[English] 日本語
Yorodumi
- PDB-7nzy: Crystal structure of human Casein Kinase I delta in complex with ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7nzy
TitleCrystal structure of human Casein Kinase I delta in complex with CGS-15943
ComponentsCasein kinase I isoform delta
KeywordsTRANSFERASE / Kinase / Inhibitor / Complex / ATP-competitive
Function / homology
Function and homology information


positive regulation of non-canonical Wnt signaling pathway / protein localization to Golgi apparatus / COPII vesicle coating / midbrain dopaminergic neuron differentiation / microtubule nucleation / tau-protein kinase / non-motile cilium assembly / protein localization to cilium / protein localization to centrosome / COPII-mediated vesicle transport ...positive regulation of non-canonical Wnt signaling pathway / protein localization to Golgi apparatus / COPII vesicle coating / midbrain dopaminergic neuron differentiation / microtubule nucleation / tau-protein kinase / non-motile cilium assembly / protein localization to cilium / protein localization to centrosome / COPII-mediated vesicle transport / tau-protein kinase activity / Golgi organization / spindle assembly / Major pathway of rRNA processing in the nucleolus and cytosol / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of mitotic centrosome proteins and complexes / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / endoplasmic reticulum-Golgi intermediate compartment membrane / AURKA Activation by TPX2 / cellular response to nerve growth factor stimulus / ciliary basal body / spindle microtubule / circadian regulation of gene expression / regulation of circadian rhythm / Wnt signaling pathway / spindle / endocytosis / Regulation of PLK1 Activity at G2/M Transition / positive regulation of canonical Wnt signaling pathway / Circadian Clock / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / non-specific serine/threonine protein kinase / protein kinase activity / cadherin binding / positive regulation of protein phosphorylation / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / centrosome / perinuclear region of cytoplasm / Golgi apparatus / signal transduction / nucleoplasm / ATP binding / nucleus / plasma membrane / cytosol
Similarity search - Function
: / 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
MALONATE ION / PHOSPHATE ION / Chem-UX2 / Casein kinase I isoform delta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsPichlo, C. / Baumann, U.
CitationJournal: J.Med.Chem. / Year: 2022
Title: Phenotypic Discovery of Triazolo[1,5- c ]quinazolines as a First-In-Class Bone Morphogenetic Protein Amplifier Chemotype.
Authors: Wesseler, F. / Lohmann, S. / Riege, D. / Halver, J. / Roth, A. / Pichlo, C. / Weber, S. / Takamiya, M. / Muller, E. / Ketzel, J. / Flegel, J. / Gihring, A. / Rastegar, S. / Bertrand, J. / ...Authors: Wesseler, F. / Lohmann, S. / Riege, D. / Halver, J. / Roth, A. / Pichlo, C. / Weber, S. / Takamiya, M. / Muller, E. / Ketzel, J. / Flegel, J. / Gihring, A. / Rastegar, S. / Bertrand, J. / Baumann, U. / Knippschild, U. / Peifer, C. / Sievers, S. / Waldmann, H. / Schade, D.
History
DepositionMar 24, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 5, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 31, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Casein kinase I isoform delta
B: Casein kinase I isoform delta
C: Casein kinase I isoform delta
D: Casein kinase I isoform delta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)147,76216
Polymers145,8314
Non-polymers1,93112
Water11,944663
1
A: Casein kinase I isoform delta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,9484
Polymers36,4581
Non-polymers4903
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Casein kinase I isoform delta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,8393
Polymers36,4581
Non-polymers3812
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Casein kinase I isoform delta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,9334
Polymers36,4581
Non-polymers4763
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Casein kinase I isoform delta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,0435
Polymers36,4581
Non-polymers5854
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.938, 82.081, 89.556
Angle α, β, γ (deg.)87.097, 74.264, 86.332
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

-
Components

#1: Protein
Casein kinase I isoform delta / CKI-delta / CKId / Tau-protein kinase CSNK1D


Mass: 36457.867 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CSNK1D, HCKID / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): TAKARA 2
References: UniProt: P48730, non-specific serine/threonine protein kinase, tau-protein kinase
#2: Chemical
ChemComp-UX2 / 9-chloranyl-2-(furan-2-yl)-[1,2,4]triazolo[1,5-c]quinazolin-5-amine


Mass: 285.689 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C13H8ClN5O / Feature type: SUBJECT OF INVESTIGATION / Comment: antagonist*YM
#3: Chemical
ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H2O4
#4: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 663 / 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: 2.37 Å3/Da / Density % sol: 48.06 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / Details: 0.2 M sodium malonate pH = 5.0, 20% (w/v) PEG 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9794 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 15, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.85→47.04 Å / Num. obs: 110137 / % possible obs: 96.27 % / Redundancy: 3.6 % / Biso Wilson estimate: 28.9 Å2 / CC1/2: 0.997 / Net I/σ(I): 9.96
Reflection shellResolution: 1.85→1.916 Å / Num. unique obs: 10873 / CC1/2: 0.797

-
Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
PHENIX1.19.1_4122refinement
XDS20180126data reduction
XDS20180126data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4TWC

4twc


Resolution: 1.85→47.04 Å / SU ML: 0.2443 / Cross valid method: FREE R-VALUE / σ(F): 2.03 / Phase error: 30.9771
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2289 1765 1.6 %
Rwork0.2049 108218 -
obs0.2053 109983 96.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 44.93 Å2
Refinement stepCycle: LAST / Resolution: 1.85→47.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9218 0 128 663 10009
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00749743
X-RAY DIFFRACTIONf_angle_d0.783313145
X-RAY DIFFRACTIONf_chiral_restr0.05041351
X-RAY DIFFRACTIONf_plane_restr0.00531681
X-RAY DIFFRACTIONf_dihedral_angle_d13.14443620
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.90.41641350.38738208X-RAY DIFFRACTION95.02
1.9-1.960.35551360.34188277X-RAY DIFFRACTION95.33
1.96-2.020.39251450.29628209X-RAY DIFFRACTION95.41
2.02-2.090.30091150.2798265X-RAY DIFFRACTION95.38
2.09-2.170.27221390.25348259X-RAY DIFFRACTION95.83
2.17-2.270.26291370.21978369X-RAY DIFFRACTION96.47
2.27-2.390.21591240.2018308X-RAY DIFFRACTION96.38
2.39-2.540.24461420.20428345X-RAY DIFFRACTION96.22
2.54-2.740.24371450.20898371X-RAY DIFFRACTION96.95
2.74-3.020.23731320.20838362X-RAY DIFFRACTION97.04
3.02-3.450.23321370.19728401X-RAY DIFFRACTION96.76
3.45-4.350.20531380.16558448X-RAY DIFFRACTION97.77
4.35-47.040.16121400.17448396X-RAY DIFFRACTION97.14

+
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