9KYS | pdb_00009kys

the Ca2+/CaM-CASK-ARD complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.76 Å
  • R-Value Free: 
    0.231 (Depositor), 0.233 (DCC) 
  • R-Value Work: 
    0.197 (Depositor), 0.199 (DCC) 
  • R-Value Observed: 
    0.199 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural basis for the Ca 2+ /CaM-mediated regulation of CASK-CaMK.

Li, W.Wang, Y.Feng, W.

(2025) Int J Biol Macromol 332: 148495-148495

  • DOI: https://doi.org/10.1016/j.ijbiomac.2025.148495
  • Primary Citation of Related Structures:  
    8Y68, 9KYS, 9M5Y, 9M6G

  • PubMed Abstract: 

    As a member of the Ca 2+ /CaM-dependent protein kinase family, CASK contains an N-terminal CaMK domain that is regulated by Ca 2+ -bound CaM, while the underlying mechanism remains to be elucidated. Here, we determine the crystal structures of CASK-CaMK in different states: apo CASK-CaMK, CASK-CaMK in complex with CaM (the CaM-CASK complex) and CASK-CaMK in complex with CaM and Mint1 (the CaM-CASK-Mint1 complex). CASK-CaMK exhibits an inhibitory conformation with the αR2 helix of the autoregulatory domain (ARD) inserting into its nucleotide-binding pocket. Contrary to conventional CaM-mediated binding paradigms, in the CaM-CASK complex, only the C-terminal lobe of CaM (C-CaM) engages with the ARD of CASK-CaMK. This C-CaM binding induces the formation of an extended ARD α-helix that reshapes the nucleotide-binding pocket of CASK-CaMK to enhance its nucleotide-binding capacity. Correspondingly, in the CaM-CASK-Mint1 complex, similar C-CaM binding to CASK-CaMK leads to a slight opening of the CASK-Mint1 complex, and only the Mint1-CID (CASK-interaction domain) core is resolved association with CASK-CaMK. Taken together, CaM likely regulates CASK-CaMK through a C-CaM-dependent mechanism to tune its nucleotide-binding and target-recognition capacities.


  • Organizational Affiliation
    • State Key Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing, 100101, China. Electronic address: liwei@ibp.ac.cn.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Calmodulin-1
A, C
153Rattus norvegicusMutation(s): 0 
Gene Names: Calm1CalmCamCam1CaMI
UniProt
Find proteins for P0DP29 (Rattus norvegicus)
Explore P0DP29 
Go to UniProtKB:  P0DP29
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0DP29
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Peripheral plasma membrane protein CASK
B, D
52Homo sapiensMutation(s): 0 
Gene Names: CASKLIN2
EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for O14936 (Homo sapiens)
Explore O14936 
Go to UniProtKB:  O14936
PHAROS:  O14936
GTEx:  ENSG00000147044 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO14936
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.76 Å
  • R-Value Free:  0.231 (Depositor), 0.233 (DCC) 
  • R-Value Work:  0.197 (Depositor), 0.199 (DCC) 
  • R-Value Observed: 0.199 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 37.662α = 90
b = 76.786β = 90
c = 130.17γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
DENZOdata reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China32071191

Revision History  (Full details and data files)

  • Version 1.0: 2025-11-12
    Type: Initial release
  • Version 1.1: 2025-11-19
    Changes: Database references