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- PDB-7p7g: Crystal structure of phosphorylated pT220 Casein Kinase I delta (... -

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Basic information

Entry
Database: PDB / ID: 7p7g
TitleCrystal structure of phosphorylated pT220 Casein Kinase I delta (CK1d), conformation 2 and 3
ComponentsCasein kinase I isoform delta
KeywordsTRANSFERASE / casein kinase / CK1d / CSNK1D / conformation plasticity / alpha G / activation segment / phosphorylation. / 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 / COPII vesicle coating / midbrain dopaminergic neuron differentiation / microtubule nucleation / protein localization to cilium / tau-protein kinase / 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 / midbrain dopaminergic neuron differentiation / microtubule nucleation / protein localization to cilium / tau-protein kinase / 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 / 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 / spindle / Wnt signaling pathway / endocytosis / positive regulation of canonical Wnt signaling pathway / Regulation of PLK1 Activity at G2/M Transition / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / Circadian Clock / 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
ADENOSINE MONOPHOSPHATE / CITRIC ACID / Casein kinase I isoform delta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsChaikuad, A. / Zhubi, R. / Knapp, S. / Structural Genomics Consortium (SGC)
CitationJournal: Mol.Cell / Year: 2022
Title: Kinase domain autophosphorylation rewires the activity and substrate specificity of CK1 enzymes.
Authors: Cullati, S.N. / Chaikuad, A. / Chen, J.S. / Gebel, J. / Tesmer, L. / Zhubi, R. / Navarrete-Perea, J. / Guillen, R.X. / Gygi, S.P. / Hummer, G. / Dotsch, V. / Knapp, S. / Gould, K.L.
History
DepositionJul 19, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 13, 2022Provider: repository / Type: Initial release
Revision 1.1Apr 20, 2022Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jun 15, 2022Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.3Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._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)70,59112
Polymers69,0102
Non-polymers1,58110
Water7,728429
1
A: Casein kinase I isoform delta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,1064
Polymers34,5051
Non-polymers6013
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Casein kinase I isoform delta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,4858
Polymers34,5051
Non-polymers9807
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.542, 64.254, 163.966
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: ARG / Beg label comp-ID: ARG / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: 0 / Auth seq-ID: 8 - 293 / Label seq-ID: 10 - 295

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

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Components

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


Mass: 34504.785 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 BL21(DE3) (bacteria) / Variant (production host): -R3-pRARE2
References: UniProt: P48730, non-specific serine/threonine protein kinase, tau-protein kinase
#2: Chemical ChemComp-CIT / CITRIC ACID / Citric acid


Mass: 192.124 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H8O7
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE / Adenosine monophosphate


Mass: 347.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 429 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.04 Å3/Da / Density % sol: 39.81 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / Details: 12% PEG 3350 and 0.1 M ammonium citrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.00009 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 15, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00009 Å / Relative weight: 1
ReflectionResolution: 1.7→44.83 Å / Num. obs: 63264 / % possible obs: 100 % / Redundancy: 10.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.095 / Rpim(I) all: 0.031 / Rrim(I) all: 0.104 / Net I/σ(I): 16
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.7-1.7410.70.9782.442460.8010.3251.084100
7.97-44.839.40.0387230.9990.0130.04199.6

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Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6RU7

6ru7


Resolution: 1.7→44.83 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.95 / SU B: 4.611 / SU ML: 0.077 / SU R Cruickshank DPI: 0.1077 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.108 / ESU R Free: 0.106 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2079 3122 4.9 %RANDOM
Rwork0.1708 ---
obs0.1726 60063 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 93.98 Å2 / Biso mean: 26.34 Å2 / Biso min: 11.44 Å2
Baniso -1Baniso -2Baniso -3
1-1.28 Å20 Å20 Å2
2---0.61 Å20 Å2
3----0.67 Å2
Refinement stepCycle: final / Resolution: 1.7→44.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4664 0 105 429 5198
Biso mean--30.57 33.35 -
Num. residues----570
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0134893
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174616
X-RAY DIFFRACTIONr_angle_refined_deg1.4841.6486583
X-RAY DIFFRACTIONr_angle_other_deg1.3881.58510616
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4735572
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.06620.916273
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.61715876
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2951540
X-RAY DIFFRACTIONr_chiral_restr0.0820.2595
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.025448
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021206
Refine LS restraints NCS

Ens-ID: 1 / Number: 8632 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.15 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.7→1.744 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.256 223 -
Rwork0.236 4410 -
all-4633 -
obs--99.98 %
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)
13.61781.52670.03247.4768-0.8242.5570.091-0.20550.15430.2058-0.1108-0.1145-0.1648-0.11220.01980.17940.030.01480.16680.00990.1008-5.512269.049675.6589
21.1834-0.53170.16031.3849-0.17141.0882-0.0392-0.11480.03990.09110.03680.1589-0.1335-0.11950.00240.03980.00730.0050.0248-0.00590.02943.418976.729553.7627
32.1232-0.5231.25122.1127-2.11557.60640.0423-0.0213-0.21180.035-0.1013-0.02630.2816-0.08580.05910.1089-0.0440.00480.0933-0.02770.046515.142560.6611-2.296
41.46960.1039-0.01821.48180.46251.33210.00880.0478-0.09840.03730.00370.05260.1451-0.1023-0.01250.033-0.0054-0.00450.0123-0.0010.0122.149173.262117.2427
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A8 - 37
2X-RAY DIFFRACTION2A38 - 294
3X-RAY DIFFRACTION3B7 - 37
4X-RAY DIFFRACTION4B38 - 293

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