7CLT

Crystal structure of the EFhd1/Swiprosin-2, a mitochondrial actin-binding protein


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.07 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.210 

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This is version 1.3 of the entry. See complete history


Literature

Structural and Biochemical Characterization of EFhd1/Swiprosin-2, an Actin-Binding Protein in Mitochondria.

Mun, S.A.Park, J.Park, K.R.Lee, Y.Kang, J.Y.Park, T.Jin, M.Yang, J.Jun, C.D.Eom, S.H.

(2020) Front Cell Dev Biol 8: 628222-628222

  • DOI: https://doi.org/10.3389/fcell.2020.628222
  • Primary Citation of Related Structures:  
    7CLT

  • PubMed Abstract: 

    Ca 2+ regulates several cellular functions, including signaling events, energy production, and cell survival. These cellular processes are mediated by Ca 2+ -binding proteins, such as EF-hand superfamily proteins. Among the EF-hand superfamily proteins, allograft inflammatory factor-1 (AIF-1) and swiprosin-1/EF-hand domain-containing protein 2 (EFhd2) are cytosolic actin-binding proteins. AIF-1 modulates the cytoskeleton and increases the migration of immune cells. EFhd2 is also a cytoskeletal protein implicated in immune cell activation and brain cell functions. EFhd1, a mitochondrial fraternal twin of EFhd2, mediates neuronal and pro-/pre-B cell differentiation and mitoflash activation. Although EFhd1 is important for maintaining mitochondrial morphology and energy synthesis, its mechanism of action remains unclear. Here, we report the crystal structure of the EFhd1 core domain comprising a C-terminus of a proline-rich region, two EF-hand domains, and a ligand mimic helix. Structural comparisons of EFhd1, EFhd2, and AIF-1 revealed similarities in their overall structures. In the structure of the EFhd1 core domain, two Zn 2+ ions were observed at the interface of the crystal contact, suggesting the possibility of Zn 2+ -mediated multimerization. In addition, we found that EFhd1 has Ca 2+ -independent β-actin-binding and Ca 2+ -dependent β-actin-bundling activities. These findings suggest that EFhd1, an actin-binding and -bundling protein in the mitochondria, may contribute to the Ca 2+ -dependent regulation of mitochondrial morphology and energy synthesis.


  • Organizational Affiliation

    School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju, South Korea.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
EF-hand domain-containing protein D1136Mus musculusMutation(s): 0 
Gene Names: Efhd1Sws2
UniProt
Find proteins for Q9D4J1 (Mus musculus)
Explore Q9D4J1 
Go to UniProtKB:  Q9D4J1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9D4J1
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.07 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.210 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 31.77α = 90
b = 47.556β = 90
c = 87.199γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Cootmodel building
HKL-2000data scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other privateKorea, Republic Of1

Revision History  (Full details and data files)

  • Version 1.0: 2021-01-06
    Type: Initial release
  • Version 1.1: 2021-01-13
    Changes: Structure summary
  • Version 1.2: 2021-02-17
    Changes: Database references
  • Version 1.3: 2023-11-29
    Changes: Data collection, Database references, Refinement description