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- PDB-8d7m: Human Casein kinase 1 delta in complex with phosphorylated human ... -

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Basic information

Entry
Database: PDB / ID: 8d7m
TitleHuman Casein kinase 1 delta in complex with phosphorylated human PERIOD2 FASP peptide
Components
  • Casein kinase I isoform delta
  • Period circadian protein homolog 2 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 / midbrain dopaminergic neuron differentiation / tau-protein kinase / 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 / midbrain dopaminergic neuron differentiation / tau-protein kinase / 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 / 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 / endoplasmic reticulum-Golgi intermediate compartment membrane / AURKA Activation by TPX2 / ciliary basal body / spindle microtubule / circadian regulation of gene expression / cellular response to nerve growth factor stimulus / regulation of circadian rhythm / Wnt signaling pathway / spindle / 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 / eukaryotic translation initiation factor 2alpha kinase activity / 3-phosphoinositide-dependent protein kinase activity / DNA-dependent protein kinase activity / ribosomal protein S6 kinase activity / histone H3S10 kinase activity / histone H2AXS139 kinase activity / histone H3S28 kinase activity / histone H4S1 kinase activity / histone H2BS14 kinase activity / histone H3T3 kinase activity / histone H2AS121 kinase activity / histone H2BS36 kinase activity / histone H3S57 kinase activity / histone H2AT120 kinase activity / AMP-activated protein kinase activity / Rho-dependent protein serine/threonine kinase activity / positive regulation of protein phosphorylation / histone H3T6 kinase activity / histone H2AS1 kinase activity / histone H3T11 kinase activity / histone H3T45 kinase activity / non-specific serine/threonine protein kinase / protein kinase activity / cadherin binding / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / centrosome / perinuclear region of cytoplasm / Golgi apparatus / signal transduction / nucleoplasm / ATP binding / nucleus / plasma membrane / cytosol
Similarity search - Function
: / Phosphorylase Kinase; domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site ...: / Phosphorylase Kinase; domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / 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)
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 13, 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: Period circadian protein homolog 2 peptide
D: Period circadian protein homolog 2 peptide


Theoretical massNumber of molelcules
Total (without water)72,1554
Polymers72,1554
Non-polymers00
Water4,576254
1
A: Casein kinase I isoform delta
C: Period circadian protein homolog 2 peptide


Theoretical massNumber of molelcules
Total (without water)36,0772
Polymers36,0772
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1160 Å2
ΔGint-13 kcal/mol
Surface area13940 Å2
MethodPISA
2
B: Casein kinase I isoform delta
D: Period circadian protein homolog 2 peptide


Theoretical massNumber of molelcules
Total (without water)36,0772
Polymers36,0772
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1170 Å2
ΔGint-12 kcal/mol
Surface area14170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.700, 135.970, 91.140
Angle α, β, γ (deg.)90.00, 94.33, 90.00
Int Tables number5
Space group name H-MC121

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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 homolog 2 peptide


Mass: 1123.022 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 254 / 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: 2.49 Å3/Da / Density % sol: 50.69 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / Details: 0.15 M Succinic Acid (5.5) 22% PEG 3350

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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: Oct 21, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03 Å / Relative weight: 1
ReflectionResolution: 2.25→46.155 Å / Num. obs: 31319 / % possible obs: 97.8 % / Redundancy: 5.7 % / CC1/2: 0.99 / Rmerge(I) obs: 0.152 / Net I/σ(I): 9.4
Reflection shellResolution: 2.25→2.32 Å / Rmerge(I) obs: 1.27 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 2767 / CC1/2: 0.55

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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→46.155 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2333 1589 5.08 %
Rwork0.1807 --
obs0.1835 31307 97.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.25→46.155 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4820 0 0 255 5075
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094928
X-RAY DIFFRACTIONf_angle_d1.1186630
X-RAY DIFFRACTIONf_dihedral_angle_d7.4922944
X-RAY DIFFRACTIONf_chiral_restr0.067694
X-RAY DIFFRACTIONf_plane_restr0.007840
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2501-2.32270.32641360.24282592X-RAY DIFFRACTION94
2.3227-2.40570.31261480.22492644X-RAY DIFFRACTION95
2.4057-2.5020.31181410.21222623X-RAY DIFFRACTION96
2.502-2.61590.26521370.20682663X-RAY DIFFRACTION96
2.6159-2.75380.2421310.18872701X-RAY DIFFRACTION98
2.7538-2.92630.24251360.1852713X-RAY DIFFRACTION98
2.9263-3.15220.26231410.19432744X-RAY DIFFRACTION99
3.1522-3.46930.21431470.17082764X-RAY DIFFRACTION99
3.4693-3.97110.22451520.16182762X-RAY DIFFRACTION100
3.9711-5.00220.19031500.15512756X-RAY DIFFRACTION100
5.0022-46.1550.21541700.1772756X-RAY DIFFRACTION99

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