8FBI

Improving the secretion of designed protein assemblies through negative design of cryptic transmembrane domains


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.61 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.233 
  • R-Value Observed: 0.238 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Improving the secretion of designed protein assemblies through negative design of cryptic transmembrane domains.

Wang, J.Y.J.Khmelinskaia, A.Sheffler, W.Miranda, M.C.Antanasijevic, A.Borst, A.J.Torres, S.V.Shu, C.Hsia, Y.Nattermann, U.Ellis, D.Walkey, C.Ahlrichs, M.Chan, S.Kang, A.Nguyen, H.Sydeman, C.Sankaran, B.Wu, M.Bera, A.K.Carter, L.Fiala, B.Murphy, M.Baker, D.Ward, A.B.King, N.P.

(2023) Proc Natl Acad Sci U S A 120: e2214556120-e2214556120

  • DOI: https://doi.org/10.1073/pnas.2214556120
  • Primary Citation of Related Structures:  
    8FBI, 8FBJ, 8FBK, 8FBN, 8FBO

  • PubMed Abstract: 
  • Computationally designed protein nanoparticles have recently emerged as a promising platform for the development of new vaccines and biologics. For many applications, secretion of designed nanoparticles from eukaryotic cells would be advantageous, but in practice, they often secrete poorly ...

    Computationally designed protein nanoparticles have recently emerged as a promising platform for the development of new vaccines and biologics. For many applications, secretion of designed nanoparticles from eukaryotic cells would be advantageous, but in practice, they often secrete poorly. Here we show that designed hydrophobic interfaces that drive nanoparticle assembly are often predicted to form cryptic transmembrane domains, suggesting that interaction with the membrane insertion machinery could limit efficient secretion. We develop a general computational protocol, the Degreaser, to design away cryptic transmembrane domains without sacrificing protein stability. The retroactive application of the Degreaser to previously designed nanoparticle components and nanoparticles considerably improves secretion, and modular integration of the Degreaser into design pipelines results in new nanoparticles that secrete as robustly as naturally occurring protein assemblies. Both the Degreaser protocol and the nanoparticles we describe may be broadly useful in biotechnological applications.


    Organizational Affiliation

    Institute for Protein Design, University of Washington, Seattle, WA 98195.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
KWOCA_39A301synthetic constructMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.61 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.233 
  • R-Value Observed: 0.238 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 115.661α = 90
b = 115.661β = 90
c = 72.079γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Bill & Melinda Gates FoundationUnited States--

Revision History  (Full details and data files)

  • Version 1.0: 2023-03-22
    Type: Initial release