9K6M | pdb_00009k6m

Crystal structure of the Dictyostelium discoideum mitochondrial calcium uptake protein (DdMICU)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 
    0.260 (Depositor), 0.260 (DCC) 
  • R-Value Work: 
    0.221 (Depositor), 0.221 (DCC) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Structure of MICU from non-metazoan Dictyostelium discoideum reveals unique characteristics.

Jin, M.Yang, J.Park, J.Kim, H.Eom, S.H.

(2025) Commun Biol 8: 782-782

  • DOI: https://doi.org/10.1038/s42003-025-08218-1
  • Primary Citation of Related Structures:  
    9K6M

  • PubMed Abstract: 

    In most eukaryotes, the mitochondrial calcium uniporter (MCU) mediates Ca 2+ influx into the mitochondrial matrix through a process regulated by MICUs and the EMRE. In Dictyostelium discoideum, a model organism for amoebozoans that lack an EMRE, the MCU complex consists solely of the MCU and MICU. Most likely, therefore, the mechanism by which DdMICU regulates the DdMCU differs from the extensively studied metazoan MCU-EMRE-MICU system. Here, we report the crystal structure of Ca 2+ -bound DdMICU at 2.5 Å resolution. Unlike human MICUs, which contain two Ca 2+ -binding EF-hand motifs, DdMICU possesses three EF-hand motifs, each with a submicromolar Ca 2+ binding affinity. The overall structure of DdMICU is comparable to that of human MICUs, and their well-conserved dimer interface interactions are similar. In addition to the face-to-face dimer observed in human MICUs, DdMICU forms a head-to-head dimer with multimeric states that equilibrate between tetrameric and dimeric forms, depending on the solution ionic strength. Moreover, the C-helix of DdMICU plays a critical role in membrane binding. These findings provide a molecular basis for the unique mechanism regulating Ca 2+ uptake by MICUs in an EMRE-free system and offer insight into the evolution and functional diversity of the MCU complex in non-metazoan organisms.


  • Organizational Affiliation
    • School of Life Sciences, Gwangju Institute of Science and Technology (GIST), Gwangju, Republic of Korea.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
EF-hand domain-containing protein
A, B
371Dictyostelium discoideumMutation(s): 0 
Gene Names: DDB_G0287825
UniProt
Find proteins for Q54JS1 (Dictyostelium discoideum)
Explore Q54JS1 
Go to UniProtKB:  Q54JS1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ54JS1
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free:  0.260 (Depositor), 0.260 (DCC) 
  • R-Value Work:  0.221 (Depositor), 0.221 (DCC) 
Space Group: I 41 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 103.937α = 90
b = 103.937β = 90
c = 297.505γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
SHELXphasing
PHASERphasing
REFMACrefinement
PHENIXrefinement
Cootmodel building

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Research Foundation (NRF, Korea)Korea, Republic OfNRF-2021R1A2C1006267
National Research Foundation (NRF, Korea)Korea, Republic OfNo. RS-2024-00344154

Revision History  (Full details and data files)

  • Version 1.0: 2025-07-30
    Type: Initial release