7YGW

Crystal structure of the Zn2+-bound EFhd1/Swiprosin-2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.72 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.199 

Starting Model: experimental
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Literature

Structural and biochemical insights into Zn 2+ -bound EF-hand proteins, EFhd1 and EFhd2.

Mun, S.A.Park, J.Kang, J.Y.Park, T.Jin, M.Yang, J.Eom, S.H.

(2023) IUCrJ 10: 233-245

  • DOI: https://doi.org/10.1107/S2052252523001501
  • Primary Citation of Related Structures:  
    7YGV, 7YGW, 7YGY

  • PubMed Abstract: 

    EF-hand proteins, which contain a Ca 2+ -binding EF-hand motif, are involved in regulating diverse cellular functions. Ca 2+ binding induces conformational changes that modulate the activities of EF-hand proteins. Moreover, these proteins occasionally modify their activities by coordinating metals other than Ca 2+ , including Mg 2+ , Pb 2+ and Zn 2+ , within their EF-hands. EFhd1 and EFhd2 are homologous EF-hand proteins with similar structures. Although separately localized within cells, both are actin-binding proteins that modulate F-actin rearrangement through Ca 2+ -independent actin-binding and Ca 2+ -dependent actin-bundling activity. Although Ca 2+ is known to affect the activities of EFhd1 and EFhd2, it is not known whether their actin-related activities are affected by other metals. Here, the crystal structures of the EFhd1 and EFhd2 core domains coordinating Zn 2+ ions within their EF-hands are reported. The presence of Zn 2+ within EFhd1 and EFhd2 was confirmed by analyzing anomalous signals and the difference between anomalous signals using data collected at the peak positions as well as low-energy remote positions at the Zn K-edge. EFhd1 and EFhd2 were also found to exhibit Zn 2+ -independent actin-binding and Zn 2+ -dependent actin-bundling activity. This suggests the actin-related activities of EFhd1 and EFhd2 could be regulated by Zn 2+ as well as Ca 2+ .


  • Organizational Affiliation

    School of Life Sciences, Gwangju Institute of Science and Technology, 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 D1130Mus 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: 1.72 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.199 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 43.959α = 90
b = 47.393β = 90
c = 63.399γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling
PHENIXphasing
Cootmodel building
HKL-2000data reduction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Research Foundation (NRF, Korea)Korea, Republic OfNRF-2021R1A2C1006267
Other private--

Revision History  (Full details and data files)

  • Version 1.0: 2023-03-15
    Type: Initial release
  • Version 1.1: 2024-05-29
    Changes: Data collection