[English] 日本語
Yorodumi
- PDB-4dgl: Crystal Structure of the CK2 Tetrameric Holoenzyme -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4dgl
TitleCrystal Structure of the CK2 Tetrameric Holoenzyme
Components
  • Casein kinase II subunit alpha
  • Casein kinase II subunit beta
KeywordsTRANSFERASE / protein kinase
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 / regulation of chromosome separation / protein kinase regulator activity / positive regulation of aggrephagy / Condensation of Prometaphase Chromosomes / WNT mediated activation of DVL ...regulation of DNA binding / adiponectin-activated signaling pathway / positive regulation of activin receptor signaling pathway / endothelial tube morphogenesis / negative regulation of viral life cycle / regulation of chromosome separation / protein kinase regulator activity / 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 / Sin3-type complex / Maturation of hRSV A proteins / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / negative regulation of signal transduction by p53 class mediator / negative regulation of blood vessel endothelial cell migration / negative regulation of apoptotic signaling pathway / positive regulation of SMAD protein signal transduction / peptidyl-threonine phosphorylation / 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 / Regulation of PTEN stability and activity / Wnt signaling pathway / fibrillar center / KEAP1-NFE2L2 pathway / positive regulation of protein catabolic process / kinase activity / rhythmic process / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / double-strand break repair / positive regulation of cell growth / protein-containing complex assembly / Regulation of TP53 Activity through Phosphorylation / secretory granule lumen / protein-macromolecule adaptor activity / ficolin-1-rich granule lumen / RNA polymerase II-specific DNA-binding transcription factor binding / non-specific serine/threonine protein kinase / regulation of cell cycle / negative regulation of translation / protein stabilization / signaling receptor binding / protein domain specific binding / negative regulation of cell population proliferation / protein serine kinase activity / protein serine/threonine kinase activity / positive regulation of cell population proliferation / apoptotic process / DNA damage response / Neutrophil degranulation / chromatin binding / chromatin / signal transduction / extracellular exosome / extracellular region / nucleoplasm / ATP binding / metal ion binding / identical protein 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 / 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 Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Casein kinase II subunit beta / Casein kinase II subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3 Å
AuthorsLolli, G. / Battistutta, R.
CitationJournal: Acs Chem.Biol. / Year: 2012
Title: Structural determinants of protein kinase CK2 regulation by autoinhibitory polymerization.
Authors: Lolli, G. / Pinna, L.A. / Battistutta, R.
History
DepositionJan 26, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 2, 2012Provider: repository / Type: Initial release
Revision 1.1May 16, 2012Group: Database references
Revision 1.2Jan 2, 2013Group: Database references
Revision 1.3Feb 28, 2024Group: 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 / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref_seq_dif.details / _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
C: Casein kinase II subunit alpha
D: Casein kinase II subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,1916
Polymers130,0604
Non-polymers1312
Water21612
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7850 Å2
ΔGint-59 kcal/mol
Surface area50900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)175.652, 175.652, 96.260
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12C
22D

NCS domain segments:

Refine code: 5

Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111SERSERLEULEUAA8 - 568 - 56
211SERSERLEULEUBB8 - 568 - 56
121GLNGLNGLYGLYAA68 - 18968 - 189
221GLNGLNGLYGLYBB68 - 18968 - 189
131LYSLYSALAALAAA191 - 203191 - 203
231LYSLYSALAALABB191 - 203191 - 203
112GLYGLYASPASPCC3 - 373 - 37
212GLYGLYASPASPDD3 - 373 - 37
122LYSLYSLYSLYSCC74 - 10274 - 102
222LYSLYSLYSLYSDD74 - 10274 - 102
132LEULEUTYRTYRCC128 - 325128 - 325
232LEULEUTYRTYRDD128 - 325128 - 325

NCS ensembles :
ID
1
2

-
Components

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


Mass: 24969.412 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CSNK2B, CK2N, G5A / Production host: Escherichia coli (E. coli) / References: UniProt: P67870
#2: Protein Casein kinase II subunit alpha / CK II alpha


Mass: 40060.762 Da / Num. of mol.: 2 / Mutation: R125Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CSNK2A1, CK2A1 / Production host: Escherichia coli (E. coli)
References: UniProt: P68400, non-specific serine/threonine protein kinase
#3: Chemical ChemComp-ZN / ZINC ION


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


Mass: 18.015 Da / Num. of mol.: 12 / 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: 3.29 Å3/Da / Density % sol: 62.65 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7
Details: PEG 3350 18%, 0.2 M sodium malonate, pH 7, vapor diffusion, temperature 293K

-
Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 9, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 3→152.119 Å / Num. all: 34036 / Num. obs: 34036 / % possible obs: 100 % / Redundancy: 19.1 % / Rsym value: 0.122 / Net I/σ(I): 23.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
3-3.1619.20.993.19466149280.99100
3.16-3.3519.20.5925.18987646720.592100
3.35-3.5919.10.3558.78445544140.355100
3.59-3.8719.20.20914.37824240780.209100
3.87-4.2419.10.12722.67246237900.127100
4.24-4.7419.10.08134.36583634390.081100
4.74-5.4819.10.07139.65770930190.071100
5.48-6.71190.06543.44884025680.065100
6.71-9.4918.70.03867.73746220010.038100
9.49-44.86317.80.02794.62003711270.02799.1

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
SCALA3.3.20data scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→152.119 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.937 / WRfactor Rfree: 0.185 / WRfactor Rwork: 0.1683 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8299 / SU B: 45.944 / SU ML: 0.324 / SU R Cruickshank DPI: 0.0816 / SU Rfree: 0.0751 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.075 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.2217 1726 5.1 %RANDOM
Rwork0.1953 ---
obs0.1966 34021 99.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 206.53 Å2 / Biso mean: 92.1847 Å2 / Biso min: 46.79 Å2
Baniso -1Baniso -2Baniso -3
1--26.57 Å2-0 Å2-0 Å2
2---26.57 Å2-0 Å2
3---53.14 Å2
Refinement stepCycle: LAST / Resolution: 3→152.119 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8863 0 2 12 8877
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.029109
X-RAY DIFFRACTIONr_angle_refined_deg1.5971.94812325
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.04551058
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.0223.374489
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.177151574
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9031572
X-RAY DIFFRACTIONr_chiral_restr0.1190.21265
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0217100
Refine LS restraints NCS

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

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A736MEDIUM POSITIONAL0.190.5
1A768LOOSE POSITIONAL0.455
1A736MEDIUM THERMAL5.922
1A768LOOSE THERMAL6.1110
2C1048MEDIUM POSITIONAL0.30.5
2C1188LOOSE POSITIONAL0.525
2C1048MEDIUM THERMAL4.182
2C1188LOOSE THERMAL5.1710
LS refinement shellResolution: 2.998→3.076 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.374 116 -
Rwork0.361 2334 -
all-2450 -
obs--96.99 %
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)
12.5774-0.4464-1.53491.66880.89641.2849-0.0959-0.2126-0.18190.3806-0.16750.38370.1825-0.26250.26340.6819-0.112-0.06920.83470.01721.009621.3811-16.4396-2.0463
20.49940.48220.6361.07590.84420.8997-0.12190.2661-0.23790.27190.22880.65310.12870.3265-0.1070.9829-0.0690.23271.08790.13421.425515.503-22.37453.0627
31.691-0.4023-0.51871.31340.72791.1613-0.1468-0.0806-0.1407-0.05190.11850.36940.0723-0.57920.02830.5787-0.0509-0.13440.6290.05020.955226.5826-7.4183-5.9363
40.99050.34380.14192.39450.48680.7522-0.0395-0.2216-0.0785-0.08980.10590.1097-0.1051-0.1107-0.06640.50350.0081-0.01440.2599-0.02120.80141.1716.715-2.4245
53.2529-0.91890.12471.9785-0.421.1916-0.10450.10780.1782-0.06010.25580.2184-0.0126-0.0992-0.15130.6043-0.0095-0.04080.270.00850.867228.896540.0641-9.1776
66.0469-1.49526.15193.28891.53929.53430.6302-0.07550.0467-0.037-0.5759-0.03661.03-0.7811-0.05430.9296-0.19730.00270.6090.18730.986716.773147.071-19.436
72.8953-1.88450.88432.2534-0.65420.3326-0.0321-0.06480.0941-0.17490.16140.29290.0721-0.1025-0.12930.5466-0.0561-0.01240.2219-0.02670.856134.170927.3028-5.5503
81.7097-0.37420.04643.60170.12280.0373-0.03250.1019-0.06-0.16530.11710.1122-0.0360.0704-0.08460.5363-0.01780.00180.1749-0.04480.762642.146510.8154-6.2818
90.5129-0.3553-0.06664.10730.86350.2638-0.1242-0.4921-0.03620.29630.01530.24070.0994-0.02840.1090.64130.05550.00490.509-0.02620.757250.4502-33.3173-1.9621
103.0476-1.4793-2.4552.69332.97983.69070.11450.12080.1386-0.1359-0.0227-0.0452-0.391-0.1144-0.09170.55220.0935-0.02390.1765-0.00760.78157.189-31.6826-14.1937
111.97050.84050.11732.02870.14943.3575-0.1568-0.1184-0.10290.36480.15720.29920.0697-0.4692-0.00040.17320.10580.07980.1563-0.02320.881346.7025-48.5296-19.1859
123.28131.9746-2.10074.3096-0.41722.7912-0.1617-0.0316-0.40260.2460.1301-0.20730.10860.05470.03160.05290.02120.01310.012-0.0370.841361.6829-48.697-26.5089
130.64660.43020.09853.1970.10630.9368-0.06760.4783-0.0314-0.6035-0.12620.10890.10340.09040.19370.5169-0.0348-0.02160.4375-0.06440.79858.63646.4875-14.1593
140.0760.1720.29671.31770.71031.36350.01940.0496-0.0478-0.41360.0193-0.18730.2945-0.0504-0.03870.4111-0.08310.03860.3573-0.08840.932565.786846.1438-2.7686
151.3491-0.2362-0.34131.89390.41492.7856-0.17410.24120.0453-0.33760.03290.3699-0.0236-0.45230.14110.1967-0.0542-0.09530.2054-0.06060.917355.256562.40451.6494
164.3553-0.01532.2065.2039-1.50986.5607-0.2084-0.01040.0024-0.2155-0.0528-0.09810.0180.45450.26120.06790.0086-0.07610.0543-0.07730.82768.959964.26099.2747
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A8 - 45
2X-RAY DIFFRACTION2A46 - 56
3X-RAY DIFFRACTION3A65 - 122
4X-RAY DIFFRACTION4A123 - 215
5X-RAY DIFFRACTION5B7 - 53
6X-RAY DIFFRACTION6B54 - 68
7X-RAY DIFFRACTION7B69 - 133
8X-RAY DIFFRACTION8B134 - 207
9X-RAY DIFFRACTION9C2 - 88
10X-RAY DIFFRACTION10C89 - 149
11X-RAY DIFFRACTION11C150 - 280
12X-RAY DIFFRACTION12C281 - 335
13X-RAY DIFFRACTION13D3 - 88
14X-RAY DIFFRACTION14D89 - 149
15X-RAY DIFFRACTION15D150 - 280
16X-RAY DIFFRACTION16D281 - 330

+
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