9B3S | pdb_00009b3s

Crystal structure of casein kinase 1 delta 1 with tethered phosphorylated tail


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 
    0.247 (Depositor), 0.249 (DCC) 
  • R-Value Work: 
    0.196 (Depositor), 0.202 (DCC) 
  • R-Value Observed: 
    0.199 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 9B3S

This is version 1.1 of the entry. See complete history

Literature

Isoform-specific C-terminal phosphorylation drives autoinhibition of Casein kinase 1.

Harold, R.L.Tulsian, N.K.Narasimamurthy, R.Yaitanes, N.Ayala Hernandez, M.G.Lee, H.W.Crosby, P.Tripathi, S.M.Virshup, D.M.Partch, C.L.

(2024) Proc Natl Acad Sci U S A 121: e2415567121-e2415567121

  • DOI: https://doi.org/10.1073/pnas.2415567121
  • Primary Citation Related Structures: 
    9B3S

  • PubMed Abstract: 

    Casein kinase 1δ (CK1δ) controls essential biological processes including circadian rhythms and wingless-related integration site (Wnt) signaling, but how its activity is regulated is not well understood. CK1δ is inhibited by autophosphorylation of its intrinsically disordered C-terminal tail. Two CK1 splice variants, δ1 and δ2, are known to have very different effects on circadian rhythms. These variants differ only in the last 16 residues of the tail, referred to as the extreme C termini (XCT), but with marked changes in potential phosphorylation sites. Here, we test whether the XCT of these variants have different effects in autoinhibition of the kinase. Using NMR and hydrogen/deuterium exchange mass spectrometry, we show that the δ1 XCT is preferentially phosphorylated by the kinase and the δ1 tail makes more extensive interactions across the kinase domain. Mutation of δ1-specific XCT phosphorylation sites increases kinase activity both in vitro and in cells and leads to changes in the circadian period, similar to what is reported in vivo. Mechanistically, loss of the phosphorylation sites in XCT disrupts tail interaction with the kinase domain. δ1 autoinhibition relies on conserved anion-binding sites around the CK1 active site, demonstrating a common mode of product inhibition of CK1δ. These findings demonstrate how a phosphorylation cycle controls the activity of this essential kinase.


  • Organizational Affiliation
    • Department of Chemistry & Biochemistry, University of California Santa Cruz, Santa Cruz, CA 95064.

Macromolecule Content 

  • Total Structure Weight: 74.12 kDa 
  • Atom Count: 5,031 
  • Modeled Residue Count: 599 
  • Deposited Residue Count: 640 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Casein kinase I isoform delta
A, B
320Homo sapiensMutation(s): 0 
Gene Names: CSNK1DHCKID
EC: 2.7.11.1 (PDB Primary Data), 2.7.11.26 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P48730 (Homo sapiens)
Explore P48730 
Go to UniProtKB:  P48730
PHAROS:  P48730
GTEx:  ENSG00000141551 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP48730
Sequence Annotations
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Reference Sequence

Small Molecules

Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
SEP
Query on SEP
A, B
L-PEPTIDE LINKINGC3 H8 N O6 PSER

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free:  0.247 (Depositor), 0.249 (DCC) 
  • R-Value Work:  0.196 (Depositor), 0.202 (DCC) 
  • R-Value Observed: 0.199 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.452α = 90
b = 135.117β = 94.36
c = 90.602γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM107069

Revision History  (Full details and data files)

  • Version 1.0: 2024-09-25
    Type: Initial release
  • Version 1.1: 2024-10-16
    Changes: Database references, Structure summary