3SRP

Structure of Rivax: A Human Ricin Vaccine

• PDB DOI: https://doi.org/10.2210/pdb3SRP/pdb
• Entry: 3SRP supersedes: 3BJG

• Classification: HYDROLASE
• Organism(s): Ricinus communis
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2011-07-07 Released: 2011-08-03 
• Deposition Author(s): Legler, P.M., Millard, C.B.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.14 Å
• R-Value Free: 0.254 
• R-Value Work: 0.216 
• R-Value Observed: 0.218 

Literature

Structure of RiVax: a recombinant ricin vaccine.

Legler, P.M., Brey, R.N., Smallshaw, J.E., Vitetta, E.S., Millard, C.B.

(2011) Acta Crystallogr D Biol Crystallogr 67: 826-830

• PubMed: 21904036 
• DOI: https://doi.org/10.1107/S0907444911026771
• Primary Citation of Related Structures:  
  3SRP


• PubMed Abstract: 
  

  RiVax is a recombinant protein that is currently under clinical development as part of a human vaccine to protect against ricin poisoning. RiVax includes ricin A-chain (RTA) residues 1-267 with two intentional amino-acid substitutions, V76M and Y80A, aimed at reducing toxicity. Here, the crystal structure of RiVax was solved to 2.1 Å resolution and it was shown that it is superposable with that of the ricin toxin A-chain from Ricinus communis with a root-mean-square deviation of 0.6 Å over 258 C(α) atoms. The RiVax structure is also compared with the recently determined structure of another potential ricin-vaccine immunogen, RTA 1-33/44-198 R48C/T77C. Finally, the locations and solvent-exposure of two toxin-neutralizing B-cell epitopes were examined and it was found that these epitopes are within or near regions predicted to be involved in catalysis. The results demonstrate the composition of the RiVax clinical material and will guide ongoing protein-engineering strategies to develop improved immunogens.

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Organizational Affiliation: 

Naval Research Laboratories, Washington, DC 20375, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content

• Total Structure Weight: 30.2 kDa 
• Atom Count: 2,218 
• Modelled Residue Count: 262 
• Deposited Residue Count: 268 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ricin A chain	A	268	Ricinus communis	Mutation(s): 2  EC: 3.2.2.22
UniProt
Find proteins for P02879 (Ricinus communis) Explore P02879  Go to UniProtKB:  P02879

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	B [auth A], C [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.14 Å
• R-Value Free: 0.254 
• R-Value Work: 0.216 
• R-Value Observed: 0.218 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.56	α = 90
b = 66.56	β = 90
c = 136.72	γ = 90

Software Package:

Software Name	Purpose
PROTEUM PLUS	data collection
AMoRE	phasing
REFMAC	refinement
SAINT	data reduction
SADABS	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-08-03 
Deposition Author(s): Legler, P.M., Millard, C.B.
• This entry supersedes: 3BJG

Revision History  

• Version 1.0: 2011-08-03
  Type: Initial release
  
• Version 1.1: 2012-01-11
  Changes: Database references
• Version 1.2: 2019-09-04
  Changes: Advisory, Data collection
• Version 1.3: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description