7UWZ

NMR solution structure of the De novo designed small beta-barrel protein 33_bp_sh3

  • Classification: DE NOVO PROTEIN
  • Organism(s): synthetic construct
  • Expression System: Escherichia coli BL21(DE3)
  • Mutation(s): No 

  • Deposited: 2022-05-04 Released: 2023-03-22 
  • Deposition Author(s): Peterson, F.C., Kim, D.E., Jensen, D.R., Saleem, A., Chow, C.M., Volkman, B.F., Baker, D.
  • Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), National Institutes of Health/National Center for Research Resources (NIH/NCRR), Department of Energy (DOE, United States), National Institutes of Health/National Cancer Institute (NIH/NCI), National Institutes of Health/National Institute on Aging (NIH/NIA), National Institutes of Health/Office of the Director

Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 20 
  • Selection Criteria: target function 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

De novo design of small beta barrel proteins.

Kim, D.E.Jensen, D.R.Feldman, D.Tischer, D.Saleem, A.Chow, C.M.Li, X.Carter, L.Milles, L.Nguyen, H.Kang, A.Bera, A.K.Peterson, F.C.Volkman, B.F.Ovchinnikov, S.Baker, D.

(2023) Proc Natl Acad Sci U S A 120: e2207974120-e2207974120

  • DOI: https://doi.org/10.1073/pnas.2207974120
  • Primary Citation of Related Structures:  
    7UR7, 7UR8, 7UWY, 7UWZ

  • PubMed Abstract: 

    Small beta barrel proteins are attractive targets for computational design because of their considerable functional diversity despite their very small size (<70 amino acids). However, there are considerable challenges to designing such structures, and there has been little success thus far. Because of the small size, the hydrophobic core stabilizing the fold is necessarily very small, and the conformational strain of barrel closure can oppose folding; also intermolecular aggregation through free beta strand edges can compete with proper monomer folding. Here, we explore the de novo design of small beta barrel topologies using both Rosetta energy-based methods and deep learning approaches to design four small beta barrel folds: Src homology 3 (SH3) and oligonucleotide/oligosaccharide-binding (OB) topologies found in nature and five and six up-and-down-stranded barrels rarely if ever seen in nature. Both approaches yielded successful designs with high thermal stability and experimentally determined structures with less than 2.4 Å rmsd from the designed models. Using deep learning for backbone generation and Rosetta for sequence design yielded higher design success rates and increased structural diversity than Rosetta alone. The ability to design a large and structurally diverse set of small beta barrel proteins greatly increases the protein shape space available for designing binders to protein targets of interest.


  • Organizational Affiliation

    Department of Biochemistry, University of Washington, Seattle, WA 98195.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
De novo designed small beta-barrel protein 33_bp_sh362synthetic constructMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 20 
  • Selection Criteria: target function 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR37 AI058072
National Institutes of Health/National Center for Research Resources (NIH/NCRR)United StatesS10 OD020000
Department of Energy (DOE, United States)United StatesDE-SC0018940
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesR01CA240339
National Institutes of Health/National Institute on Aging (NIH/NIA)United States5U19AG065156
National Institutes of Health/Office of the DirectorUnited StatesDP5OD026389

Revision History  (Full details and data files)

  • Version 1.0: 2023-03-22
    Type: Initial release
  • Version 1.1: 2024-05-15
    Changes: Data collection, Database references