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- PDB-6gzm: Crystal Structure of Human CKIdelta with A86 -

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Basic information

Entry
Database: PDB / ID: 6gzm
TitleCrystal Structure of Human CKIdelta with A86
ComponentsCasein kinase I isoform delta
KeywordsTRANSFERASE / CDK9 / kinase inhibitor / A86
Function / homology
Function and homology information


positive regulation of non-canonical Wnt signaling pathway / protein localization to Golgi apparatus / COPII vesicle coating / tau-protein kinase / midbrain dopaminergic neuron differentiation / microtubule nucleation / protein localization to cilium / non-motile cilium assembly / protein localization to centrosome / COPII-mediated vesicle transport ...positive regulation of non-canonical Wnt signaling pathway / protein localization to Golgi apparatus / COPII vesicle coating / tau-protein kinase / midbrain dopaminergic neuron differentiation / microtubule nucleation / protein localization to cilium / non-motile cilium assembly / protein localization to centrosome / COPII-mediated vesicle transport / tau-protein kinase activity / Golgi organization / Major pathway of rRNA processing in the nucleolus and cytosol / spindle assembly / endoplasmic reticulum-Golgi intermediate compartment membrane / 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 / AURKA Activation by TPX2 / spindle microtubule / circadian regulation of gene expression / regulation of circadian rhythm / spindle / Wnt signaling pathway / endocytosis / : / Regulation of PLK1 Activity at G2/M Transition / positive regulation of canonical Wnt signaling pathway / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / actin cytoskeleton / protein phosphorylation / non-specific serine/threonine protein kinase / protein kinase activity / cilium / ciliary basal body / cadherin binding / 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 / cytoplasm
Similarity search - Function
: / 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 ...: / 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 Alpha / Alpha Beta
Similarity search - Domain/homology
CITRIC ACID / Chem-LCI / Casein kinase I isoform delta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.59 Å
AuthorsBen-neriah, Y. / Venkatachalam, A. / Minzel, W. / Fink, A. / Snir-Alkalay, I. / Vacca, J.
CitationJournal: Cell / Year: 2018
Title: Small Molecules Co-targeting CKI alpha and the Transcriptional Kinases CDK7/9 Control AML in Preclinical Models.
Authors: Minzel, W. / Venkatachalam, A. / Fink, A. / Hung, E. / Brachya, G. / Burstain, I. / Shaham, M. / Rivlin, A. / Omer, I. / Zinger, A. / Elias, S. / Winter, E. / Erdman, P.E. / Sullivan, R.W. / ...Authors: Minzel, W. / Venkatachalam, A. / Fink, A. / Hung, E. / Brachya, G. / Burstain, I. / Shaham, M. / Rivlin, A. / Omer, I. / Zinger, A. / Elias, S. / Winter, E. / Erdman, P.E. / Sullivan, R.W. / Fung, L. / Mercurio, F. / Li, D. / Vacca, J. / Kaushansky, N. / Shlush, L. / Oren, M. / Levine, R. / Pikarsky, E. / Snir-Alkalay, I. / Ben-Neriah, Y.
History
DepositionJul 4, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 29, 2018Provider: repository / Type: Initial release
Revision 1.1Sep 5, 2018Group: Data collection / Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Oct 3, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)69,8739
Polymers68,6212
Non-polymers1,2517
Water14,988832
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3520 Å2
ΔGint-9 kcal/mol
Surface area27050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.232, 73.659, 89.204
Angle α, β, γ (deg.)90.00, 103.57, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 34310.613 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CSNK1D, HCKID / Production host: Escherichia coli (E. coli)
References: UniProt: P48730, non-specific serine/threonine protein kinase, tau-protein kinase
#2: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-LCI / [4-[[4-[5-(cyclopropylmethyl)-1-methyl-pyrazol-4-yl]-5-fluoranyl-pyrimidin-2-yl]amino]cyclohexyl]azanium


Mass: 345.438 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H26FN6 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 832 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.29 Å3/Da / Density % sol: 46.32 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: The construct used for crystallization was that of the wild type protein with the mutation R13N. Crystals of CK1d in complex with A-86 were obtained using hanging drop vapour diffusion set- ...Details: The construct used for crystallization was that of the wild type protein with the mutation R13N. Crystals of CK1d in complex with A-86 were obtained using hanging drop vapour diffusion set-ups. CK1d at a concentration of 13.6 mg/ml (50 mM HEPES, 266 mM NaCl, 1 mM EDTA, 1 mM DTT, 5 mM B-OG, pH 7.5) was pre-incubated with 2 mM (5.1-fold molar excess) of A-86 (150 mM in DMSO) for 1 h. 1 ul of the protein solution was then mixed with 1 ul of reservoir solution (0.1 M Na3-Citrate, pH 4.9, 18 %(w/v) PEG 3350) and equilibrated at 20 C over 0.4 ml of reservoir solution. Well diffracting crystals appeared over night

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Data collection

DiffractionMean temperature: 110.15 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.966 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Dec 19, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.966 Å / Relative weight: 1
ReflectionResolution: 1.59→29.19 Å / Num. obs: 80180 / % possible obs: 96.5 % / Redundancy: 2.4 % / Rrim(I) all: 0.09 / Net I/σ(I): 7.1
Reflection shellResolution: 1.59→1.68 Å / Redundancy: 2.4 % / Num. unique obs: 11624 / Rrim(I) all: 0.57 / % possible all: 96.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3uyt

3uyt


Resolution: 1.59→29.19 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.922 / SU B: 3.08 / SU ML: 0.104 / Cross valid method: THROUGHOUT / ESU R: 0.107 / ESU R Free: 0.117 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24976 3911 4.9 %RANDOM
Rwork0.18869 ---
obs0.19153 75238 95.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 28.076 Å2
Baniso -1Baniso -2Baniso -3
1--0.44 Å20 Å2-0.39 Å2
2--2.91 Å2-0 Å2
3----2.05 Å2
Refinement stepCycle: 1 / Resolution: 1.59→29.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4788 0 87 832 5707
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0195374
X-RAY DIFFRACTIONr_bond_other_d0.0020.025045
X-RAY DIFFRACTIONr_angle_refined_deg1.5331.9857256
X-RAY DIFFRACTIONr_angle_other_deg0.985311702
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1795649
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.78622.677254
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.52415977
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.6341546
X-RAY DIFFRACTIONr_chiral_restr0.0940.2755
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.025921
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021201
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.7672.5042503
X-RAY DIFFRACTIONr_mcbond_other2.7672.5042504
X-RAY DIFFRACTIONr_mcangle_it3.8383.7533136
X-RAY DIFFRACTIONr_mcangle_other3.8373.7523137
X-RAY DIFFRACTIONr_scbond_it3.5132.8332871
X-RAY DIFFRACTIONr_scbond_other3.5122.8332872
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.2514.0964095
X-RAY DIFFRACTIONr_long_range_B_refined10.40332.3226660
X-RAY DIFFRACTIONr_long_range_B_other9.76430.7446338
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.59→1.631 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.286 286 -
Rwork0.284 5512 -
obs--95.03 %

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