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- PDB-6rch: Crystal structure of Casein kinase I isoform delta (CK1 delta) co... -

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Basic information

Entry
Database: PDB / ID: 6rch
TitleCrystal structure of Casein kinase I isoform delta (CK1 delta) complexed with SR4133 inhibitor
ComponentsCasein kinase I isoform delta
KeywordsTRANSFERASE / CK1 delta / CK1d / kinase inhibitor / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


positive regulation of non-canonical Wnt signaling pathway / protein localization to Golgi apparatus / midbrain dopaminergic neuron differentiation / COPII vesicle coating / 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 / midbrain dopaminergic neuron differentiation / COPII vesicle coating / 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 / Major pathway of rRNA processing in the nucleolus and cytosol / spindle assembly / 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 / circadian regulation of gene expression / spindle microtubule / regulation of circadian rhythm / Wnt signaling pathway / spindle / endocytosis / Regulation of PLK1 Activity at G2/M Transition / Circadian Clock / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / positive regulation of canonical Wnt signaling pathway / 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
Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; 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. ...Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; 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
Chem-K0B / Casein kinase I isoform delta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsChaikuad, A. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Roush, W.R. / Knapp, S. / Structural Genomics Consortium (SGC)
CitationJournal: To Be Published
Title: Crystal structure of Casein kinase I isoform delta (CK1 delta) complexed with SR4133 inhibitor
Authors: Chaikuad, A. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Roush, W.R. / Knapp, S. / Structural Genomics Consortium (SGC)
History
DepositionApr 11, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 25, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 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_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim
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_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)70,45318
Polymers68,8502
Non-polymers1,60316
Water13,980776
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3230 Å2
ΔGint-98 kcal/mol
Surface area28130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.106, 74.072, 88.967
Angle α, β, γ (deg.)90.000, 103.180, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: GLU / Beg label comp-ID: GLU / End auth comp-ID: MET / End label comp-ID: MET / Refine code: _ / Auth seq-ID: 2 - 292 / Label seq-ID: 4 - 294

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 34424.805 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CSNK1D, HCKID / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-R3-pRARE2
References: UniProt: P48730, non-specific serine/threonine protein kinase, tau-protein kinase

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Non-polymers , 5 types, 792 molecules

#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-K0B / ~{N}-[[4,5-bis(fluoranyl)-1~{H}-benzimidazol-2-yl]methyl]-2-morpholin-4-yl-9-naphthalen-2-yl-purin-6-amine


Mass: 512.513 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H22F2N8O
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 776 / 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: 46.25 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 5.9
Details: 25% PEG3350, 0.2M sodium sulfate, 0.1M citrate pH 5.9

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 23, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.45→86.622 Å / Num. obs: 108708 / % possible obs: 99 % / Redundancy: 5.7 % / CC1/2: 0.978 / Rpim(I) all: 0.077 / Rrim(I) all: 0.188 / Rsym value: 0.171 / Net I/av σ(I): 6.5 / Net I/σ(I): 6.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allRsym value% possible all
1.45-1.535.40.4393.1154810.8580.2040.4860.43997.1
1.53-1.625.80.3464.1148900.1560.380.34698.6
1.62-1.735.60.2795140880.1280.3070.27998.9
1.73-1.875.90.2336.1131190.1040.2550.23399.2
1.87-2.055.60.197.1121810.0880.210.1999.5
2.05-2.295.90.1738.6109840.0770.1890.17399.7
2.29-2.655.60.1588.997360.0730.1750.15899.9
2.65-3.2460.1549.982820.0680.1690.154100
3.24-4.595.70.14610.364190.0660.160.146100
4.59-19.7215.70.1510.435280.0680.1660.1598.6

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Processing

Software
NameVersionClassification
SCALA3.3.22data scaling
REFMAC5.8.0123refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4HNF

4hnf


Resolution: 1.45→86.62 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.956 / SU B: 2.069 / SU ML: 0.04 / SU R Cruickshank DPI: 0.0618 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.062 / ESU R Free: 0.062
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1783 5329 4.9 %RANDOM
Rwork0.1554 ---
obs0.1566 103364 99.01 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 62.46 Å2 / Biso mean: 16.295 Å2 / Biso min: 3.54 Å2
Baniso -1Baniso -2Baniso -3
1--0.17 Å2-0 Å20.04 Å2
2--0.2 Å20 Å2
3----0.04 Å2
Refinement stepCycle: final / Resolution: 1.45→86.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4775 0 103 776 5654
Biso mean--24.37 27.62 -
Num. residues----586
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0195141
X-RAY DIFFRACTIONr_bond_other_d0.010.024915
X-RAY DIFFRACTIONr_angle_refined_deg1.6151.9676942
X-RAY DIFFRACTIONr_angle_other_deg1.521311308
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9475632
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.68922.672247
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.2315940
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.8961547
X-RAY DIFFRACTIONr_chiral_restr0.1010.2722
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.025961
X-RAY DIFFRACTIONr_gen_planes_other0.0080.021276
Refine LS restraints NCS

Ens-ID: 1 / Number: 34218 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.16 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.45→1.488 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.205 368 -
Rwork0.205 7352 -
all-7720 -
obs--95.76 %
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)
13.7657-2.8695-2.996.8966.968512.5626-0.05910.20230.3997-0.23820.5396-0.3507-0.54920.9357-0.48050.0553-0.06220.00850.1840.02110.0685-12.65366.73510.616
20.3227-0.00290.040.1074-0.02110.1849-0.00360.0058-0.02070.0030.0179-0.009-0.01590.0025-0.01430.01510.00250.0040.02470.00150.0149-27.23761.04430.945
30.35370.5382-0.30240.8801-0.862.9793-0.0157-0.05830.02310.0015-0.09620.0153-0.23760.19570.11190.0446-0.017-0.00440.05580.00230.0115-15.579105.0792.343
40.387-0.0092-0.00820.23640.05510.2741-0.00990.00880.0186-0.01320.01210.0069-0.00980.0246-0.00210.0215-0.0053-0.00220.02610.00180.0019-29.74297.68319.473
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 17
2X-RAY DIFFRACTION2A18 - 294
3X-RAY DIFFRACTION3B1 - 70
4X-RAY DIFFRACTION4B71 - 293

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