8ZLX | pdb_00008zlx

Crystal Structure of mPPEF2 IQ motif/apo-CaM Complex

• PDB DOI: https://doi.org/10.2210/pdb8ZLX/pdb

• Classification: PROTEIN BINDING
• Organism(s): Mus musculus
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): No 


• Deposited: 2024-05-21 Released: 2025-03-05 
• Deposition Author(s): Liu, J., Ding, Y.Z., Li, J.C., Liu, W.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.291 (Depositor), 0.289 (DCC) 
• R-Value Work: 
  0.208 (Depositor), 0.212 (DCC) 
• R-Value Observed: 
  0.212 (Depositor) 

Starting Model: experimental

Literature

Structural insights into the dual Ca 2+ -sensor-mediated activation of the PPEF phosphatase family.

Liu, J., Wu, C., Liu, Y., Chen, Q., Ding, Y., Lin, Z., Pan, L., Xiao, K., Li, J., Liu, Z., Liu, W.

(2025) Nat Commun 16: 3120-3120

• PubMed: 40169586 
• DOI: https://doi.org/10.1038/s41467-025-58261-z
• Primary Citation of Related Structures:  
  8ZLW, 8ZLX


• PubMed Abstract: 
  

  Serine/threonine-protein phosphatases with EF-hands (PPEFs) are a family of highly conserved proteins implicated in cancer and neuronal degeneration. The initially characterized member, Drosophila melanogaster retinal degeneration C (RDGC) contains a calmodulin (CaM)-interacting extended-IQ motif and a Ca ²⁺ -binding EF-like/EF-hand tandem. However, the molecular regulation of PPEF is poorly understood. In this study, we use cryogenic-electron microscopy to delineate the structures of the RDGC/CaM holoenzyme. In the absence of Ca ²⁺ , CaM and the EF-like/EF-hand tandem allow the extended-IQ motif to block substrate access to the catalytic sites, constituting an auto-inhibitory mechanism. Upon Ca ²⁺ binding, CaM and the EF-like/EF-hand tandem drive drastic conformational changes in the extended-IQ motif to unlock the catalytic sites. This dual Ca ²⁺ -sensor-mediated activation is evolutionarily conserved in mammals. This study provides mechanistic insight into the molecular activation of PPEFs, paving the way for the development of therapeutic strategies for PPEF-related human diseases.

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Organizational Affiliation: 
• Shenzhen Key Laboratory for Neuronal Structural Biology, Biomedical Research Institute, Shenzhen Peking University-The Hong Kong University of Science and Technology Medical Center, Shenzhen, 518036, Guangdong, China.
Department of Immunology and Microbiology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, Guangdong, China.
Institute for Biological Electron Microscopy, Southern University of Science and Technology, Shenzhen, 518055, Guangdong, China.
State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, 200032, China.
HKUST Shenzhen-Hong Kong Collaborative Innovation Research Institute, Futian, Shenzhen, China.
Innovation Centre of Ministry of Education for Development and Diseases, School of Medicine, South China University of Technology, Guangzhou, 510006, Guangdong, China. [e-mail].
Department of Immunology and Microbiology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, Guangdong, China. [e-mail].
Institute for Biological Electron Microscopy, Southern University of Science and Technology, Shenzhen, 518055, Guangdong, China. [e-mail].
Shenzhen Key Laboratory of Biomolecular Assembling and Regulation, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, Guangdong, China. [e-mail].
Shenzhen Key Laboratory for Neuronal Structural Biology, Biomedical Research Institute, Shenzhen Peking University-The Hong Kong University of Science and Technology Medical Center, Shenzhen, 518036, Guangdong, China. [e-mail].
Institute of Geriatric Medicine, Peking University Shenzhen Hospital, Shenzhen Peking University-The Hong Kong University of Science and Technology Medical Center, Shenzhen, 518036, China. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 8-mer - A4B4 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 8-mer - A4B3C1 

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

Macromolecule Content 

• Total Structure Weight: 81.22 kDa 
• Atom Count: 5,059 
• Modeled Residue Count: 662 
• Deposited Residue Count: 716 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Calmodulin (CaM)	A [auth B], B [auth D], E [auth C], H [auth A]	155	Mus musculus	Mutation(s): 0  Gene Names: CALM3
UniProt
Find proteins for A0A7N4P457 (Sarcophilus harrisii) Explore A0A7N4P457  Go to UniProtKB:  A0A7N4P457

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine/threonine-protein phosphatase with EF-hands 2	C [auth d], D [auth a], F [auth b], G [auth c]	24	Mus musculus	Mutation(s): 0  Gene Names: Ppef2 EC: 3.1.3.16
UniProt
Find proteins for O35385 (Mus musculus) Explore O35385  Go to UniProtKB:  O35385

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.291 (Depositor), 0.289 (DCC) 
• R-Value Work:  0.208 (Depositor), 0.212 (DCC) 
• R-Value Observed: 0.212 (Depositor) 

Space Group: P 4₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 134.451	α = 90
b = 134.451	β = 90
c = 35.944	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-3000	data scaling
HKL-3000	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-03-05 
Deposition Author(s): Liu, J., Ding, Y.Z., Li, J.C., Liu, W.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	31870746

Revision History  

• Version 1.0: 2025-03-05
  Type: Initial release
  
• Version 1.1: 2025-04-09
  Changes: Database references