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- PDB-6ru8: Crystal structure of Casein Kinase I delta (CK1d) in complex with... -

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Basic information

Entry
Database: PDB / ID: 6ru8
TitleCrystal structure of Casein Kinase I delta (CK1d) in complex with triple phosphorylated p63 PAD3P 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 / squamous basal epithelial stem cell differentiation involved in prostate gland acinus development / negative regulation of keratinocyte differentiation / negative regulation of intracellular estrogen receptor signaling pathway / polarized epithelial cell differentiation / proximal/distal pattern formation / protein localization to Golgi apparatus / positive regulation of fibroblast apoptotic process / positive regulation of cell cycle G1/S phase transition / skin morphogenesis / COPII vesicle coating / cranial skeletal system development / midbrain dopaminergic neuron differentiation / sympathetic nervous system development / microtubule nucleation / post-anal tail morphogenesis / tau-protein kinase / non-motile cilium assembly / protein localization to cilium / 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 / Regulation of TP53 Activity through Association with Co-factors / hair follicle morphogenesis / WW domain binding / tau-protein kinase activity / regulation of epidermal cell division / positive regulation of Notch signaling pathway / TP53 regulates transcription of several additional cell death genes whose specific roles in p53-dependent apoptosis remain uncertain / TP53 Regulates Transcription of Caspase Activators and Caspases / epithelial cell development / positive regulation of stem cell proliferation / 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 / establishment of skin barrier / spindle assembly / Pyroptosis / Major pathway of rRNA processing in the nucleolus and cytosol / positive regulation of osteoblast differentiation / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of mitotic centrosome proteins and complexes / keratinocyte differentiation / MDM2/MDM4 family protein binding / Notch signaling pathway / 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 / spindle microtubule / determination of adult lifespan / promoter-specific chromatin binding / TP53 Regulates Metabolic Genes / RNA polymerase II transcription regulatory region sequence-specific DNA binding / positive regulation of apoptotic signaling pathway / protein tetramerization / circadian regulation of gene expression / regulation of circadian rhythm / Wnt signaling pathway / spindle / endocytosis / cellular senescence / Regulation of PLK1 Activity at G2/M Transition / positive regulation of canonical Wnt signaling pathway / p53 binding / Circadian Clock / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / DNA-binding transcription activator activity, RNA polymerase II-specific / spermatogenesis / neuron apoptotic process / transcription by RNA polymerase II / damaged DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / non-specific serine/threonine protein kinase / protein kinase activity / cadherin binding / chromatin remodeling / positive regulation of protein phosphorylation / 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 ...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
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: 1.92 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 / 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 / _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
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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
E: Tumor protein 63
F: Tumor protein 63
G: Tumor protein 63
H: Tumor protein 63
hetero molecules


Theoretical massNumber of molelcules
Total (without water)146,34435
Polymers143,1848
Non-polymers3,16027
Water9,458525
1
A: Casein kinase I isoform delta
E: Tumor protein 63
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,65210
Polymers35,7962
Non-polymers8578
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2330 Å2
ΔGint-26 kcal/mol
Surface area14270 Å2
MethodPISA
2
B: Casein kinase I isoform delta
F: Tumor protein 63
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,68610
Polymers35,7962
Non-polymers8918
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3460 Å2
ΔGint-35 kcal/mol
Surface area14510 Å2
MethodPISA
3
C: Casein kinase I isoform delta
G: Tumor protein 63
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,5969
Polymers35,7962
Non-polymers8007
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3040 Å2
ΔGint-16 kcal/mol
Surface area13930 Å2
MethodPISA
4
D: Casein kinase I isoform delta
H: Tumor protein 63
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,4096
Polymers35,7962
Non-polymers6134
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2660 Å2
ΔGint-22 kcal/mol
Surface area14650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.727, 84.131, 89.287
Angle α, β, γ (deg.)108.600, 105.830, 91.570
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: _ / Beg auth comp-ID: GLU / Beg label comp-ID: GLU / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: _ / Auth seq-ID: 2 - 294 / Label seq-ID: 4 - 296

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13AA
23DD
14BB
24CC
15BB
25DD
16CC
26DD

NCS ensembles :
ID
1
2
3
4
5
6

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Components

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Protein / Protein/peptide , 2 types, 8 molecules ABCDEFGH

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


Mass: 34424.805 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
#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: 1371.088 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q9H3D4

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Non-polymers , 5 types, 552 molecules

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


Mass: 427.201 Da / Num. of mol.: 4 / 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.: 18 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#6: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 525 / 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: 2.31 Å3/Da / Density % sol: 46.81 %
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: 1.92→48.84 Å / Num. obs: 90338 / % possible obs: 92.2 % / Redundancy: 3.9 % / CC1/2: 0.994 / Rmerge(I) obs: 0.096 / Rpim(I) all: 0.056 / Rrim(I) all: 0.111 / Net I/σ(I): 7.2 / Num. measured all: 348255 / Scaling rejects: 149
Reflection shell

Diffraction-ID: 1 / Redundancy: 3.9 %

Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.92-1.990.6762.188190.8430.3970.78591.5
7.44-48.840.06213.616700.9930.0360.07199.4

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Processing

Software
NameVersionClassification
Aimless0.7.3data scaling
REFMAC5.8.0232refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4HNF

4hnf


Resolution: 1.92→48.84 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.946 / SU B: 7.175 / SU ML: 0.102 / SU R Cruickshank DPI: 0.1705 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.171 / ESU R Free: 0.149
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2106 4513 5 %RANDOM
Rwork0.1718 ---
obs0.1737 85820 92.16 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 109.91 Å2 / Biso mean: 37.523 Å2 / Biso min: 19.65 Å2
Baniso -1Baniso -2Baniso -3
1--0.46 Å20.14 Å20.05 Å2
2--1.41 Å21.22 Å2
3----1.31 Å2
Refinement stepCycle: final / Resolution: 1.92→48.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9796 0 197 525 10518
Biso mean--41.74 43.43 -
Num. residues----1206
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.01310305
X-RAY DIFFRACTIONr_bond_other_d0.0010.0179580
X-RAY DIFFRACTIONr_angle_refined_deg1.2881.65113890
X-RAY DIFFRACTIONr_angle_other_deg1.2731.58122178
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.72551235
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.02420.732560
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.952151836
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9731586
X-RAY DIFFRACTIONr_chiral_restr0.0690.21270
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0211328
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022342
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A99410.07
12B99410.07
21A94900.09
22C94900.09
31A97580.09
32D97580.09
41B94950.09
42C94950.09
51B97650.09
52D97650.09
61C97420.07
62D97420.07
LS refinement shellResolution: 1.92→1.97 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.322 327 -
Rwork0.262 6334 -
all-6661 -
obs--91.74 %
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)
10.2642-0.23130.18550.4066-0.3150.98020.01330.00240.0169-0.0286-0.0211-0.0020.08920.08690.00780.05330.02470.00660.02260.00810.007819.7691-28.968417.3454
20.33680.1899-0.14570.1941-0.22270.7009-0.0072-0.0013-0.01770.0085-0.0046-0.0083-0.07570.05970.01170.0674-0.00510.01080.02370.00930.00721.8116-55.509-18.2609
30.38560.2063-0.14640.1962-0.16110.65580.0174-0.0150.0292-0.0220.03620.0512-0.0371-0.0528-0.05360.03540.00660.00170.05070.03310.02633.5205-72.845920.5156
40.4121-0.22570.18310.1844-0.19650.90470.02860.0048-0.04640.01380.05070.06740.0634-0.0762-0.07930.0360.01610.01050.05680.04510.0421.1764-11.5162-21.1079
56.3823-0.8604-0.12280.89240.85841.0322-0.0529-0.1237-0.24240.08210.05990.03990.1954-0.0052-0.0070.1309-0.0363-0.00490.03930.01980.049512.0727-40.42713.3021
67.587-0.9251-0.57990.318-0.11550.8528-0.05290.11380.39950.01860.0923-0.0082-0.18740.0129-0.03940.0991-0.0179-0.00480.08170.02810.043516.5696-44.0639-14.5828
75.63052.99860.27453.0339-0.95660.86380.0875-0.33380.09510.2057-0.11070.0439-0.1212-0.08690.02320.10810.03140.03090.1289-0.04490.0858-0.8568-59.179121.8657
82.898-1.8127-0.27375.62050.28741.9842-0.09650.5896-0.25860.1173-0.23440.32760.1205-0.28650.33090.0884-0.0405-0.01220.1546-0.07610.1026-2.8954-25.3934-22.9384
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 294
2X-RAY DIFFRACTION2B2 - 294
3X-RAY DIFFRACTION3C2 - 294
4X-RAY DIFFRACTION4D2 - 294
5X-RAY DIFFRACTION5E582 - 591
6X-RAY DIFFRACTION6F582 - 593
7X-RAY DIFFRACTION7G582 - 590
8X-RAY DIFFRACTION8H582 - 590

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