4WVM | pdb_00004wvm

Stonustoxin structure

• PDB DOI: https://doi.org/10.2210/pdb4WVM/pdb

• Classification: TOXIN
• Organism(s): Synanceia horrida
• Mutation(s): No 


• Deposited: 2014-11-06 Released: 2015-12-02 
• Deposition Author(s): Ellisdon, A.M., Panjikar, S., Whisstock, J.C., McGowan, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free: 
  0.236 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.207 (Depositor), 0.231 (DCC) 
• R-Value Observed: 
  0.209 (Depositor) 

Literature

Stonefish toxin defines an ancient branch of the perforin-like superfamily.

Ellisdon, A.M., Reboul, C.F., Panjikar, S., Huynh, K., Oellig, C.A., Winter, K.L., Dunstone, M.A., Hodgson, W.C., Seymour, J., Dearden, P.K., Tweten, R.K., Whisstock, J.C., McGowan, S.

(2015) Proc Natl Acad Sci U S A 112: 15360-15365

• PubMed: 26627714 
• DOI: https://doi.org/10.1073/pnas.1507622112
• Primary Citation Related Structures: 
  4WVM


• PubMed Abstract: 
  

  The lethal factor in stonefish venom is stonustoxin (SNTX), a heterodimeric cytolytic protein that induces cardiovascular collapse in humans and native predators. Here, using X-ray crystallography, we make the unexpected finding that SNTX is a pore-forming member of an ancient branch of the Membrane Attack Complex-Perforin/Cholesterol-Dependent Cytolysin (MACPF/CDC) superfamily. SNTX comprises two homologous subunits (α and β), each of which comprises an N-terminal pore-forming MACPF/CDC domain, a central focal adhesion-targeting domain, a thioredoxin domain, and a C-terminal tripartite motif family-like PRY SPla and the RYanodine Receptor immune recognition domain. Crucially, the structure reveals that the two MACPF domains are in complex with one another and arranged into a stable early prepore-like assembly. These data provide long sought after near-atomic resolution insights into how MACPF/CDC proteins assemble into prepores on the surface of membranes. Furthermore, our analyses reveal that SNTX-like MACPF/CDCs are distributed throughout eukaryotic life and play a broader, possibly immune-related function outside venom.

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Organizational Affiliation: 
• Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Melbourne, VIC, 3800, Australia; Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Melbourne, VIC, 3800, Australia;
Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Melbourne, VIC, 3800, Australia; Australian Synchrotron, Macromolecular Crystallography, Melbourne, VIC, 3168, Australia;
Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Melbourne, VIC, 3800, Australia;
Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Melbourne, VIC, 3800, Australia; Biomedicine Discovery Institute and Department of Pharmacology, Monash University, Melbourne, VIC, 3800, Australia;
Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Melbourne, VIC, 3800, Australia; Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Melbourne, VIC, 3800, Australia; Biomedicine Discovery Institute and Department of Microbiology, Monash University, Melbourne, VIC, 3800, Australia;
Biomedicine Discovery Institute and Department of Pharmacology, Monash University, Melbourne, VIC, 3800, Australia;
Centre for Biodiscovery and Molecular Development of Therapeutics, Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, QLD, 4870, Australia;
Department of Biochemistry and Genetics Otago, University of Otago, Dunedin, 9054 Aotearoa-New Zealand;
Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104.
Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Melbourne, VIC, 3800, Australia; Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Melbourne, VIC, 3800, Australia; [e-mail] [e-mail].
Biomedicine Discovery Institute and Department of Microbiology, Monash University, Melbourne, VIC, 3800, Australia; [e-mail] [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 159.14 kDa 
• Atom Count: 9,691 
• Modeled Residue Count: 1,228 
• Deposited Residue Count: 1,403 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Stonustoxin subunit alpha	A	703	Synanceia horrida	Mutation(s): 0
UniProt
Find proteins for Q98989 (Synanceia horrida) Explore Q98989  Go to UniProtKB:  Q98989

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Stonustoxin subunit beta	B	700	Synanceia horrida	Mutation(s): 0
UniProt
Find proteins for Q91453 (Synanceia horrida) Explore Q91453  Go to UniProtKB:  Q91453

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free:  0.236 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.207 (Depositor), 0.231 (DCC) 
• R-Value Observed: 0.209 (Depositor) 

Space Group: P 4₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 107.911	α = 90
b = 107.911	β = 90
c = 244.345	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
Coot	model building
XSCALE	data scaling
SHELXDE	phasing
XDS	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-12-02 
Deposition Author(s): Ellisdon, A.M., Panjikar, S., Whisstock, J.C., McGowan, S.

Revision History  

• Version 1.0: 2015-12-02
  Type: Initial release
  
• Version 1.1: 2015-12-16
  Changes: Database references
• Version 1.2: 2015-12-30
  Changes: Database references
• Version 1.3: 2017-11-22
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.4: 2023-12-27
  Changes: Data collection, Database references