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- PDB-6ru6: Crystal structure of Casein Kinase I delta (CK1d) in complex with... -

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Basic information

Entry
Database: PDB / ID: 6ru6
TitleCrystal structure of Casein Kinase I delta (CK1d) in complex with monophosphorylated p63 PAD1P 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 / prostatic bud formation / negative regulation of mesoderm development / female genitalia morphogenesis / positive regulation of non-canonical Wnt signaling pathway / establishment of planar polarity / positive regulation of keratinocyte proliferation ...ectoderm and mesoderm interaction / epidermal cell division / cloacal septation / positive regulation of somatic stem cell population maintenance / prostatic bud formation / negative regulation of mesoderm development / female genitalia morphogenesis / positive regulation of non-canonical Wnt signaling pathway / establishment of planar polarity / positive regulation of keratinocyte proliferation / negative regulation of keratinocyte differentiation / squamous basal epithelial stem cell differentiation involved in prostate gland acinus development / polarized epithelial cell differentiation / negative regulation of intracellular estrogen receptor signaling pathway / proximal/distal pattern formation / protein localization to Golgi apparatus / positive regulation of fibroblast apoptotic process / positive regulation of cell cycle G1/S phase transition / WW domain binding / skin morphogenesis / cranial skeletal system development / midbrain dopaminergic neuron differentiation / COPII vesicle coating / sympathetic nervous system development / microtubule nucleation / post-anal tail morphogenesis / tau-protein kinase / non-motile cilium assembly / protein localization to cilium / embryonic forelimb morphogenesis / 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 / Regulation of TP53 Activity through Association with Co-factors / hair follicle morphogenesis / tau-protein kinase activity / positive regulation of Notch signaling pathway / regulation of epidermal cell division / TP53 regulates transcription of several additional cell death genes whose specific roles in p53-dependent apoptosis remain uncertain / positive regulation of stem cell proliferation / epithelial cell development / TP53 Regulates Transcription of Caspase Activators and Caspases / Golgi organization / odontogenesis of dentin-containing tooth / negative regulation of cellular senescence / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / keratinocyte proliferation / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / Major pathway of rRNA processing in the nucleolus and cytosol / spindle assembly / establishment of skin barrier / Pyroptosis / positive regulation of osteoblast differentiation / keratinocyte differentiation / MDM2/MDM4 family protein binding / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Notch signaling pathway / 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 / stem cell proliferation / skeletal system development / determination of adult lifespan / promoter-specific chromatin binding / positive regulation of apoptotic signaling pathway / TP53 Regulates Metabolic Genes / protein tetramerization / RNA polymerase II transcription regulatory region sequence-specific DNA binding / circadian regulation of gene expression / spindle microtubule / regulation of circadian rhythm / Wnt signaling pathway / spindle / endocytosis / Regulation of PLK1 Activity at G2/M Transition / cellular senescence / Circadian Clock / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / positive regulation of canonical Wnt signaling pathway / p53 binding / spermatogenesis / DNA-binding transcription activator activity, RNA polymerase II-specific / neuron apoptotic process / transcription by RNA polymerase II / damaged DNA binding / non-specific serine/threonine protein kinase / DNA-binding transcription factor activity, RNA polymerase II-specific / protein kinase activity / chromatin remodeling / cadherin binding / positive regulation of protein phosphorylation / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor 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 / SAM domain (Sterile alpha motif) ...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 / 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
PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / Casein kinase I isoform delta / Tumor protein 63
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
C: Tumor protein 63
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,86815
Polymers70,2423
Non-polymers1,62612
Water2,504139
1
A: Casein kinase I isoform delta
C: Tumor protein 63
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,78011
Polymers35,8172
Non-polymers9639
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2990 Å2
ΔGint2 kcal/mol
Surface area14580 Å2
MethodPISA
2
B: Casein kinase I isoform delta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,0884
Polymers34,4251
Non-polymers6633
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1220 Å2
ΔGint-11 kcal/mol
Surface area14440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)171.937, 48.924, 85.199
Angle α, β, γ (deg.)90.000, 109.720, 90.000
Int Tables number5
Space group name H-MC121
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

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Protein / Protein/peptide , 2 types, 3 molecules ABC

#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: 1392.387 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q9H3D4

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Non-polymers , 5 types, 151 molecules

#3: Chemical ChemComp-ACP / PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / ADENOSINE-5'-[BETA, GAMMA-METHYLENE]TRIPHOSPHATE


Mass: 505.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H18N5O12P3 / Comment: AMP-PCP, energy-carrying molecule analogue*YM
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 139 / 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: 2.4 Å3/Da / Density % sol: 48.77 %
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: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 27, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.05→49.26 Å / Num. obs: 42000 / % possible obs: 99.4 % / Redundancy: 5 % / CC1/2: 0.996 / Rmerge(I) obs: 0.117 / Rpim(I) all: 0.057 / Rrim(I) all: 0.131 / Net I/σ(I): 8.3 / Num. measured all: 208293 / Scaling rejects: 6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.05-2.125.10.784241260.8370.3820.87699.5
7.94-49.264.60.05221.17680.9970.0260.05897.1

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Processing

Software
NameVersionClassification
Aimless0.7.3data scaling
REFMAC5.8.0238refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4HNF

4hnf


Resolution: 2.05→49.26 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.915 / SU B: 15.451 / SU ML: 0.189 / SU R Cruickshank DPI: 0.219 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.219 / ESU R Free: 0.189
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.257 2074 4.9 %RANDOM
Rwork0.2108 ---
obs0.2131 39925 99.29 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 147.12 Å2 / Biso mean: 50.924 Å2 / Biso min: 27.26 Å2
Baniso -1Baniso -2Baniso -3
1--3.58 Å20 Å21.77 Å2
2---2.25 Å2-0 Å2
3---3.63 Å2
Refinement stepCycle: final / Resolution: 2.05→49.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4697 0 100 139 4936
Biso mean--75 50.12 -
Num. residues----574
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0134925
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174627
X-RAY DIFFRACTIONr_angle_refined_deg1.2781.6736621
X-RAY DIFFRACTIONr_angle_other_deg1.1661.59110698
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4485575
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.44920.543276
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.31115895
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.6831544
X-RAY DIFFRACTIONr_chiral_restr0.0580.2603
X-RAY DIFFRACTIONr_gen_planes_refined0.010.025368
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021134
Refine LS restraints NCS

Ens-ID: 1 / Number: 8992 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.1 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.05→2.103 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.321 142 -
Rwork0.318 2947 -
all-3089 -
obs--99.81 %
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)
13.7448-0.3619-0.45250.62671.0472.667-0.1672-0.57880.18290.07680.0768-0.1130.3143-0.1030.09040.0564-0.00780.04680.1569-0.06980.13-41.08230.26429.005
21.0461-0.13180.0920.30050.05730.1264-0.0216-0.07290.122-0.0016-0.0165-0.00790.0232-0.0330.0380.02660.00560.03620.1151-0.01950.0782-23.11917.09819.102
30.9664-0.08470.73244.3969-0.26451.1148-0.0001-0.0569-0.09910.3583-0.0663-0.0279-0.0152-0.06630.06650.0432-0.00980.03820.0839-0.04420.178228.514-12.60116.108
41.7832-0.1980.06640.25460.21080.7009-0.0425-0.0596-0.16840.02540.04230.02010.0371-0.06280.00020.0238-0.00070.04280.0922-0.00380.089511.117.11418.412
54.6486-5.9696-4.71027.67566.05434.8554-0.2748-0.075-0.0040.37460.14240.02630.3423-0.03650.13240.0576-0.04150.08580.3732-0.09550.1918-27.98510.09132.266
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 62
2X-RAY DIFFRACTION2A63 - 294
3X-RAY DIFFRACTION3B3 - 85
4X-RAY DIFFRACTION4B86 - 294
5X-RAY DIFFRACTION5C579 - 586

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