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- PDB-7p7h: Crystal structure of Casein Kinase I delta (CK1d) with alphaG-in ... -

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Basic information

Entry
Database: PDB / ID: 7p7h
TitleCrystal structure of Casein Kinase I delta (CK1d) with alphaG-in conformation
ComponentsCasein kinase I isoform delta
KeywordsTRANSFERASE / casein kinase / CK1d / CSNK1D / conformation plasticity / alpha G / activation segment. / 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 / 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 / cytoplasm / 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 / Casein kinase I isoform delta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 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)69,5444
Polymers68,8502
Non-polymers6942
Water1,72996
1
A: Casein kinase I isoform delta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,7722
Polymers34,4251
Non-polymers3471
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Casein kinase I isoform delta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,7722
Polymers34,4251
Non-polymers3471
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.029, 73.377, 90.608
Angle α, β, γ (deg.)90.000, 103.640, 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: LEU / Beg label comp-ID: LEU / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: _ / Auth seq-ID: 3 - 294 / Label seq-ID: 5 - 296

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

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Components

#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 BL21(DE3) (bacteria) / Variant (production host): -R3-pRARE2
References: UniProt: P48730, non-specific serine/threonine protein kinase, tau-protein kinase
#2: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


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


Mass: 18.015 Da / Num. of mol.: 96 / 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: 2.3 Å3/Da / Density % sol: 46.53 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 18% PEG 6000, 1 M LiCl and 0.1 M citrate, pH 5.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.00002 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Jul 4, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00002 Å / Relative weight: 1
ReflectionResolution: 2.4→44.03 Å / Num. obs: 23044 / % possible obs: 94.5 % / Redundancy: 4.7 % / CC1/2: 0.98 / Rmerge(I) obs: 0.169 / Rpim(I) all: 0.095 / Rrim(I) all: 0.213 / Net I/σ(I): 7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.4-2.534.50.8081.733650.6970.4551.02195
7.59-44.035.10.0587340.9960.0270.06591.2

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Processing

Software
NameVersionClassification
Aimless0.7.7data scaling
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6RU7

6ru7


Resolution: 2.4→44.03 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.912 / SU B: 26.719 / SU ML: 0.289 / SU R Cruickshank DPI: 0.8065 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.806 / ESU R Free: 0.316 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2684 1027 4.5 %RANDOM
Rwork0.223 ---
obs0.2251 22004 93.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 122.57 Å2 / Biso mean: 43.573 Å2 / Biso min: 17.88 Å2
Baniso -1Baniso -2Baniso -3
1--1.13 Å2-0 Å2-0.13 Å2
2--1.8 Å2-0 Å2
3----0.54 Å2
Refinement stepCycle: final / Resolution: 2.4→44.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4776 0 46 96 4918
Biso mean--53.89 38.86 -
Num. residues----584
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0134936
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174696
X-RAY DIFFRACTIONr_angle_refined_deg1.2381.6476642
X-RAY DIFFRACTIONr_angle_other_deg1.1181.58610794
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9795582
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.3420.791278
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.60815902
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1011542
X-RAY DIFFRACTIONr_chiral_restr0.0490.2604
X-RAY DIFFRACTIONr_gen_planes_refined0.010.025522
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021232
Refine LS restraints NCS

Ens-ID: 1 / Number: 9024 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.12 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.4→2.462 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.293 72 -
Rwork0.289 1642 -
all-1714 -
obs--94.64 %
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)
16.6228-0.8196-2.18875.60532.09963.2146-0.1245-0.36290.622-0.05610.18650.5905-0.0442-0.2967-0.06210.3815-0.02340.00090.24160.03780.235629.808525.0065-4.1607
21.95150.3866-0.15671.1702-0.46292.50420.0104-0.1770.36690.0075-0.0803-0.1106-0.21030.54130.070.52890.00880.02860.1869-0.00930.102826.881619.015714.094
32.48520.50390.48591.7010.4661.6323-0.0626-0.16320.21450.1403-0.00870.1974-0.12690.00850.07130.47460.01490.05290.07880.00690.042213.119615.807423.8658
45.7303-1.56652.08343.0982-1.65091.8473-0.0069-0.11230.69510.01030.08830.1654-0.1071-0.1184-0.08140.42690.02230.02670.3484-0.03930.2885-9.740320.252675.9351
51.75380.5874-0.15271.10740.12491.2629-0.05450.10020.0157-0.0370.08540.18480.105-0.3578-0.03080.4993-0.01780.02610.15280.0370.04241.898413.827663.6454
61.58561.18180.30542.110.11253.0486-0.09150.18770.0823-0.18160.13640.170.0164-0.0725-0.04490.4415-0.04130.05110.1906-0.01880.03310.862318.507349.9723
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 37
2X-RAY DIFFRACTION2A38 - 176
3X-RAY DIFFRACTION3A177 - 294
4X-RAY DIFFRACTION4B3 - 46
5X-RAY DIFFRACTION5B47 - 159
6X-RAY DIFFRACTION6B160 - 294

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