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- PDB-7p7f: Crystal structure of phosphorylated pT220 Casein Kinase I delta (... -

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Basic information

Entry
Database: PDB / ID: 7p7f
TitleCrystal structure of phosphorylated pT220 Casein Kinase I delta (CK1d), conformation 1
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 / 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 / ADENOSINE MONOPHOSPHATE / Casein kinase I isoform delta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.96 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
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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
C: Casein kinase I isoform delta
D: Casein kinase I isoform delta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)141,29835
Polymers138,0194
Non-polymers3,27931
Water11,512639
1
A: Casein kinase I isoform delta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,2026
Polymers34,5051
Non-polymers6975
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Casein kinase I isoform delta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,51311
Polymers34,5051
Non-polymers1,00810
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Casein kinase I isoform delta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,2468
Polymers34,5051
Non-polymers7427
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Casein kinase I isoform delta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,33710
Polymers34,5051
Non-polymers8329
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.061, 81.813, 89.088
Angle α, β, γ (deg.)90.270, 105.950, 93.600
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LEULEUAA3 - 2945 - 296
21LEULEUBB3 - 2945 - 296
12ARGARGAA4 - 2946 - 296
22ARGARGCC4 - 2946 - 296
13ARGARGAA4 - 2946 - 296
23ARGARGDD4 - 2946 - 296
14ARGARGBB4 - 2946 - 296
24ARGARGCC4 - 2946 - 296
15ARGARGBB4 - 2946 - 296
25ARGARGDD4 - 2946 - 296
16ARGARGCC4 - 2946 - 296
26ARGARGDD4 - 2946 - 296

NCS ensembles :
ID
1
2
3
4
5
6

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Components

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Protein , 1 types, 4 molecules ABCD

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


Mass: 34504.785 Da / Num. of mol.: 4
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

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Non-polymers , 5 types, 670 molecules

#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


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


Mass: 267.241 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H13N5O4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 639 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationY

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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: 2.49 Å3/Da / Density % sol: 50.51 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 5.9
Details: 20% PEG 3350, 0.1 M sodium sulfate, and 0.1 M citrate, pH 5.9

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.99999 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Feb 6, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99999 Å / Relative weight: 1
ReflectionResolution: 1.96→47.09 Å / Num. obs: 88717 / % possible obs: 93 % / Redundancy: 3.8 % / CC1/2: 0.998 / Rmerge(I) obs: 0.048 / Rpim(I) all: 0.034 / Rrim(I) all: 0.067 / Net I/σ(I): 12.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.96-2.033.80.413285680.9290.3040.59791.7
7.59-47.093.90.03216330.9960.0190.03799.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
Aimless0.7.4data scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6RU7

6ru7


Resolution: 1.96→47.09 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.952 / SU B: 8.702 / SU ML: 0.122 / SU R Cruickshank DPI: 0.1887 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.189 / ESU R Free: 0.158 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.221 4541 5.1 %RANDOM
Rwork0.1879 ---
obs0.1896 84176 92.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 140.25 Å2 / Biso mean: 42.477 Å2 / Biso min: 21.26 Å2
Baniso -1Baniso -2Baniso -3
1--0.51 Å20.68 Å2-0.53 Å2
2--3.37 Å20.39 Å2
3----2.32 Å2
Refinement stepCycle: final / Resolution: 1.96→47.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9434 0 203 639 10276
Biso mean--53.27 43.82 -
Num. residues----1154
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0139911
X-RAY DIFFRACTIONr_bond_other_d0.0010.0179247
X-RAY DIFFRACTIONr_angle_refined_deg1.4121.6513325
X-RAY DIFFRACTIONr_angle_other_deg1.3111.58221402
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8251171
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.88920.688552
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.262151796
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6891585
X-RAY DIFFRACTIONr_chiral_restr0.0730.21204
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0210890
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022277
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A99450.05
12B99450.05
21A93100.1
22C93100.1
31A93300.09
32D93300.09
41B92890.1
42C92890.1
51B93510.09
52D93510.09
61C96870.07
62D96870.07
LS refinement shellResolution: 1.96→2.011 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.305 361 -
Rwork0.263 6088 -
all-6449 -
obs--92.15 %
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)
10.67380.2237-0.38060.3104-0.83394.62640.1776-0.16790.06880.0967-0.04720.081-0.56040.2414-0.13050.1884-0.10270.06210.1763-0.02530.051129.919328.7175-39.12
20.51540.2132-0.28870.16710.1662.04330.05710.03720.0331-0.03820.11050.0057-0.25980.0875-0.16760.0913-0.02540.02320.23120.04090.024415.240918.8209-20.6128
30.7471-0.35410.16350.8114-0.52815.20030.09370.1826-0.0647-0.01560.02940.09150.6740.132-0.12310.16650.066-0.05020.1622-0.01620.033429.9887-29.477339.4286
40.5999-0.20650.1690.1680.02371.51470.0306-0.0533-0.04860.02250.07170.02120.15420.1136-0.10230.07550.0243-0.02090.22110.03470.019315.1392-19.593420.9149
51.0776-0.05630.09720.0244-0.03590.96850.03910.0745-0.0661-0.00540.01190.0046-0.052-0.1798-0.0510.03510.0092-0.00740.2240.04130.0158-4.987-15.9503-21.3786
60.3781-0.15280.11130.1168-0.00061.25830.0566-0.037-0.04070.01750.07660.02790.08030.0746-0.13320.0640.004-0.01310.18330.03550.02729.1554-20.7113-7.9774
71.09210.1515-0.0120.1239-0.04440.87080.0674-0.06610.0636-0.0086-0.01210.0110.0438-0.1416-0.05530.033-0.007700.23620.04440.0147-4.869315.196321.6628
80.35150.23330.0670.20510.02261.33330.0377-0.010.0393-0.02480.04530.0374-0.08030.0552-0.0830.0792-0.00010.01050.19890.03160.01789.305419.97878.2865
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 85
2X-RAY DIFFRACTION2A86 - 294
3X-RAY DIFFRACTION3B3 - 85
4X-RAY DIFFRACTION4B86 - 294
5X-RAY DIFFRACTION5C4 - 176
6X-RAY DIFFRACTION6C177 - 294
7X-RAY DIFFRACTION7D4 - 176
8X-RAY DIFFRACTION8D177 - 294

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