHAIN D AND (RESSEQ 2:44 OR RESSEQ 53:103 OR RESSEQ 108:330 )D53 - 103
431CHAIN D AND (RESSEQ 2:44 OR RESSEQ 53:103 OR RESSEQ 108:330 )D108 - 330

-
Components

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


Mass: 40096.770 Da / Num. of mol.: 4 / Fragment: catalytic subunit, C-terminal truncation 1-335
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: CK2 / Plasmid: pProEx / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P19139, non-specific serine/threonine protein kinase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 31 / 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: 61.61 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: Li2SO4, PEG 3350, Bis-Tris buffer, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.95→50 Å / Num. all: 40253 / Num. obs: 40213 / % possible obs: 99 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 7.2 % / Biso Wilson estimate: 41.99 Å2 / Rmerge(I) obs: 0.154 / Rsym value: 0.11 / Net I/σ(I): 14.2
Reflection shellResolution: 3→3.11 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.648 / Mean I/σ(I) obs: 2.85 / Rsym value: 0.551 / % possible all: 100

-
Processing

Software
NameClassification
PHENIXrefinement
HKL-2000data collection
HKL-2000data reduction
SCALEPACKdata scaling
PHASESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.003→19.574 Å / SU ML: 0.38 / Isotropic thermal model: RESTRAINED / σ(F): 0.08 / Phase error: 24.93 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2571 1935 5.04 %
Rwork0.2161 --
obs0.2181 38373 95.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 15.392 Å2 / ksol: 0.314 e/Å3
Displacement parametersBiso mean: 27.5 Å2
Baniso -1Baniso -2Baniso -3
1-5.22 Å20 Å20 Å2
2--5.22 Å20 Å2
3----10.44 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.43 Å0.38 Å
Luzzati d res low-5 Å
Luzzati sigma a0.44 Å0.42 Å
Refinement stepCycle: LAST / Resolution: 3.003→19.574 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10748 0 40 31 10819
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00611062
X-RAY DIFFRACTIONf_angle_d0.93414972
X-RAY DIFFRACTIONf_dihedral_angle_d18.6444006
X-RAY DIFFRACTIONf_chiral_restr0.0671575
X-RAY DIFFRACTIONf_plane_restr0.0031913
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A2655X-RAY DIFFRACTIONPOSITIONAL0.031
12B2655X-RAY DIFFRACTIONPOSITIONAL0.031
13C2663X-RAY DIFFRACTIONPOSITIONAL0.012
14D2663X-RAY DIFFRACTIONPOSITIONAL0.031
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.003-3.07780.34731250.28132261X-RAY DIFFRACTION84
3.0778-3.16070.30441260.25842430X-RAY DIFFRACTION89
3.1607-3.25330.27641520.23592520X-RAY DIFFRACTION93
3.2533-3.35780.27921440.21982610X-RAY DIFFRACTION96
3.3578-3.47720.21891510.21072604X-RAY DIFFRACTION97
3.4772-3.61550.28041470.20592613X-RAY DIFFRACTION96
3.6155-3.7790.26381430.20412638X-RAY DIFFRACTION97
3.779-3.97660.22921270.20242627X-RAY DIFFRACTION96
3.9766-4.22350.23831290.18232652X-RAY DIFFRACTION97
4.2235-4.54580.21911320.18572691X-RAY DIFFRACTION98
4.5458-4.99630.21221290.17122690X-RAY DIFFRACTION98
4.9963-5.70360.23631560.20072663X-RAY DIFFRACTION98
5.7036-7.12780.2571290.23672709X-RAY DIFFRACTION98
7.1278-19.57410.27791450.23742730X-RAY DIFFRACTION98
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3so4.paramso4.top

+
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