7SQ4

Designed trefoil knot protein, variant 2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.49 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.231 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

De novo design of knotted tandem repeat proteins.

Doyle, L.A.Takushi, B.Kibler, R.D.Milles, L.F.Orozco, C.T.Jones, J.D.Jackson, S.E.Stoddard, B.L.Bradley, P.

(2023) Nat Commun 14: 6746-6746

  • DOI: https://doi.org/10.1038/s41467-023-42388-y
  • Primary Citation of Related Structures:  
    7SQ3, 7SQ4, 7SQ5, 8ETQ

  • PubMed Abstract: 

    De novo protein design methods can create proteins with folds not yet seen in nature. These methods largely focus on optimizing the compatibility between the designed sequence and the intended conformation, without explicit consideration of protein folding pathways. Deeply knotted proteins, whose topologies may introduce substantial barriers to folding, thus represent an interesting test case for protein design. Here we report our attempts to design proteins with trefoil (3 1 ) and pentafoil (5 1 ) knotted topologies. We extended previously described algorithms for tandem repeat protein design in order to construct deeply knotted backbones and matching designed repeat sequences (N = 3 repeats for the trefoil and N = 5 for the pentafoil). We confirmed the intended conformation for the trefoil design by X ray crystallography, and we report here on this protein's structure, stability, and folding behaviour. The pentafoil design misfolded into an asymmetric structure (despite a 5-fold symmetric sequence); two of the four repeat-repeat units matched the designed backbone while the other two diverged to form local contacts, leading to a trefoil rather than pentafoil knotted topology. Our results also provide insights into the folding of knotted proteins.


  • Organizational Affiliation

    Division of Basic Sciences, Fred Hutchinson Cancer Center, 1100 Fairview Ave. North, Seattle, WA, 98109, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Designed trefoil knot protein, variant 2153synthetic 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: X-RAY DIFFRACTION
  • Resolution: 1.49 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.231 
  • Space Group: P 21 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.81α = 90
b = 55.81β = 90
c = 55.81γ = 90
Software Package:
Software NamePurpose
HKL-2000data scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM123378
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM115545

Revision History  (Full details and data files)

  • Version 1.0: 2022-06-29
    Type: Initial release
  • Version 1.1: 2023-11-15
    Changes: Data collection, Database references