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- PDB-8d7p: Human Casein kinase 1 delta in complex with phosphorylated Drosop... -

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Basic information

Entry
Database: PDB / ID: 8d7p
TitleHuman Casein kinase 1 delta in complex with phosphorylated Drosophila PERIOD peptide
Components
  • Casein kinase I isoform delta
  • Period circadian protein peptide
KeywordsTRANSFERASE/CIRCADIAN CLOCK PROTEIN / Transferase / CIRCADIAN CLOCK PROTEIN / Kinase / complex / TRANSFERASE-CIRCADIAN CLOCK PROTEIN complex
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
: / 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 ...: / 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
Casein kinase I isoform delta
Similarity search - Component
Biological speciesHomo sapiens (human)
Drosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsPhilpott, J.M. / Freeberg, A.M. / Tripathi, S.M. / Partch, C.L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: Mol.Cell / Year: 2023
Title: PERIOD phosphorylation leads to feedback inhibition of CK1 activity to control circadian period.
Authors: Philpott, J.M. / Freeberg, A.M. / Park, J. / Lee, K. / Ricci, C.G. / Hunt, S.R. / Narasimamurthy, R. / Segal, D.H. / Robles, R. / Cai, Y. / Tripathi, S. / McCammon, J.A. / Virshup, D.M. / ...Authors: Philpott, J.M. / Freeberg, A.M. / Park, J. / Lee, K. / Ricci, C.G. / Hunt, S.R. / Narasimamurthy, R. / Segal, D.H. / Robles, R. / Cai, Y. / Tripathi, S. / McCammon, J.A. / Virshup, D.M. / Chiu, J.C. / Lee, C. / Partch, C.L.
History
DepositionJun 7, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 17, 2023Provider: repository / Type: Initial release
Revision 1.1May 31, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 6, 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
D: Period circadian protein peptide
C: Period circadian protein peptide


Theoretical massNumber of molelcules
Total (without water)74,1534
Polymers74,1534
Non-polymers00
Water2,432135
1
A: Casein kinase I isoform delta
C: Period circadian protein peptide


Theoretical massNumber of molelcules
Total (without water)37,0772
Polymers37,0772
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1110 Å2
ΔGint-8 kcal/mol
Surface area14240 Å2
MethodPISA
2
B: Casein kinase I isoform delta
D: Period circadian protein peptide


Theoretical massNumber of molelcules
Total (without water)37,0772
Polymers37,0772
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1520 Å2
ΔGint-12 kcal/mol
Surface area14000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.780, 56.740, 65.940
Angle α, β, γ (deg.)108.93, 95.63, 108.69
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 34954.344 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CSNK1D, HCKID / Production host: Escherichia coli (E. coli)
References: UniProt: P48730, non-specific serine/threonine protein kinase, tau-protein kinase
#2: Protein/peptide Period circadian protein peptide


Mass: 2122.232 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Drosophila melanogaster (fruit fly)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 135 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.34 Å3/Da / Density % sol: 42.75 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 0.16M Succinic Acid (5.5) 23% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.03 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 10, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03 Å / Relative weight: 1
ReflectionResolution: 2.25→60.77 Å / Num. obs: 27457 / % possible obs: 93.7 % / Redundancy: 3.1 % / CC1/2: 0.98 / Rmerge(I) obs: 0.116 / Net I/σ(I): 5.5
Reflection shellResolution: 2.25→2.32 Å / Rmerge(I) obs: 0.312 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 2505 / CC1/2: 0.85

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Processing

Software
NameVersionClassification
PHENIX(1.15.2_3472)refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6PXO

6pxo


Resolution: 2.25→48.514 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 28.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2511 1303 4.75 %
Rwork0.1963 --
obs0.199 27427 93.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.25→48.514 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4864 0 0 135 4999
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094971
X-RAY DIFFRACTIONf_angle_d1.0696682
X-RAY DIFFRACTIONf_dihedral_angle_d8.6492974
X-RAY DIFFRACTIONf_chiral_restr0.059697
X-RAY DIFFRACTIONf_plane_restr0.006852
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.25-2.34010.29021390.22672858X-RAY DIFFRACTION92
2.3401-2.44660.34781510.2292894X-RAY DIFFRACTION93
2.4466-2.57560.32861630.22962853X-RAY DIFFRACTION93
2.5756-2.7370.28121240.22322891X-RAY DIFFRACTION94
2.737-2.94830.28521410.20792883X-RAY DIFFRACTION93
2.9483-3.24490.29011400.20962949X-RAY DIFFRACTION94
3.2449-3.71430.22051620.18472916X-RAY DIFFRACTION95
3.7143-4.6790.19841570.16292910X-RAY DIFFRACTION95
4.679-48.5140.20871260.18512970X-RAY DIFFRACTION95

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