6FDB

Positively supercharged variant of the computationally designed cage protein O3-33


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.62 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.225 
  • R-Value Observed: 0.229 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Rational Engineering of a Designed Protein Cage for siRNA Delivery.

Edwardson, T.G.W.Mori, T.Hilvert, D.

(2018) J Am Chem Soc 140: 10439-10442

  • DOI: https://doi.org/10.1021/jacs.8b06442
  • Primary Citation of Related Structures:  
    6FDB

  • PubMed Abstract: 

    Oligonucleotide therapeutics have transformative potential in modern medicine but are poor drug candidates in themselves unless fitted with compensatory carrier systems. We describe a simple approach to transform a designed porous protein cage into a nucleic acid delivery vehicle. By introducing arginine mutations to the lumenal surface, a positively supercharged capsule is created, which can encapsidate oligonucleotides in vitro with high binding affinity. We demonstrate that the siRNA-loaded cage is taken up by mammalian cells and releases its cargo to induce RNAi and knockdown gene expression. These general concepts could also be applied to alternative scaffold designs, expediting the development of artificial protein cages toward delivery applications.


  • Organizational Affiliation

    Laboratory of Organic Chemistry , ETH Zurich , 8093 Zurich , Switzerland.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Propanediol utilization protein
A, B, C, D, E
A, B, C, D, E, F, G, H
192Salmonella entericaMutation(s): 16 
Gene Names: A7S24_10320A7S72_11360BUJ19_10850CBI64_04620CEP91_14370IN36_13565IN77_10790IN95_23850NGUA18_00608
UniProt
Find proteins for A0A0M0QF47 (Salmonella enterica)
Explore A0A0M0QF47 
Go to UniProtKB:  A0A0M0QF47
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0M0QF47
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.62 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.225 
  • R-Value Observed: 0.229 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 136.865α = 90
b = 136.865β = 90
c = 559.097γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-08-22
    Type: Initial release
  • Version 1.1: 2018-08-29
    Changes: Data collection, Database references
  • Version 1.2: 2024-01-17
    Changes: Data collection, Database references, Refinement description