4RUD

Crystal structure of a three finger toxin

• PDB DOI: https://doi.org/10.2210/pdb4RUD/pdb

• Classification: TOXIN
• Organism(s): Micrurus fulvius
• Expression System: Xenopus laevis
• Mutation(s): No 


• Deposited: 2014-11-18 Released: 2016-05-18 
• Deposition Author(s): Jobichen, C., Sivaraman, J.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.237 
• R-Value Work: 0.201 
• R-Value Observed: 0.204 

Literature

Fulditoxin, representing a new class of dimeric snake toxins, defines novel pharmacology at nicotinic ACh receptors.

Foo, C.S., Jobichen, C., Hassan-Puttaswamy, V., Dekan, Z., Tae, H.S., Bertrand, D., Adams, D.J., Alewood, P.F., Sivaraman, J., Nirthanan, S., Kini, R.M.

(2020) Br J Pharmacol 177: 1822-1840

• PubMed: 31877243 
• DOI: https://doi.org/10.1111/bph.14954
• Primary Citation of Related Structures:  
  4RUD


• PubMed Abstract: 
  

  Animal toxins have contributed significantly to our understanding of the neurobiology of receptors and ion channels. We studied the venom of the coral snake Micrurus fulvius fulvius and identified and characterized the structure and pharmacology of a new homodimeric neurotoxin, fulditoxin, that exhibited novel pharmacology at nicotinic ACh receptors (nAChRs).

---

Organizational Affiliation: 

Protein Science Laboratory, Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore, Singapore.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 13.22 kDa 
• Atom Count: 1,041 
• Modelled Residue Count: 116 
• Deposited Residue Count: 116 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Three-finger toxin 3b	A, B	58	Micrurus fulvius	Mutation(s): 0
UniProt
Find proteins for U3EPL2 (Micrurus fulvius) Explore U3EPL2  Go to UniProtKB:  U3EPL2

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	C [auth A], D [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.237 
• R-Value Work: 0.201 
• R-Value Observed: 0.204 
• Space Group: P 4 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.8	α = 90
b = 58.8	β = 90
c = 70.567	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
PHASER	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-05-18 
Deposition Author(s): Jobichen, C., Sivaraman, J.

Revision History  

• Version 1.0: 2016-05-18
  Type: Initial release
  
• Version 1.1: 2017-11-22
  Changes: Refinement description
• Version 1.2: 2018-07-18
  Changes: Data collection, Database references
• Version 1.3: 2020-01-22
  Changes: Database references, Source and taxonomy, Structure summary
• Version 1.4: 2022-08-24
  Changes: Database references, Derived calculations
• Version 1.5: 2023-11-08
  Changes: Data collection, Refinement description