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- PDB-6ru7: Crystal structure of Casein Kinase I delta (CK1d) in complex with... -

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Basic information

Entry
Database: PDB / ID: 6ru7
TitleCrystal structure of Casein Kinase I delta (CK1d) in complex with double phosphorylated p63 PAD2P peptide
Components
  • Casein kinase I isoform delta
  • Tumor protein 63
KeywordsTRANSFERASE / CK1 delta / CK1delta / CSNK1D / TP63 / p63 / kinase substrate complex / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


ectoderm and mesoderm interaction / epidermal cell division / cloacal septation / positive regulation of somatic stem cell population maintenance / negative regulation of mesoderm development / prostatic bud formation / female genitalia morphogenesis / positive regulation of non-canonical Wnt signaling pathway / positive regulation of keratinocyte proliferation / establishment of planar polarity ...ectoderm and mesoderm interaction / epidermal cell division / cloacal septation / positive regulation of somatic stem cell population maintenance / negative regulation of mesoderm development / prostatic bud formation / female genitalia morphogenesis / positive regulation of non-canonical Wnt signaling pathway / positive regulation of keratinocyte proliferation / establishment of planar polarity / squamous basal epithelial stem cell differentiation involved in prostate gland acinus development / negative regulation of keratinocyte differentiation / polarized epithelial cell differentiation / negative regulation of intracellular estrogen receptor signaling pathway / proximal/distal pattern formation / positive regulation of fibroblast apoptotic process / protein localization to Golgi apparatus / skin morphogenesis / COPII vesicle coating / positive regulation of cell cycle G1/S phase transition / midbrain dopaminergic neuron differentiation / cranial skeletal system development / sympathetic nervous system development / post-anal tail morphogenesis / tau-protein kinase / microtubule nucleation / protein localization to cilium / non-motile cilium assembly / embryonic forelimb morphogenesis / Differentiation of Keratinocytes in Interfollicular Epidermis in Mammalian Skin / embryonic hindlimb morphogenesis / protein localization to centrosome / COPII-mediated vesicle transport / TP53 Regulates Transcription of Death Receptors and Ligands / Activation of PUMA and translocation to mitochondria / tau-protein kinase activity / Regulation of TP53 Activity through Association with Co-factors / hair follicle morphogenesis / WW domain binding / regulation of epidermal cell division / positive regulation of Notch signaling pathway / TP53 Regulates Transcription of Caspase Activators and Caspases / positive regulation of stem cell proliferation / epithelial cell development / Golgi organization / odontogenesis of dentin-containing tooth / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / TP53 regulates transcription of several additional cell death genes whose specific roles in p53-dependent apoptosis remain uncertain / negative regulation of cellular senescence / keratinocyte proliferation / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / Pyroptosis / establishment of skin barrier / positive regulation of osteoblast differentiation / Major pathway of rRNA processing in the nucleolus and cytosol / spindle assembly / keratinocyte differentiation / Notch signaling pathway / MDM2/MDM4 family protein binding / 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 / positive regulation of apoptotic signaling pathway / stem cell proliferation / skeletal system development / RNA polymerase II transcription regulatory region sequence-specific DNA binding / determination of adult lifespan / TP53 Regulates Metabolic Genes / spindle microtubule / protein tetramerization / promoter-specific chromatin binding / circadian regulation of gene expression / cellular response to nerve growth factor stimulus / regulation of circadian rhythm / spindle / Wnt signaling pathway / endocytosis / cellular senescence / p53 binding / positive regulation of canonical Wnt signaling pathway / : / Regulation of PLK1 Activity at G2/M Transition / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / actin cytoskeleton / DNA-binding transcription activator activity, RNA polymerase II-specific / neuron apoptotic process / spermatogenesis / transcription by RNA polymerase II / damaged DNA binding / eukaryotic translation initiation factor 2alpha kinase activity / DNA-binding transcription factor activity, RNA polymerase II-specific / 3-phosphoinositide-dependent protein kinase activity / DNA-dependent protein kinase activity / ribosomal protein S6 kinase activity / histone H3S10 kinase activity / histone H2AXS139 kinase activity
Similarity search - Function
Tumour protein p63, SAM domain / : / p53 family signature. / p53, tetramerisation domain / P53 tetramerisation motif / p53, DNA-binding domain / P53 DNA-binding domain / p53 tumour suppressor family / p53-like tetramerisation domain superfamily / p53/RUNT-type transcription factor, DNA-binding domain superfamily ...Tumour protein p63, SAM domain / : / p53 family signature. / p53, tetramerisation domain / P53 tetramerisation motif / p53, DNA-binding domain / P53 DNA-binding domain / p53 tumour suppressor family / p53-like tetramerisation domain superfamily / p53/RUNT-type transcription factor, DNA-binding domain superfamily / SAM domain (Sterile alpha motif) / p53-like transcription factor, DNA-binding / Sterile alpha motif. / Sterile alpha motif domain / Sterile alpha motif/pointed domain superfamily / 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
ADENOSINE-5'-DIPHOSPHATE / Casein kinase I isoform delta / Tumor protein 63
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.08 Å
AuthorsChaikuad, A. / Tuppi, M. / Gebel, J. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Dotsch, V. / Knapp, S. / Structural Genomics Consortium (SGC)
CitationJournal: Nat.Chem.Biol. / Year: 2020
Title: p63 uses a switch-like mechanism to set the threshold for induction of apoptosis.
Authors: Gebel, J. / Tuppi, M. / Chaikuad, A. / Hotte, K. / Schroder, M. / Schulz, L. / Lohr, F. / Gutfreund, N. / Finke, F. / Henrich, E. / Mezhyrova, J. / Lehnert, R. / Pampaloni, F. / Hummer, G. / ...Authors: Gebel, J. / Tuppi, M. / Chaikuad, A. / Hotte, K. / Schroder, M. / Schulz, L. / Lohr, F. / Gutfreund, N. / Finke, F. / Henrich, E. / Mezhyrova, J. / Lehnert, R. / Pampaloni, F. / Hummer, G. / Stelzer, E.H.K. / Knapp, S. / Dotsch, V.
History
DepositionMay 27, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 13, 2020Provider: repository / Type: Initial release
Revision 1.1Aug 12, 2020Group: Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / pdbx_struct_conn_angle / struct_conn / struct_conn_type
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_label_seq_id / _struct_conn_type.id
Revision 1.2Sep 30, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Jan 24, 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
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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
C: Tumor protein 63
D: Tumor protein 63
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,22124
Polymers72,2894
Non-polymers1,93320
Water4,035224
1
A: Casein kinase I isoform delta
C: Tumor protein 63
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,21514
Polymers36,1442
Non-polymers1,07112
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3970 Å2
ΔGint-0 kcal/mol
Surface area15130 Å2
MethodPISA
2
B: Casein kinase I isoform delta
D: Tumor protein 63
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,00610
Polymers36,1442
Non-polymers8628
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2910 Å2
ΔGint-3 kcal/mol
Surface area14730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)171.779, 48.673, 87.631
Angle α, β, γ (deg.)90.000, 109.930, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-511-

HOH

21B-512-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12C
22D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A3 - 294
2010B3 - 294
1020C620 - 631
2020D620 - 631

NCS ensembles :
ID
1
2

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Components

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Protein / Protein/peptide , 2 types, 4 molecules ABCD

#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: Protein/peptide Tumor protein 63 / p63 / Chronic ulcerative stomatitis protein / CUSP / Keratinocyte transcription factor KET / ...p63 / Chronic ulcerative stomatitis protein / CUSP / Keratinocyte transcription factor KET / Transformation-related protein 63 / TP63 / Tumor protein p73-like / p73L / p40 / p51


Mass: 1719.545 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q9H3D4

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Non-polymers , 4 types, 244 molecules

#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 224 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.38 Å3/Da / Density % sol: 48.37 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop
Details: 10-20% PEG 3350, 0.1-0.2 M sodium sulfate and 0.1 M citrate, pH 4.6-5.9
PH range: 4.6-5.9

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 20, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.08→46.6 Å / Num. obs: 41053 / % possible obs: 99.3 % / Redundancy: 6 % / CC1/2: 0.996 / Rmerge(I) obs: 0.114 / Rpim(I) all: 0.05 / Rrim(I) all: 0.125 / Net I/σ(I): 8.6 / Num. measured all: 248293 / Scaling rejects: 27
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.08-2.196.20.83259970.8650.360.90799.6
6.58-46.65.80.05619.613580.9970.0240.06197.5

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Processing

Software
NameVersionClassification
Aimless0.7.2data scaling
REFMAC5.8.0232refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4HNF

4hnf


Resolution: 2.08→46.6 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.943 / SU B: 10.187 / SU ML: 0.128 / SU R Cruickshank DPI: 0.2041 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.204 / ESU R Free: 0.171
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2182 2017 4.9 %RANDOM
Rwork0.1754 ---
obs0.1775 39030 99.19 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 143.55 Å2 / Biso mean: 44.001 Å2 / Biso min: 25.45 Å2
Baniso -1Baniso -2Baniso -3
1--1.45 Å20 Å20.9 Å2
2---1.24 Å20 Å2
3---1.6 Å2
Refinement stepCycle: final / Resolution: 2.08→46.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4935 0 127 224 5286
Biso mean--52.29 47.95 -
Num. residues----608
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0135208
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174887
X-RAY DIFFRACTIONr_angle_refined_deg1.3231.6566992
X-RAY DIFFRACTIONr_angle_other_deg1.2611.58111311
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0915619
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.19820.638282
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.05415931
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7341544
X-RAY DIFFRACTIONr_chiral_restr0.0680.2639
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.025690
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021180
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A94100.1
12B94100.1
21C2210.18
22D2210.18
LS refinement shellResolution: 2.08→2.134 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.286 148 -
Rwork0.26 2905 -
all-3053 -
obs--99.61 %
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)
11.1335-0.3353-0.060.24430.06810.2463-0.0254-0.0950.14450.00530.0368-0.04960.0119-0.0146-0.01140.00190.00460.00610.1378-0.01320.1593-26.516419.644921.1253
20.7246-0.1443-0.02340.41650.01060.2343-0.073-0.0079-0.06050.05070.0269-0.01010.0205-0.01770.04610.0133-0.00190.02080.1092-0.00740.174615.64771.273117.9884
33.65042.3682-1.14562.05910.23513.98380.386-0.46210.08870.4823-0.26040.22870.21190.0298-0.12560.22470.00390.05910.34860.00650.1967-26.16411.128435.3028
43.19662.21710.94936.06453.08345.09260.1236-0.3625-0.35020.61950.1824-0.39930.68150.0733-0.3060.21670.0112-0.0570.18960.09020.181311.9491-5.533530.0147
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 294
2X-RAY DIFFRACTION2B3 - 294
3X-RAY DIFFRACTION3C579 - 593
4X-RAY DIFFRACTION4D581 - 593

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