5GWF

FraC with GlcNAc(6S) bound


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.163 
  • R-Value Work: 0.118 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Haemolytic actinoporins interact with carbohydrates using their lipid-binding module

Tanaka, K.Caaveiro, J.M.M.Morante, K.Tsumoto, K.

(2017) Philos. Trans. R. Soc. Lond., B, Biol. Sci. 372: --

  • DOI: 10.1098/rstb.2016.0216

  • PubMed Abstract: 
  • Pore-forming toxins (PFTs) are proteins endowed with metamorphic properties that enable them to stably fold in water solutions as well as in cellular membranes. PFTs produce lytic pores on the plasma membranes of target cells conducive to lesions, pl ...

    Pore-forming toxins (PFTs) are proteins endowed with metamorphic properties that enable them to stably fold in water solutions as well as in cellular membranes. PFTs produce lytic pores on the plasma membranes of target cells conducive to lesions, playing key roles in the defensive and offensive molecular systems of living organisms. Actinoporins are a family of potent haemolytic toxins produced by sea anemones vigorously studied as a paradigm of α-helical PFTs, in the context of lipid-protein interactions, and in connection with nanopore technologies. We have recently reported that fragaceatoxin C (FraC), an actinoporin, engages biological membranes with a large adhesive motif allowing the simultaneous attachment of up to four lipid molecules prior to pore formation. Since actinoporins also interact with carbohydrates, we sought to understand the molecular and energetic basis of glycan recognition by FraC. By employing structural and biophysical methodologies, we show that FraC engages glycans with low affinity using its lipid-binding module. Contrary to other PFTs requiring separate domains for glycan and lipid recognition, the small single-domain actinoporins economize resources by achieving dual recognition with a single binding module. This mechanism could enhance the recruitment of actinoporins to the surface of target tissues in their marine environment.This article is part of the themed issue 'Membrane pores: from structure and assembly, to medicine and technology'.


    Organizational Affiliation

    Department of Chemistry and Biotechnology, The University of Tokyo, Bunkyo-ku, Tokyo 113-8656, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DELTA-actitoxin-Afr1a
A, B, C, D
180Actinia fragaceaMutation(s): 0 
Find proteins for B9W5G6 (Actinia fragacea)
Go to UniProtKB:  B9W5G6
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NGY
Query on NGY

Download SDF File 
Download CCD File 
B, D
2-(acetylamino)-2-deoxy-6-O-sulfo-alpha-D-glucopyranose
Sulfated glycosaminoglycan
C8 H15 N O9 S
WJFVEEAIYIOATH-PVFLNQBWSA-N
 Ligand Interaction
CL
Query on CL

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Download CCD File 
A, B, C, D
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
B, C
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.163 
  • R-Value Work: 0.118 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 77.160α = 90.00
b = 44.400β = 92.76
c = 114.360γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
SCALAdata scaling
MOSFLMdata reduction
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
JSPSJapan25249115
JSPSJapan15K06962

Revision History 

  • Version 1.0: 2017-06-21
    Type: Initial release
  • Version 1.1: 2017-12-06
    Type: Database references