[English] 日本語
Yorodumi
- PDB-1jwh: Crystal Structure of Human Protein Kinase CK2 Holoenzyme -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1jwh
TitleCrystal Structure of Human Protein Kinase CK2 Holoenzyme
Components(Casein kinase ...) x 2
KeywordsTRANSFERASE / casein kinase 2 / CK2 holoenzyme / protein kinase CK2
Function / homology
Function and homology information


regulation of DNA binding / adiponectin-activated signaling pathway / positive regulation of activin receptor signaling pathway / endothelial tube morphogenesis / protein kinase regulator activity / negative regulation of viral life cycle / regulation of chromosome separation / positive regulation of aggrephagy / WNT mediated activation of DVL / Condensation of Prometaphase Chromosomes ...regulation of DNA binding / adiponectin-activated signaling pathway / positive regulation of activin receptor signaling pathway / endothelial tube morphogenesis / protein kinase regulator activity / negative regulation of viral life cycle / regulation of chromosome separation / positive regulation of aggrephagy / WNT mediated activation of DVL / Condensation of Prometaphase Chromosomes / protein kinase CK2 complex / symbiont-mediated disruption of host cell PML body / Receptor Mediated Mitophagy / Sin3-type complex / Synthesis of PC / 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 apoptotic signaling pathway / positive regulation of Wnt signaling pathway / chaperone-mediated protein folding / negative regulation of ubiquitin-dependent protein catabolic process / Signal transduction by L1 / Hsp90 protein binding / peptidyl-threonine phosphorylation / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / PML body / Wnt signaling pathway / Regulation of PTEN stability and activity / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / positive regulation of protein catabolic process / rhythmic process / KEAP1-NFE2L2 pathway / double-strand break repair / protein-macromolecule adaptor activity / kinase activity / positive regulation of cell growth / protein-containing complex assembly / peptidyl-serine phosphorylation / secretory granule lumen / Regulation of TP53 Activity through Phosphorylation / ficolin-1-rich granule lumen / negative regulation of translation / RNA polymerase II-specific DNA-binding transcription factor binding / protein stabilization / regulation of cell cycle / non-specific serine/threonine protein kinase / cell cycle / protein domain specific binding / negative regulation of cell population proliferation / signaling receptor binding / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / apoptotic process / DNA damage response / chromatin binding / positive regulation of cell population proliferation / chromatin / Neutrophil degranulation / signal transduction / extracellular exosome / extracellular region / nucleoplasm / ATP binding / identical protein binding / metal ion binding / nucleus / plasma membrane / 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 / Casein Kinase 2, subunit alpha ...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 / Casein Kinase 2, subunit alpha / N-terminal domain of TfIIb / Single Sheet / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; 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 Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / PHOSPHATE ION / Casein kinase II subunit beta / Casein kinase II subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsNiefind, K. / Guerra, B. / Ermakowa, I. / Issinger, O.G.
Citation
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.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2000
Title: Crystallization and Preliminary Characterization of Crystals of Human Protein Kinase CK2
Authors: Niefind, K. / Guerra, B. / Ermakowa, I. / Issinger, O.G.
History
DepositionSep 4, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 4, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 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 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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, alpha chain
B: Casein kinase II, alpha chain
C: Casein kinase II beta chain
D: Casein kinase II beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,72214
Polymers130,4214
Non-polymers1,30210
Water3,765209
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8780 Å2
ΔGint-90 kcal/mol
Surface area51680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)175.990, 175.990, 93.666
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63
DetailsThe asymmetric unit contains one complete CK2 tetramer comprising two catalytic and two regulatory subunits.

-
Components

-
Casein kinase ... , 2 types, 4 molecules ABCD

#1: Protein Casein kinase II, alpha chain / CK II / catalytic subunit


Mass: 40240.902 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P68400, EC: 2.7.1.37
#2: Protein Casein kinase II beta chain / CK II / regulatory subunit


Mass: 24969.412 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P67870

-
Non-polymers , 4 types, 219 molecules

#3: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 209 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

-
Sample preparation

CrystalDensity Matthews: 3.22 Å3/Da / Density % sol: 61.8 %
Description: WHILE THE OVERALL DATA COMPLETENESS FOR THE GIVEN RESOLUTION RANGE (59.3 A - 3.1 A) WAS 98.4 % ONLY 78.7 % OF ALL POSSIBLE DATA WERE USED IN REFINEMENT WITH CNS. THE REASON FOR THIS ...Description: WHILE THE OVERALL DATA COMPLETENESS FOR THE GIVEN RESOLUTION RANGE (59.3 A - 3.1 A) WAS 98.4 % ONLY 78.7 % OF ALL POSSIBLE DATA WERE USED IN REFINEMENT WITH CNS. THE REASON FOR THIS DISCREPANCY WAS THAT THE DATA HAD NOT BEEN WILSON SCALED AFTER PROCESSING AND ALL NEGATIVE INTENSITIES HAD BEEN SET TO ZERO WHEN THE INTENSITIES HAD BEEN CONVERTED TO STRUCTURE AMPLITUDES. ALL THESE ZERO DATA WERE IGNORED DURING REFINEMENT WITH CNS.
Crystal growTemperature: 285 K / Method: vapor diffusion, sitting drop / pH: 9.3
Details: initial composition of the drop: 3 ul rhCK2 stock solution [5 mg/ml enzyme in 25 mM Tris/HCl, 300 mM NaCl, 1 mM dithiothreitole, pH 8.5], 1.5 ul reservoir solution [20 % (w/v) PEG3350, 200 ...Details: initial composition of the drop: 3 ul rhCK2 stock solution [5 mg/ml enzyme in 25 mM Tris/HCl, 300 mM NaCl, 1 mM dithiothreitole, pH 8.5], 1.5 ul reservoir solution [20 % (w/v) PEG3350, 200 mM dipotassium hydrogenphosphate], 3 ul 1 mM adenylyl imidodiphosphate (AMPPNP), 3 ul 2 mM magnesium chloride, 2 ul 10 % (w/v) polyethylene glycol 400 dodecylether (Thesit), pH 9.3, VAPOR DIFFUSION, SITTING DROP, temperature 285K
Crystal grow
*PLUS
Temperature: 12 ℃ / pH: 8.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
15.0 mg/mlprotein1drop
225 mMTris-HCl1drop
3300 mM1dropNaCl
41 mMdithiothreitol1droppH8.5
52.0 mM1dropMgCl2
61 mMAMPPNP1drop
710 %(w/v)PEG4001dropdodecylether
820 %(w/v)PEG33501reservoir
9200 mMpotassium phosphate1reservoirpH9.3

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.8428 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 26, 2000
RadiationMonochromator: silicon 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8428 Å / Relative weight: 1
ReflectionResolution: 3.1→59.3 Å / Num. obs: 29935 / % possible obs: 98.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.8 % / Biso Wilson estimate: 92.2 Å2 / Limit h max: 49 / Limit h min: 0 / Limit k max: 48 / Limit k min: 0 / Limit l max: 30 / Limit l min: 0 / Observed criterion F max: 2867098.76 / Observed criterion F min: 1.5 / Rsym value: 0.096 / Net I/σ(I): 16.7
Reflection shellResolution: 3.1→3.2 Å / Redundancy: 6 % / Mean I/σ(I) obs: 2.6 / Rsym value: 42 / % possible all: 90.4
Reflection
*PLUS
Num. measured all: 268848 / Rmerge(I) obs: 0.096
Reflection shell
*PLUS
% possible obs: 90.4 % / Rmerge(I) obs: 0.42

-
Processing

Software
NameVersionClassification
AMoREphasing
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: POLY-ALANINE BACKBONE OF CK2A FROM ZEA MAYS (PDB ENTRY 1DAW)

1daw


Resolution: 3.1→59.3 Å / Rfactor Rfree error: 0.011 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MLF
RfactorNum. reflection% reflectionSelection details
Rfree0.338 935 3.9 %Random
Rwork0.267 ---
obs-23733 78.7 %-
Solvent computationSolvent model: CNS bulk solvent model used / Bsol: 27.2984 Å2 / ksol: 0.269435 e/Å3
Displacement parametersBiso max: 243.39 Å2 / Biso mean: 90.96 Å2 / Biso min: 3.08 Å2
Baniso -1Baniso -2Baniso -3
1--32.76 Å226.71 Å20 Å2
2---32.76 Å20 Å2
3---65.51 Å2
Refine Biso
ClassRefine-IDTreatment
polymerX-RAY DIFFRACTIONisotropic
waterX-RAY DIFFRACTIONisotropic
nonpolymerX-RAY DIFFRACTIONisotropic
Refine analyze
FreeObs
Luzzati coordinate error0.6 Å0.46 Å
Luzzati d res low-5 Å
Luzzati sigma a1.05 Å0.88 Å
Luzzati d res high-3.1
Refinement stepCycle: LAST / Resolution: 3.1→59.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8947 0 68 209 9224
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d22.2
X-RAY DIFFRACTIONc_improper_angle_d1.05
X-RAY DIFFRACTIONc_mcbond_it12.239
X-RAY DIFFRACTIONc_mcangle_it17.412
X-RAY DIFFRACTIONc_scbond_it19.2612
X-RAY DIFFRACTIONc_scangle_it24.1415
Refine LS restraints NCSNCS model details: RESTRAINTS
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkRfactor Rfree errorNum. reflection allNum. reflection obs% reflection obs (%)
3.1-3.240.458812.20.45822440.0513736232562.2
3.24-3.410.352952.50.34725090.0363733260469.7
3.41-3.630.3281082.90.3226440.0323771275273
3.63-3.910.2911253.30.28929260.0263767305181
3.91-4.30.218962.60.22326060.0223753270272
4.3-4.920.2021343.60.21530180.0173772315283.6
4.92-6.20.2371423.80.26232360.023777337889.4
6.2-59.110.25415440.24236150.023872376997.3
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top
X-RAY DIFFRACTION4anp.paranp.top
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Highest resolution: 3.1 Å / Lowest resolution: 60 Å / σ(F): 0 / % reflection Rfree: 4 % / Rfactor obs: 0.267
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 91 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.2
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.05
X-RAY DIFFRACTIONc_mcbond_it12.239
X-RAY DIFFRACTIONc_scbond_it19.2612
X-RAY DIFFRACTIONc_mcangle_it17.412
X-RAY DIFFRACTIONc_scangle_it24.1415
LS refinement shell
*PLUS
Rfactor Rfree: 0.458 / % reflection Rfree: 2.2 % / Rfactor Rwork: 0.458

+
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