5I2O

Structure of EF-hand containing protein


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.185 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural implications of Ca(2+)-dependent actin-bundling function of human EFhd2/Swiprosin-1.

Park, K.R.Kwon, M.S.An, J.Y.Lee, J.G.Youn, H.S.Lee, Y.Kang, J.Y.Kim, T.G.Lim, J.J.Park, J.S.Lee, S.H.Song, W.K.Cheong, H.K.Jun, C.D.Eom, S.H.

(2016) Sci Rep 6: 39095-39095

  • DOI: https://doi.org/10.1038/srep39095
  • Primary Citation of Related Structures:  
    5I2L, 5I2O, 5I2Q

  • PubMed Abstract: 

    EFhd2/Swiprosin-1 is a cytoskeletal Ca 2+ -binding protein implicated in Ca 2+ -dependent cell spreading and migration in epithelial cells. EFhd2 domain architecture includes an N-terminal disordered region, a PxxP motif, two EF-hands, a ligand mimic helix and a C-terminal coiled-coil domain. We reported previously that EFhd2 displays F-actin bundling activity in the presence of Ca 2+ and this activity depends on the coiled-coil domain and direct interaction of the EFhd2 core region. However, the molecular mechanism for the regulation of F-actin binding and bundling by EFhd2 is unknown. Here, the Ca 2+ -bound crystal structure of the EFhd2 core region is presented and structures of mutants defective for Ca 2+ -binding are also described. These structures and biochemical analyses reveal that the F-actin bundling activity of EFhd2 depends on the structural rigidity of F-actin binding sites conferred by binding of the EF-hands to Ca 2+ . In the absence of Ca 2+ , the EFhd2 core region exhibits local conformational flexibility around the EF-hand domain and C-terminal linker, which retains F-actin binding activity but loses the ability to bundle F-actin. In addition, we establish that dimerisation of EFhd2 via the C-terminal coiled-coil domain, which is necessary for F-actin bundling, occurs through the parallel coiled-coil interaction.


  • Organizational Affiliation

    School of Life Science, Gwangju Institute of Science and Technology (GIST), 123 Cheomdangwagi-ro, Buk-gu, Gwangju 61005, Republic of Korea.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
EF-hand domain-containing protein D2120Homo sapiensMutation(s): 1 
Gene Names: EFHD2SWS1
UniProt & NIH Common Fund Data Resources
Find proteins for Q96C19 (Homo sapiens)
Explore Q96C19 
Go to UniProtKB:  Q96C19
PHAROS:  Q96C19
GTEx:  ENSG00000142634 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ96C19
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download Ideal Coordinates CCD File 
B [auth A]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.185 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 36.254α = 90
b = 51.529β = 90
c = 53.567γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data collection
HKL-2000data processing
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-12-28
    Type: Initial release
  • Version 1.1: 2023-11-08
    Changes: Data collection, Database references, Refinement description