[English] 日本語
Yorodumi
- PDB-1qf8: TRUNCATED FORM OF CASEIN KINASE II BETA SUBUNIT (2-182) FROM HOMO... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1qf8
TitleTRUNCATED FORM OF CASEIN KINASE II BETA SUBUNIT (2-182) FROM HOMO SAPIENS
ComponentsCASEIN KINASE II
KeywordsTRANSFERASE / CASEIN KINASE BETA SUBUNIT (1-182) / SER/THR PROTEIN KINASE / ZN FINGER
Function / homology
Function and homology information


regulation of DNA binding / adiponectin-activated signaling pathway / positive regulation of activin receptor 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 / adiponectin-activated signaling pathway / positive regulation of activin receptor 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 / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / Maturation of hRSV A proteins / positive regulation of SMAD protein signal transduction / negative regulation of blood vessel endothelial cell migration / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / Signal transduction by L1 / peptidyl-threonine phosphorylation / PML body / Wnt signaling pathway / Regulation of PTEN stability and activity / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / KEAP1-NFE2L2 pathway / protein-macromolecule adaptor activity / protein-containing complex assembly / secretory granule lumen / RNA polymerase II-specific DNA-binding transcription factor binding / Regulation of TP53 Activity through Phosphorylation / ficolin-1-rich granule lumen / protein domain specific binding / negative regulation of cell population proliferation / signaling receptor binding / protein serine/threonine kinase activity / chromatin binding / Neutrophil degranulation / chromatin / signal transduction / extracellular exosome / extracellular region / nucleoplasm / identical protein binding / nucleus / metal ion binding / 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 / MAD / Resolution: 1.74 Å
AuthorsChantalat, L. / Leroy, D. / Filhol, O. / Nueda, A. / Benitez, M.J. / Chambaz, E. / Cochet, C. / Dideberg, O.
CitationJournal: EMBO J. / Year: 1999
Title: Crystal structure of the human protein kinase CK2 regulatory subunit reveals its zinc finger-mediated dimerization.
Authors: Chantalat, L. / Leroy, D. / Filhol, O. / Nueda, A. / Benitez, M.J. / Chambaz, E.M. / Cochet, C. / Dideberg, O.
History
DepositionApr 7, 1999Deposition site: PDBE / Processing site: RCSB
Revision 1.0Apr 19, 2000Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software / Item: _software.name
Revision 1.4Dec 27, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_conn_type / struct_ref_seq_dif / struct_site
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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_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_type.id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: CASEIN KINASE II
B: CASEIN KINASE II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,2615
Polymers43,1062
Non-polymers1553
Water5,837324
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)132.230, 132.230, 63.780
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212
Components on special symmetry positions
IDModelComponents
11A-331-

HOH

-
Components

#1: Protein CASEIN KINASE II


Mass: 21552.885 Da / Num. of mol.: 2 / Fragment: BETA SUBUNIT (RESIDUES 1-182)
Source method: isolated from a genetically manipulated source
Details: TRUNCATED, CONTAINS RESIDUES 1-182 / Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P67870, EC: 2.7.1.37
#2: Chemical ChemComp-ZN / ZINC ION


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


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 324 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Nonpolymer detailsZINC FINGER
Sequence detailsRESIDUES 183-215 HAVE BEEN DELETED

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.7 Å3/Da / Density % sol: 60 %
Crystal growTemperature: 281 K / Method: vapor diffusion, sitting drop / pH: 9
Details: CRYSTALS OF CK2 BETA (1-182) WERE GROWN AT 281 K IN 4 MICROLITER SITTING DROPS CONTAINING A 1:1 MIXTURE OF PROTEIN SOLUTION (18 MG/ML) IN 10 MM TRIS (PH 7) AND RESERVOIR SOLUTION WITH 15% ...Details: CRYSTALS OF CK2 BETA (1-182) WERE GROWN AT 281 K IN 4 MICROLITER SITTING DROPS CONTAINING A 1:1 MIXTURE OF PROTEIN SOLUTION (18 MG/ML) IN 10 MM TRIS (PH 7) AND RESERVOIR SOLUTION WITH 15% PEG 5K MME, 500 MM NACL, 460 MM MGCL2 3% DIOXANE, pH 9, VAPOR DIFFUSION, SITTING DROP
Crystal
*PLUS
Crystal grow
*PLUS
pH: 9.2 / Method: vapor diffusion, hanging drop / Details: Chantalat, L., (1999) Acta Crystallogr., D55, 895.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
118 mg/mlprotein1drop
214-20 %mPEG50001reservoir
40.46 M1reservoirMgCl2
510 mMdithiothreitol1reservoir
63 %dioxane1reservoir
70.4 M1reservoirNaCl
3bicine1reservoir

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.88, 0.978668, 0.978418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 1, 1998 / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.881
20.9786681
30.9784181
ReflectionResolution: 1.7→30 Å / Num. obs: 634684 / % possible obs: 99.4 % / Observed criterion σ(I): 0 / Redundancy: 10.2 % / Biso Wilson estimate: 19.3 Å2 / Rmerge(I) obs: 0.043 / Net I/σ(I): 34
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 10 % / Rmerge(I) obs: 0.326 / Mean I/σ(I) obs: 7.05 / % possible all: 99.7
Reflection
*PLUS
Num. obs: 62119 / Num. measured all: 634684
Reflection shell
*PLUS
% possible obs: 99.7 %

-
Processing

Software
NameVersionClassification
MLPHAREphasing
SOLOMONphasing
CNS0.4refinement
DENZOdata reduction
CCP4(AGROVATAdata scaling
SCALAdata scaling
TRUNCATEdata scaling
RefinementMethod to determine structure: MAD / Resolution: 1.74→20 Å / Rfactor Rfree error: 0.003 / Data cutoff high rms absF: 2101218.05 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.219 5818 10 %RANDOM
Rwork0.194 ---
obs-57967 99.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 52.66 Å2 / ksol: 0.412 e/Å3
Displacement parametersBiso mean: 23.8 Å2
Baniso -1Baniso -2Baniso -3
1-2.08 Å20 Å20 Å2
2--2.08 Å20 Å2
3----4.15 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.21 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.13 Å0.12 Å
Refinement stepCycle: LAST / Resolution: 1.74→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2704 0 3 324 3031
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.96
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it0.781.5
X-RAY DIFFRACTIONc_mcangle_it1.32
X-RAY DIFFRACTIONc_scbond_it2.612
X-RAY DIFFRACTIONc_scangle_it3.282.5
LS refinement shellResolution: 1.74→1.85 Å / Rfactor Rfree error: 0.008 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.25 958 10 %
Rwork0.226 8605 -
obs--100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
Software
*PLUS
Name: CNS / Version: 0.4 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 10 % / Rfactor obs: 0.1933
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 23.8 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.8
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.96
X-RAY DIFFRACTIONc_mcbond_it1.5
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.25 / % reflection Rfree: 10 % / Rfactor Rwork: 0.226

+
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