[English] 日本語
Yorodumi
- PDB-3eed: Crystal structure of human protein kinase CK2 regulatory subunit ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3eed
TitleCrystal structure of human protein kinase CK2 regulatory subunit (CK2beta; mutant 1-193)
ComponentsCasein kinase II subunit beta
KeywordsTRANSFERASE / protein kinase CK2 / casein kinase 2 / casein kinase II / eukaryotic protein kinases / Phosphoprotein / Wnt signaling pathway
Function / homology
Function and homology information


regulation of DNA binding / positive regulation of activin receptor signaling pathway / adiponectin-activated signaling pathway / endothelial tube morphogenesis / negative regulation of viral life cycle / protein kinase regulator activity / Condensation of Prometaphase Chromosomes / WNT mediated activation of DVL / protein kinase CK2 complex / symbiont-mediated disruption of host cell PML body ...regulation of DNA binding / positive regulation of activin receptor signaling pathway / adiponectin-activated signaling pathway / endothelial tube morphogenesis / negative regulation of viral life cycle / protein kinase regulator activity / 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 / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / negative regulation of blood vessel endothelial cell migration / positive regulation of SMAD protein signal transduction / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / peptidyl-threonine phosphorylation / Signal transduction by L1 / PML body / Wnt signaling pathway / Regulation of PTEN stability and activity / fibrillar center / KEAP1-NFE2L2 pathway / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / protein-containing complex assembly / protein-macromolecule adaptor activity / secretory granule lumen / Regulation of TP53 Activity through Phosphorylation / RNA polymerase II-specific DNA-binding transcription factor binding / ficolin-1-rich granule lumen / protein domain specific binding / signaling receptor binding / negative regulation of cell population proliferation / protein serine/threonine kinase activity / chromatin binding / Neutrophil degranulation / chromatin / signal transduction / extracellular exosome / extracellular region / nucleoplasm / metal ion binding / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
protein kinase ck2 holoenzyme, chain C, domain 1 / protein kinase ck2 holoenzyme, chain C, domain 1 / Casein kinase II, regulatory subunit / Casein kinase II, regulatory subunit, N-terminal / Casein kinase II subunit beta-like / Casein kinase II regulatory subunit / Casein kinase II regulatory subunit signature. / Casein kinase II regulatory subunit / N-terminal domain of TfIIb - #20 / N-terminal domain of TfIIb ...protein kinase ck2 holoenzyme, chain C, domain 1 / protein kinase ck2 holoenzyme, chain C, domain 1 / Casein kinase II, regulatory subunit / Casein kinase II, regulatory subunit, N-terminal / Casein kinase II subunit beta-like / Casein kinase II regulatory subunit / Casein kinase II regulatory subunit signature. / Casein kinase II regulatory subunit / N-terminal domain of TfIIb - #20 / N-terminal domain of TfIIb / Single Sheet / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Casein kinase II subunit beta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsNiefind, K. / Raaf, J. / Issinger, O.-G.
Citation
Journal: Protein Sci. / Year: 2008
Title: The interaction of CK2{alpha} and CK2{beta}, the subunits of protein kinase CK2, requires CK2{beta} in a preformed conformation and is enthalpically driven
Authors: Raaf, J. / Brunstein, E. / Issinger, O.-G. / Niefind, K.
#1: 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.
History
DepositionSep 4, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 16, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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 / diffrn_source / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _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 beta
B: Casein kinase II subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,4047
Polymers44,9852
Non-polymers4195
Water1,47782
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2820 Å2
ΔGint-50 kcal/mol
Surface area20490 Å2
MethodPISA
2
A: Casein kinase II subunit beta
B: Casein kinase II subunit beta
hetero molecules

A: Casein kinase II subunit beta
B: Casein kinase II subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,80814
Polymers89,9704
Non-polymers83810
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_554y,x,-z-11
Buried area6680 Å2
ΔGint-117 kcal/mol
Surface area39960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.463, 116.463, 76.088
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22B

NCS domain segments:

Component-ID: 1 / Refine code: 2

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11VALVALLEULEUAA7 - 567 - 56
21VALVALLEULEUBB7 - 567 - 56
12GLNGLNILEILEAA68 - 19268 - 192
22GLNGLNILEILEBB68 - 19268 - 192

NCS ensembles :
ID
1
2

-
Components

#1: Protein Casein kinase II subunit beta / CK II beta / Phosvitin / G5a


Mass: 22492.488 Da / Num. of mol.: 2 / Fragment: regulatory subunit, UNP residues 1-193
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pT7-7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P67870
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 82 / 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: 2.87 Å3/Da / Density % sol: 57.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.3
Details: 25.5% PEG 8000, 15% glycerol, 0.17M ammonium sulfate, 0.085M sodium cacodylate, pH 6.3, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X12 / Wavelength: 0.9 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 25, 2005
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.8→29.74 Å / Num. all: 13382 / Num. obs: 13382 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 13.1 % / Biso Wilson estimate: 71 Å2 / Rmerge(I) obs: 0.099 / Rsym value: 0.099 / Net I/σ(I): 29.9
Reflection shellResolution: 2.8→2.9 Å / Mean I/σ(I) obs: 4.6 / % possible all: 100

-
Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.4.0073refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1JWH (CHAINS C and D)

1jwh


Resolution: 2.8→29.12 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.934 / SU B: 22.332 / SU ML: 0.221 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.318 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21616 1321 9.9 %RANDOM
Rwork0.17163 ---
all0.17619 12061 --
obs0.17619 12061 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 52.049 Å2
Baniso -1Baniso -2Baniso -3
1-0.47 Å20 Å20 Å2
2--0.47 Å20 Å2
3----0.94 Å2
Refinement stepCycle: LAST / Resolution: 2.8→29.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3000 0 17 82 3099
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0223112
X-RAY DIFFRACTIONr_bond_other_d0.0010.022140
X-RAY DIFFRACTIONr_angle_refined_deg1.1231.9614216
X-RAY DIFFRACTIONr_angle_other_deg0.7363.0035170
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6855362
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.36523.902164
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.48215502
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.8961518
X-RAY DIFFRACTIONr_chiral_restr0.0590.2418
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213456
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02654
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.2561830
X-RAY DIFFRACTIONr_mcbond_other0.5386728
X-RAY DIFFRACTIONr_mcangle_it3.65292956
X-RAY DIFFRACTIONr_scbond_it3.14661282
X-RAY DIFFRACTIONr_scangle_it4.38791260
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A296TIGHT POSITIONAL0.030.05
1A409MEDIUM POSITIONAL0.030.5
1B296TIGHT THERMAL0.080.5
1B409MEDIUM THERMAL0.082
2A729TIGHT POSITIONAL0.030.05
2A1026MEDIUM POSITIONAL0.040.5
2B729TIGHT THERMAL0.090.5
2B1026MEDIUM THERMAL0.092
LS refinement shellResolution: 2.8→2.872 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.372 74 -
Rwork0.292 880 -
obs--100 %
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)
12.41770.0966-0.22284.25441.63315.15470.03720.1722-0.28370.07670.0202-0.44490.48730.5517-0.0574-0.15980.101-0.0582-0.1250.0167-0.0777-19.31-34.262-25.498
21.12230.8771.36835.03041.933.41090.1794-0.0162-0.09820.5219-0.20450.18730.1992-0.17680.0251-0.1474-0.03210-0.1960.0252-0.2155-28.535-18.419-14.462
31.4103-4.46010.111635.36217.06488.0381-0.45610.43340.46560.93540.67460.6009-0.1427-1.1647-0.2186-0.1373-0.01340.10840.04980.0033-0.1165-33.7197.302-1.846
43.01150.67061.8423.7388-0.28045.9776-0.0596-0.35950.05720.7412-0.0148-0.6397-0.33470.87720.0743-0.03-0.0759-0.09490.0943-0.0002-0.0325-8.72712.5261.53
52.19870.71030.38214.92880.94613.19040.0076-0.0490.01950.0209-0.00250.04290.1275-0.0448-0.005-0.22840.01030.0411-0.23250.0425-0.1877-23.5832.53-10.242
612.099517.87151.13926.6192.71724.9271-0.8310.3690.4486-1.42870.92750.4757-0.0528-0.5749-0.0964-0.17460.00890.0158-0.0843-0.0245-0.0464-39.393-18.085-23.608
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA6 - 596 - 59
2X-RAY DIFFRACTION1AA65 - 10565 - 105
3X-RAY DIFFRACTION2AA106 - 180106 - 180
4X-RAY DIFFRACTION3AA181 - 193181 - 193
5X-RAY DIFFRACTION4BB6 - 596 - 59
6X-RAY DIFFRACTION4BB65 - 10565 - 105
7X-RAY DIFFRACTION5BB106 - 180106 - 180
8X-RAY DIFFRACTION6BB181 - 193181 - 193

+
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