6FDB | pdb_00006fdb

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

• PDB DOI: https://doi.org/10.2210/pdb6FDB/pdb

• Classification: DE NOVO PROTEIN
• Organism(s): Salmonella enterica
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2017-12-22 Released: 2018-08-22 
• Deposition Author(s): Edwardson, T., Mori, T., Hilvert, D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.62 Å
• R-Value Free: 
  0.288 (Depositor), 0.289 (DCC) 
• R-Value Work: 
  0.225 (Depositor), 0.230 (DCC) 
• R-Value Observed: 
  0.229 (Depositor) 

Starting Model: experimental

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

• PubMed: 30091604 
• DOI: https://doi.org/10.1021/jacs.8b06442
• Primary Citation 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.

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Organizational Affiliation: 
• Laboratory of Organic Chemistry , ETH Zurich , 8093 Zurich , Switzerland.

Biological Assembly 1  

Global Symmetry: Octahedral - O  (Explore in 3D)
Global Stoichiometry: Homo 24-mer - A24 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 161.07 kDa 
• Atom Count: 10,624 
• Modeled Residue Count: 1,472 
• Deposited Residue Count: 1,536 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Propanediol utilization protein	A, B, C, D, E, F, G, H	192	Salmonella enterica	Mutation(s): 16  Gene Names: A7S24_10320, A7S72_11360, BUJ19_10850, CBI64_04620, CEP91_14370, IN36_13565, IN77_10790, IN95_23850, NGUA18_00608
UniProt
Find proteins for A0A0M0QF47 (Salmonella enterica) Explore A0A0M0QF47  Go to UniProtKB:  A0A0M0QF47

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.62 Å
• R-Value Free:  0.288 (Depositor), 0.289 (DCC) 
• R-Value Work:  0.225 (Depositor), 0.230 (DCC) 
• R-Value Observed: 0.229 (Depositor) 

Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 136.865	α = 90
b = 136.865	β = 90
c = 559.097	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-08-22 
Deposition Author(s): Edwardson, T., Mori, T., Hilvert, D.

Revision History  

• 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