7C28

Unusual quaternary structure of a homodimeric synergistic toxin from mamba snake venom


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.241 
  • R-Value Observed: 0.246 

wwPDB Validation 3D Report Full Report



Literature

Unusual quaternary structure of a homodimeric synergistic-type toxin from mamba snake venom defines its molecular evolution.

Aoki-Shioi, N.Jobichen, C.Sivaraman, J.Kini, R.M.

(2020) Biochem J 

  • DOI: 10.1042/BCJ20200529
  • Primary Citation of Related Structures:  
    7C28

  • PubMed Abstract: 
  • Snake venoms are complex mixtures of enzymes and non-enzymatic proteins that have evolved to immobilize and kill prey animals. Among them, three-finger toxins (3FTxs) belong to the largest superfamily of non-enzymatic proteins. They share a common st ...

    Snake venoms are complex mixtures of enzymes and non-enzymatic proteins that have evolved to immobilize and kill prey animals. Among them, three-finger toxins (3FTxs) belong to the largest superfamily of non-enzymatic proteins. They share a common structure of three b-stranded loops extending like fingers from a central core containing all four conserved disulfide bonds. Most 3FTxs are monomers and through subtle changes in their amino acid sequences they interact with different receptors, ion channels and enzymes to exhibit a wide variety of biological effects. The 3FTxs have further expanded their pharmacological space through covalent or noncovalent dimerization. Synergistic-type toxins (SynTxs) isolated from mamba venoms, highly deadly venomous snake, although nontoxic have been known to enhance toxicity of other venom proteins. However, the details of three-dimensional structure and molecular mechanism of activity of this unusual class of 3FTxs are unclear. We determined the first three-dimensional structure of a SynTx isolated from Dendroaspis jamesoni jamesoni (Jameson's mamba) venom. The SynTx forms a unique homodimer that is held together by an interchain disulfide bond. The dimeric interface is elaborate and encompasses loops II and III. In addition to the inter-subunit disulfide bond, the hydrogen bonds and hydrophobic interactions between the monomers contribute to the dimer formation. Besides, two sulfate ions that mediate interactions between the monomers. This unique quaternary structure is evolved through noncovalent homodimers such as k-bungarotoxins. This novel dimerization further enhances the diversity in structure and function of 3FTxs.


    Organizational Affiliation

    National University of Singapore, SINGAPORE, Singapore.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Synergistic-type venom protein S2C4AB65Dendroaspis jamesoni kaimosaeMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.241 
  • R-Value Observed: 0.246 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 52.439α = 90
b = 55.982β = 90
c = 102.818γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
DENZOdata reduction
SCALEPACKdata scaling
Auto-Rickshawphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2020-10-14
    Type: Initial release