[English] 日本語
Yorodumi
- PDB-4fbx: Complex structure of human protein kinase CK2 catalytic subunit c... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4fbx
TitleComplex structure of human protein kinase CK2 catalytic subunit crystallized in the presence of a bisubstrate inhibitor
Components
  • Casein kinase II subunit alpha
  • bisubstrate inhibitor
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / protein kinase fold / protein phosphorylation / Bisubstrate inhibitor / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


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 / Synthesis of PC / Sin3-type complex / Maturation of hRSV A proteins ...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 / 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 apoptotic signaling pathway / positive regulation of Wnt signaling pathway / negative regulation of double-strand break repair via homologous recombination / chaperone-mediated protein folding / Signal transduction by L1 / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / peptidyl-threonine phosphorylation / Hsp90 protein binding / PML body / Wnt signaling pathway / Regulation of PTEN stability and activity / positive regulation of protein catabolic process / rhythmic process / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / KEAP1-NFE2L2 pathway / double-strand break repair / kinase activity / peptidyl-serine phosphorylation / positive regulation of cell growth / Regulation of TP53 Activity through Phosphorylation / protein stabilization / regulation of cell cycle / non-specific serine/threonine protein kinase / negative regulation of translation / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / positive regulation of cell population proliferation / DNA damage response / apoptotic process / 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. / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Serine/Threonine protein kinases, catalytic domain / Protein kinase domain / Protein kinase, ATP binding site ...Casein Kinase 2, subunit alpha / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Serine/Threonine protein kinases, catalytic domain / Protein kinase 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 Alpha / Alpha Beta
Similarity search - Domain/homology
bisubstrate inhibitor / Casein kinase II subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.33 Å
AuthorsEnkvist, E. / Viht, K. / Bischoff, N. / Vahter, J. / Saaver, S. / Raidaru, G. / Issinger, O.-G. / Niefind, K. / Uri, A.
Citation
Journal: Org.Biomol.Chem. / Year: 2012
Title: A subnanomolar fluorescent probe for protein kinase CK2 interaction studies.
Authors: Enkvist, E. / Viht, K. / Bischoff, N. / Vahter, J. / Saaver, S. / Raidaru, G. / Issinger, O.G. / Niefind, K. / Uri, A.
#1: Journal: J.Mol.Biol. / Year: 2003
Title: Crystal structure of a C-terminal deletion mutant of human protein kinase CK2 catalytic subunit.
Authors: Ermakova, I. / Boldyreff, B. / Issinger, O.G. / Niefind, K.
#2: Journal: J.Mol.Biol. / Year: 2008
Title: The catalytic subunit of human protein kinase CK2 structurally deviates from its maize homologue in complex with the nucleotide competitive inhibitor emodin.
Authors: Raaf, J. / Klopffleisch, K. / Issinger, O.G. / Niefind, K.
#3: Journal: Cell.Mol.Life Sci. / Year: 2009
Title: Protein kinase CK2 in health and disease: Protein kinase CK2: from structures to insights.
Authors: Niefind, K. / Raaf, J. / Issinger, O.G.
History
DepositionMay 23, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 17, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 31, 2012Group: Database references
Revision 1.2Dec 12, 2012Group: Other
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.0Jul 10, 2024Group: Data collection / Non-polymer description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / entity
Item: _chem_comp.formula / _chem_comp.formula_weight / _entity.formula_weight

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)41,4817
Polymers41,3042
Non-polymers1775
Water2,198122
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)72.114, 72.114, 135.056
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

-
Components

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


Mass: 40066.742 Da / Num. of mol.: 1
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: Protein/peptide bisubstrate inhibitor


Type: Polypeptide / Class: Enzyme inhibitor / Mass: 1237.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / References: bisubstrate inhibitor
#3: Chemical
ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 122 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCHAIN B IS A BISUBSTRATE INHIBITOR, I.E. A MODIFIED CK2 SUBSTRATE PEPTIDE TO WHICH AN ATP- ...CHAIN B IS A BISUBSTRATE INHIBITOR, I.E. A MODIFIED CK2 SUBSTRATE PEPTIDE TO WHICH AN ATP-COMPETITIVE INHIBITOR MOIETY IS LINKED. ONLY THE LATTER IS DEFINED IN THE ELECTRON DENSITY WHILE THE PEPTIDIC PART IS COMPLETELY FLEXIBLE PROBABLY DUE TO ITS HIGH NEGATIVE CHARGE DENSITY.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.16 Å3/Da / Density % sol: 42.98 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: The concentrated enzyme solution contained 6.2 mg/ml protein dissolved in 500 mM NaCl, 25 mM Tris/HCl, pH 8.5. Nine volume parts of this protein stock solution were mixed with one part 12 mM ...Details: The concentrated enzyme solution contained 6.2 mg/ml protein dissolved in 500 mM NaCl, 25 mM Tris/HCl, pH 8.5. Nine volume parts of this protein stock solution were mixed with one part 12 mM ARC-1154 dissolved in 100% dimethyl sulfoxide. The CK2alpha1-335/ARC-1154 mixture was incubated for 30 min at room temperature. The best crystals grew with a reservoir solution composed of 4.4 M NaCl, 100 mM citric acid, pH 5.25 and mixing 2 microliter of this reservoir solution with microliter CK2alpha1-335/ARC-1154 mixture, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SEALED TUBE / Type: OTHER / Wavelength: 1.5418 Å
DetectorType: AGILENT ATLAS CCD / Detector: CCD / Date: Dec 14, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.33→32.25 Å / Num. all: 15941 / Num. obs: 15925 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8 % / Biso Wilson estimate: 38.8 Å2 / Rmerge(I) obs: 0.095 / Rsym value: 0.095 / Net I/σ(I): 18.8

-
Processing

Software
NameVersionClassification
PHENIXmodel building
PHENIX(phenix.refine: 1.7.3_928)refinement
XDSdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.33→31.807 Å / SU ML: 0.37 / σ(F): 1.35 / Phase error: 23.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2492 924 5.82 %Random
Rwork0.1988 ---
obs0.2018 15868 99.9 %-
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 36.043 Å2 / ksol: 0.361 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.0349 Å20 Å20 Å2
2---0.0349 Å20 Å2
3---0.0698 Å2
Refinement stepCycle: LAST / Resolution: 2.33→31.807 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2829 0 5 122 2956
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032905
X-RAY DIFFRACTIONf_angle_d0.6773930
X-RAY DIFFRACTIONf_dihedral_angle_d13.761098
X-RAY DIFFRACTIONf_chiral_restr0.054405
X-RAY DIFFRACTIONf_plane_restr0.003505
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.33-2.45290.37341100.27752093X-RAY DIFFRACTION100
2.4529-2.60650.32361410.26042071X-RAY DIFFRACTION100
2.6065-2.80760.28991200.23092095X-RAY DIFFRACTION100
2.8076-3.08990.27571420.21772115X-RAY DIFFRACTION100
3.0899-3.53650.25321520.19572104X-RAY DIFFRACTION100
3.5365-4.45370.1971250.15942168X-RAY DIFFRACTION100
4.4537-31.80970.21711340.18222298X-RAY DIFFRACTION100
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)
10.5073-0.1326-0.46660.54890.20421.15510.0063-0.0496-0.02970.1075-0.0083-0.17310.31670.028800.26370.0886-0.0320.2229-0.03090.190921.4813-2.422128.1565
21.4434-0.0124-0.31210.7826-0.65911.4880.01880.19310.25320.13740.0246-0.0625-0.0232-0.13070.02070.02630.0241-0.02030.1690.01690.17779.909716.266622.6869
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ 2:129)
2X-RAY DIFFRACTION2CHAIN A AND (RESSEQ 130:334)

+
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://pdbjlvh1.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