8ZLW | pdb_00008zlw

Crystal Structure of RDGC IQ motif/dCaM Complex

• PDB DOI: https://doi.org/10.2210/pdb8ZLW/pdb

• Classification: PROTEIN BINDING
• Organism(s): Escherichia coli #1/H766, Drosophila melanogaster
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): No 


• Deposited: 2024-05-21 Released: 2025-04-02 
• Deposition Author(s): Liu, J., Ding, Y.Z., Li, J.C., Liu, W.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.254 (Depositor), 0.259 (DCC) 
• R-Value Work: 
  0.216 (Depositor), 0.218 (DCC) 
• R-Value Observed: 
  0.218 (Depositor) 

Starting Models: 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 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.

---

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 3-mer - A1B1C1 

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

Macromolecule Content 

• Total Structure Weight: 62.36 kDa 
• Atom Count: 4,219 
• Modeled Residue Count: 539 
• Deposited Residue Count: 562 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Maltodextrin-binding protein	A	376	Escherichia coli #1/H766	Mutation(s): 0  Gene Names: malE, JW3994
UniProt
Find proteins for A0ACD6BAW2 (Serratia sp. (strain FS14)) Explore A0ACD6BAW2  Go to UniProtKB:  A0ACD6BAW2

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Calmodulin	B [auth N]	153	Drosophila melanogaster	Mutation(s): 0  Gene Names: Cam, CG8472
UniProt
Find proteins for P62152 (Drosophila melanogaster) Explore P62152  Go to UniProtKB:  P62152

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine/threonine-protein phosphatase rdgC	C [auth R]	33	Drosophila melanogaster	Mutation(s): 0  Gene Names: rdgC, CG44746 EC: 3.1.3.16
UniProt
Find proteins for P40421 (Drosophila melanogaster) Explore P40421  Go to UniProtKB:  P40421

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.254 (Depositor), 0.259 (DCC) 
• R-Value Work:  0.216 (Depositor), 0.218 (DCC) 
• R-Value Observed: 0.218 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.664	α = 90
b = 61.59	β = 94.17
c = 88.002	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-04-02 
Deposition Author(s): Liu, J., Ding, Y.Z., Li, J.C., Liu, W.

---

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

Revision History  

• Version 1.0: 2025-04-02
  Type: Initial release
  
• Version 1.1: 2025-04-09
  Changes: Database references