[English] 日本語
Yorodumi
- PDB-7psu: Structure of protein kinase CK2alpha mutant K198R associated with... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7psu
TitleStructure of protein kinase CK2alpha mutant K198R associated with the Okur-Chung Neurodevelopmental Syndrome
ComponentsCasein kinase II subunit alpha
KeywordsTRANSFERASE / protein kinase CK2 / casein kinase 2 / CSNK2A1 mutant K198R / Okur-Chung Neurodevelopmental Syndrome
Function / homology
Function and homology information


regulation of chromosome separation / 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 / Maturation of hRSV A proteins / Sin3-type complex ...regulation of chromosome separation / 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 / Maturation of hRSV A proteins / Sin3-type complex / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / negative regulation of apoptotic signaling pathway / 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 / peptidyl-threonine phosphorylation / Hsp90 protein binding / PML body / Wnt signaling pathway / Regulation of PTEN stability and activity / positive regulation of protein catabolic process / KEAP1-NFE2L2 pathway / kinase activity / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / rhythmic process / double-strand break repair / peptidyl-serine phosphorylation / positive regulation of cell growth / Regulation of TP53 Activity through Phosphorylation / eukaryotic translation initiation factor 2alpha kinase activity / 3-phosphoinositide-dependent protein kinase activity / DNA-dependent protein kinase activity / ribosomal protein S6 kinase activity / histone H3S10 kinase activity / histone H2AXS139 kinase activity / histone H3S28 kinase activity / histone H4S1 kinase activity / histone H2BS14 kinase activity / histone H3T3 kinase activity / histone H2AS121 kinase activity / Rho-dependent protein serine/threonine kinase activity / histone H2BS36 kinase activity / histone H3S57 kinase activity / histone H2AT120 kinase activity / AMP-activated protein kinase activity / histone H2AS1 kinase activity / histone H3T6 kinase activity / histone H3T11 kinase activity / histone H3T45 kinase activity / non-specific serine/threonine protein kinase / regulation of cell cycle / protein stabilization / negative regulation of translation / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / apoptotic process / positive regulation of cell population proliferation / DNA damage response / signal transduction / nucleoplasm / ATP binding / identical protein binding / nucleus / plasma membrane / cytosol
Similarity search - Function
Casein Kinase 2, subunit alpha / 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
Similarity search - Domain/homology
Casein kinase II subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.77 Å
AuthorsWerner, C. / Gast, A. / Lindenblatt, D. / Nickelsen, K. / Niefind, K. / Jose, J. / Hochscherf, J.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)NI 643/4-2 Germany
CitationJournal: Front Mol Biosci / Year: 2022
Title: Structural and Enzymological Evidence for an Altered Substrate Specificity in Okur-Chung Neurodevelopmental Syndrome Mutant CK2 alpha Lys198Arg.
Authors: Werner, C. / Gast, A. / Lindenblatt, D. / Nickelsen, A. / Niefind, K. / Jose, J. / Hochscherf, J.
History
DepositionSep 23, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 23, 2022Provider: repository / Type: Initial release
Revision 1.1May 4, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)96,31022
Polymers94,8162
Non-polymers1,49420
Water11,998666
1
A: Casein kinase II subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,23412
Polymers47,4081
Non-polymers82611
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Casein kinase II subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,07610
Polymers47,4081
Non-polymers6689
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)127.824, 127.824, 123.180
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 2 through 220 or resid 222 through 333 or resid 401 through 404))
d_2ens_1(chain "B" and (resid 2 through 220 or resid 222 through 333 or resid 402 through 405))

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1SERCYSA1 - 219
d_12ens_1LEUARGA221 - 332
d_13ens_1EDOEDOB
d_14ens_1EDOEDOC
d_15ens_1EDOEDOD
d_16ens_1EDOEDOE
d_21ens_1SERCYSG1 - 219
d_22ens_1LEUARGG221 - 332
d_23ens_1EDOEDOH
d_24ens_1EDOEDOI
d_25ens_1EDOEDOJ
d_26ens_1EDOEDOK

NCS oper: (Code: givenMatrix: (0.008050919572, -0.997033362091, 0.0765484001891), (0.999967353957, 0.0080799830039, 6.99672190945E-5), (-0.000688269424194, 0.0765453378863, 0.99706586419)Vector: -64. ...NCS oper: (Code: given
Matrix: (0.008050919572, -0.997033362091, 0.0765484001891), (0.999967353957, 0.0080799830039, 6.99672190945E-5), (-0.000688269424194, 0.0765453378863, 0.99706586419)
Vector: -64.513990966, -62.1681353152, 32.71122664)

-
Components

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


Mass: 47407.930 Da / Num. of mol.: 2 / Mutation: K198R
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
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 666 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.16 Å3/Da / Density % sol: 61.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: The crystallization drops were composed of a 1:1 mix of the protein solution (5 mg/mL in 500 mM NaCl, 25 mM TRIS/HCl buffer, pH 8,5) and the reservoir solution containing [0.2 M lithium ...Details: The crystallization drops were composed of a 1:1 mix of the protein solution (5 mg/mL in 500 mM NaCl, 25 mM TRIS/HCl buffer, pH 8,5) and the reservoir solution containing [0.2 M lithium sulfate, 25 % (w/v) PEG 3350 and 0.1 M Bis/TRIS/HCl, pH 6.5]. The crystals were optimized by macroseeding and transferred into a cryo-protectant solution composed of 70 microliter of the reservoir solution and 30 microliter ethylene glycol.

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.87313 Å
DetectorType: DECTRIS PILATUS3 X 2M / Detector: PIXEL / Date: Apr 10, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87313 Å / Relative weight: 1
ReflectionResolution: 1.774→88.698 Å / Num. obs: 65649 / % possible obs: 66.5 % / Redundancy: 44.4 % / Biso Wilson estimate: 3.97 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.587 / Rpim(I) all: 0.087 / Rrim(I) all: 0.594 / Rsym value: 0.587 / Net I/σ(I): 18.1
Reflection shellResolution: 1.774→1.98 Å / Rmerge(I) obs: 2.814 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 3280 / CC1/2: 0.709 / Rpim(I) all: 0.448 / Rrim(I) all: 2.85 / Rsym value: 2.814 / % possible all: 12

-
Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
autoPROCdata processing
autoPROCdata reduction
STARANISO2.3.73data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2PVR

2pvr


Resolution: 1.77→50.9 Å / SU ML: 0.1676 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.2961
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2183 1332 2.03 %
Rwork0.1802 64295 -
obs0.1809 65627 66.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 20.22 Å2
Refinement stepCycle: LAST / Resolution: 1.77→50.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5612 0 83 666 6361
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00385834
X-RAY DIFFRACTIONf_angle_d0.64747877
X-RAY DIFFRACTIONf_chiral_restr0.0465809
X-RAY DIFFRACTIONf_plane_restr0.00671008
X-RAY DIFFRACTIONf_dihedral_angle_d11.59782196
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 2.60761872272 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.77-1.8400.2662392X-RAY DIFFRACTION4.04
1.84-1.910.3267270.23451123X-RAY DIFFRACTION11.81
1.91-20.2389510.21852268X-RAY DIFFRACTION23.72
2-2.10.2662860.2054114X-RAY DIFFRACTION43.09
2.1-2.240.23541660.20267635X-RAY DIFFRACTION79.72
2.24-2.410.23711780.19279613X-RAY DIFFRACTION99.76
2.41-2.650.23632080.18519622X-RAY DIFFRACTION99.85
2.65-3.030.18932130.17499674X-RAY DIFFRACTION99.97
3.03-3.820.19861690.15619806X-RAY DIFFRACTION99.98
3.82-50.90.20342340.168910048X-RAY DIFFRACTION99.14
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)
10.978606869786-0.3242977424420.1013180447470.658016039012-0.007354061615680.8952512251420.0449473286609-0.0569042709894-0.01045138101090.0100665744301-0.0324930803765-0.02910379609120.03841021526270.128342216626-0.01864435973650.06060607383930.02159431886020.007727260480530.0801683736042-0.03095268593360.05315229856951.83136200068-48.693962946815.1865270831
20.260133442392-0.595334177554-0.1446381347481.609848053580.3224553360770.080162990433-0.214695596733-0.5678770857040.1725280849740.905457656808-0.04111889036150.5214118298830.0429108133859-0.3008804696350.235158194410.4521905580060.07776111164880.04606971308440.537212360183-0.1630834844970.3010809137731.50389236304-39.050195897831.4402625826
30.152311851652-0.0504576598796-0.08575964097460.3439458046370.1103167232150.255660935253-0.00400568472036-0.1860273750050.1409416081050.135319747590.08092540965230.0591901183911-0.0563355699804-0.03833551394980.1842354607950.05341723007950.1411737730140.07456450073460.124237251755-0.09795401219640.0738794220237-17.5429612213-38.271704496125.5639532421
40.3231902063540.326222652030.03357255105950.7405918099970.5422222477640.965101891055-0.07342350009330.0556698008169-0.0239375252726-0.1112243043020.129762123309-0.133395861924-0.1259407395840.110938998762-0.03743329003330.126542928259-0.02283830125130.01003260613830.0763387577458-0.01143690853690.0500846869929-16.7696835475-66.166806328238.7995924552
53.93934623759-0.355377163375-0.6354100718453.838556316640.9497618641554.01829717402-0.0363061346909-0.1655869557050.06785118048240.181222573656-0.0381389562620.118545493631-0.0955756402302-0.1481700902720.0439986641460.0871020047686-0.0433833952337-0.0363611406140.0869541041365-0.02621387514220.0804625018118-12.4096489294-54.365102354453.2012230487
60.746768381627-0.297446357351-0.03034382756210.897029788995-0.03214606354840.665967349729-0.00409299336049-0.008978566278760.09862394136610.0142082537993-0.0122395778413-0.131829697181-0.09191144277610.1280914878370.01336697202040.048266451397-0.03474683436220.01777883488650.0329372917383-0.003706803281690.030777573818-14.3726512159-59.313940783643.588973868
70.5957339631260.426192711904-0.4580860090750.610932463662-0.4383783533970.3919078904960.141008472019-0.3431511299490.09021840578070.262531269597-0.099866580970.0451383831653-0.1362722733830.162593903226-0.03523366871130.100116315785-0.03726852059610.03942456633040.15884482416-0.01214830485560.0774435051774-28.1178226971-65.711826622457.0805856851
80.6482336796640.399874457803-0.04138189840490.690206250833-0.1700899799960.8340290477240.057888221682-0.103166867062-0.0507008979420.0961969118895-0.0351584479336-0.0485323286706-0.03373728121370.007841619462830.01450366167130.038187462722-0.0345949118877-9.74271816557E-50.04277830861790.008419908166310.0439672968666-20.4080146525-74.597250824151.3735025391
92.88645303261-0.9304970605382.325481704862.05534534666-0.5946411737223.59218906679-0.01844600932740.03177684726530.03088195597870.1420595200620.00478328554146-0.0944946513762-0.0512984983260.1645243892410.04029393718150.133331438554-0.0530302093602-0.0523145618140.1435057804360.05828057736940.075215090785-16.9018095347-84.362633540763.8093109208
101.18814827455-0.116778544874-1.498988601472.346602186990.3841075405374.43025112477-0.0992911637857-0.27732406632-0.215398491330.0821567229023-0.0261633288435-0.6620791754730.3813250403750.5709069886790.1637556793430.2311767773970.00295530324648-0.04683925941420.1595115873070.08730369213630.346939728311-16.7459036538-96.10308704655.4666490038
110.9083205672060.262283924023-0.639872472790.505387640249-0.3539781266881.119491339580.0625974454779-0.03538732034750.08774866560450.0968160882340.02887238832490.142653811455-0.0732687710786-0.0877614637755-0.1123065302730.106638520119-0.09174206209260.01636438219930.1258183535770.04832948249480.091540660355-34.7705942303-80.37969626558.3053528524
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 2 through 108 )AA2 - 1081 - 107
22chain 'A' and (resid 109 through 129 )AA109 - 129108 - 128
33chain 'A' and (resid 130 through 333 )AA130 - 333129 - 332
44chain 'B' and (resid 2 through 44 )BG2 - 441 - 43
55chain 'B' and (resid 45 through 74 )BG45 - 7444 - 73
66chain 'B' and (resid 75 through 108 )BG75 - 10874 - 107
77chain 'B' and (resid 109 through 149 )BG109 - 149108 - 148
88chain 'B' and (resid 150 through 227 )BG150 - 227149 - 226
99chain 'B' and (resid 228 through 249 )BG228 - 249227 - 248
1010chain 'B' and (resid 250 through 280 )BG250 - 280249 - 279
1111chain 'B' and (resid 281 through 333 )BG281 - 333280 - 332

+
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