7EKZ

Structural and functional insights into Hydra Actinoporin-Like Toxin 1 (HALT-1)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.43 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.163 
  • R-Value Observed: 0.166 

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This is version 1.1 of the entry. See complete history


Literature

Structural and functional analysis of Hydra Actinoporin-Like Toxin 1 (HALT-1).

Ker, D.S.Sha, H.X.Jonet, M.A.Hwang, J.S.Ng, C.L.

(2021) Sci Rep 11: 20649-20649

  • DOI: https://doi.org/10.1038/s41598-021-99879-5
  • Primary Citation of Related Structures:  
    7EKZ

  • PubMed Abstract: 

    Actinoporins are a family of α-pore-forming toxins (α-PFTs) that have been identified in sea anemones. Recently, a freshwater Hydra Actinoporin-Like Toxin (HALT) gene family was found in Hydra magnipapillata. Unlike sea anemone actinoporins that use sphingomyelin as their main recognition target, the HALTs proteins may recognise alternative lipid molecules as their target. To unveil the structural insights into lipid preference of HALTs protein as compared to sea anemone actinoporins, we have determined the first crystal structure of actinoporin-like toxin, HALT-1 at 1.43 Å resolution with an acetylated lysine residue K76. Despite the overall structure of HALT-1 sharing a high structural similarity to sea anemone actinoporins, the atomic resolution structure revealed several unique structural features of HALT-1 that may influence the lipid preference and oligomerisation interface. The HALT-1 contains a RAG motif in place of the highly conserved RGD motif found in sea anemone actinoporins. The RAG motif contributed to a sharper β9-β10 turn, which may sway its oligomerisation interface in comparison to sea anemone actinoporins. In the lipid-binding region, the HALT-1 contains a shorter α2 helix and a longer α2-β9 loop due to deletion and subsequently an insertion of five amino acid residues in comparison to the sea anemone actinoporins. Structure comparison and molecular docking analysis further revealed that the HALT-1 lipid-binding site may favour sphingolipids with sulfate or phosphate head group more than the sphingomyelin. The structure of HALT-1 reported here provides a new insight for a better understanding of the evolution and lipid recognition mechanism of actinoporin.


  • Organizational Affiliation

    Department of Biological Sciences, School of Medical and Life Sciences, Sunway University, No. 5, Jalan Universiti, 47500, Bandar Sunway, Selangor, Malaysia.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
HALT-1189Hydra vulgarisMutation(s): 0 
UniProt
Find proteins for A0A8B7DWS6 (Hydra vulgaris)
Explore A0A8B7DWS6 
Go to UniProtKB:  A0A8B7DWS6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A8B7DWS6
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.43 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.163 
  • R-Value Observed: 0.166 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 47.1α = 90
b = 49.59β = 90
c = 77.094γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
MOSFLMdata reduction
Aimlessdata scaling
BALBESphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Universiti Kebangsaan MalaysiaMalaysiaGP-2019-K019584
Universiti Kebangsaan MalaysiaMalaysiaGP-2020-K019584

Revision History  (Full details and data files)

  • Version 1.0: 2022-02-16
    Type: Initial release
  • Version 1.1: 2023-11-29
    Changes: Data collection, Refinement description