7LDF

High resolution NMR solution structure of a de novo designed minimal thioredoxin fold protein


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the lowest energy 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Sampling of structure and sequence space of small protein folds.

Linsky, T.W.Noble, K.Tobin, A.R.Crow, R.Carter, L.Urbauer, J.L.Baker, D.Strauch, E.M.

(2022) Nat Commun 13: 7151-7151

  • DOI: https://doi.org/10.1038/s41467-022-34937-8
  • Primary Citation of Related Structures:  
    7LDF

  • PubMed Abstract: 

    Nature only samples a small fraction of the sequence space that can fold into stable proteins. Furthermore, small structural variations in a single fold, sometimes only a few amino acids, can define a protein's molecular function. Hence, to design proteins with novel functionalities, such as molecular recognition, methods to control and sample shape diversity are necessary. To explore this space, we developed and experimentally validated a computational platform that can design a wide variety of small protein folds while sampling shape diversity. We designed and evaluated stability of about 30,000 de novo protein designs of eight different folds. Among these designs, about 6,200 stable proteins were identified, including some predicted to have a first-of-its-kind minimalized thioredoxin fold. Obtained data revealed protein folding rules for structural features such as helix-connecting loops. Beyond serving as a resource for protein engineering, this massive and diverse dataset also provides training data for machine learning. We developed an accurate classifier to predict the stability of our designed proteins. The methods and the wide range of protein shapes provide a basis for designing new protein functions without compromising stability.


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Minimal thioredoxin fold protein, ems_thioM_80271synthetic constructMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the lowest energy 

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 StatesR01AI140245
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR21AI143399

Revision History  (Full details and data files)

  • Version 1.0: 2022-07-13
    Type: Initial release
  • Version 1.1: 2022-09-14
    Changes: Advisory, Derived calculations
  • Version 1.2: 2022-12-14
    Changes: Database references
  • Version 1.3: 2024-05-15
    Changes: Data collection, Database references