8ZLW | pdb_00008zlw

Crystal Structure of RDGC IQ motif/dCaM Complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 
    0.254 (Depositor), 0.258 (DCC) 
  • R-Value Work: 
    0.216 (Depositor), 0.218 (DCC) 
  • R-Value Observed: 
    0.218 (Depositor) 

Starting Models: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


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

  • 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.


  • 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.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Maltodextrin-binding protein376Escherichia coli #1/H766Mutation(s): 0 
Gene Names: malEJW3994
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
CalmodulinB [auth N]153Drosophila melanogasterMutation(s): 0 
Gene Names: CamCG8472
UniProt
Find proteins for P62152 (Drosophila melanogaster)
Explore P62152 
Go to UniProtKB:  P62152
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UniProt GroupP62152
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Serine/threonine-protein phosphatase rdgCC [auth R]33Drosophila melanogasterMutation(s): 0 
Gene Names: rdgCCG44746
EC: 3.1.3.16
UniProt
Find proteins for P40421 (Drosophila melanogaster)
Explore P40421 
Go to UniProtKB:  P40421
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UniProt GroupP40421
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free:  0.254 (Depositor), 0.258 (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 = 52.664α = 90
b = 61.59β = 94.17
c = 88.002γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China31870746

Revision History  (Full details and data files)

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