3MK9

Stabilized Ricin Immunogen 1-33/44-198


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.08 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.211 

wwPDB Validation   3D Report Full Report


This is version 1.5 of the entry. See complete history


Literature

Introduction of a disulfide bond leads to stabilization and crystallization of a ricin immunogen.

Compton, J.R.Legler, P.M.Clingan, B.V.Olson, M.A.Millard, C.B.

(2011) Proteins 79: 1048-1060

  • DOI: https://doi.org/10.1002/prot.22933
  • Primary Citation of Related Structures:  
    3LC9, 3MK9

  • PubMed Abstract: 

    RTA1-33/44-198 is a catalytically inactive, single-domain derivative of the ricin toxin A-chain (RTA) engineered to serve as a stable protein scaffold for presentation of native immunogenic epitopes (Olson et al., Protein Eng Des Sel 2004;17:391-397). To improve the stability and solubility of RTA1-33/44-198 further, we have undertaken the design challenge of introducing a disulfide (SS) bond. Nine pairs of residues were selected for placement of the SS-bond based on molecular dynamics simulation studies of the modeled single-domain chain. Disulfide formation at either of two positions (R48C/T77C or V49C/E99C) involving a specific surface loop (44-55) increased the protein melting temperature by ~5°C compared with RTA1-33/44-198 and by ~13°C compared with RTA. Prolonged stability studies of the R48C/T77C variant (> 60 days at 37°C, pH 7.4) confirmed a > 40% reduction in self-aggregation compared with RTA1-33/44-198 lacking the SS-bond. The R48C/T77C variant retained affinity for anti-RTA antibodies capable of neutralizing ricin toxin, including a monoclonal that recognizes a human B-cell epitope. Introduction of either R48C/T77C or V49C/E99C promoted crystallization of RTA1-33/44-198, and the X-ray structures of the variants were solved to 2.3 A or 2.1 A resolution, respectively. The structures confirm formation of an intramolecular SS-bond, and reveal a single-domain fold that is significantly reduced in volume compared with RTA. Loop 44 to 55 is partly disordered as predicted by simulations, and is positioned to form self-self interactions between symmetry-related molecules. We discuss the importance of RTA loop 34 to 55 as a nucleus for unfolding and aggregation, and draw conclusions for ongoing structure-based minimalist design of RTA-based immunogens.


  • Organizational Affiliation

    Division of Biochemistry, Walter Reed Army Institute of Research, Silver Spring, Maryland 20910, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ricin189Ricinus communisMutation(s): 2 
EC: 3.2.2.22
UniProt
Find proteins for P02879 (Ricinus communis)
Explore P02879 
Go to UniProtKB:  P02879
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP02879
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
B [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.08 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.211 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.744α = 90
b = 72.767β = 90
c = 96.382γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
AMoREphasing
CNSrefinement
SAINTdata reduction
SADABSdata scaling
PROTEUM PLUSdata collection

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-11-10
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2012-01-25
    Changes: Database references
  • Version 1.3: 2019-07-17
    Changes: Data collection, Refinement description
  • Version 1.4: 2021-10-06
    Changes: Database references, Derived calculations
  • Version 1.5: 2023-09-06
    Changes: Data collection, Refinement description