9KYS | pdb_00009kys

the Ca2+/CaM-CASK-ARD complex

• PDB DOI: https://doi.org/10.2210/pdb9KYS/pdb

• Classification: STRUCTURAL PROTEIN
• Organism(s): Rattus norvegicus, Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-12-09 Released: 2025-11-12 
• Deposition Author(s): Li, W., Wang, Y., Feng, W.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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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

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

• PubMed: 41151710 
• DOI: https://doi.org/10.1016/j.ijbiomac.2025.148495
• Primary Citation 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.

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Organizational Affiliation: 
• State Key Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing, 100101, China. Electronic address: [e-mail].
State Key Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing, 100101, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China.
State Key Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing, 100101, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 46.25 kDa 
• Atom Count: 3,088 
• Modeled Residue Count: 346 
• Deposited Residue Count: 410 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Calmodulin-1	A, C	153	Rattus norvegicus	Mutation(s): 0  Gene Names: Calm1, Calm, Cam, Cam1, CaMI
UniProt
Find proteins for P0DP29 (Rattus norvegicus) Explore P0DP29  Go to UniProtKB:  P0DP29

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Peripheral plasma membrane protein CASK	B, D	52	Homo sapiens	Mutation(s): 0  Gene Names: CASK, LIN2 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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA (Subject of Investigation/LOI)	E [auth A], F [auth A], G [auth A], H [auth A], I [auth C], J [auth C], K [auth C], L [auth C]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

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 = 37.662	α = 90
b = 76.786	β = 90
c = 130.17	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
DENZO	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-11-12 
Deposition Author(s): Li, W., Wang, Y., Feng, W.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	32071191

Revision History  

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