8FRE

Designed loop protein RBL4


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.234 
  • R-Value Observed: 0.236 

Starting Model: in silico
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

De novo design of buttressed loops for sculpting protein functions.

Jiang, H.Jude, K.M.Wu, K.Fallas, J.Ueda, G.Brunette, T.J.Hicks, D.R.Pyles, H.Yang, A.Carter, L.Lamb, M.Li, X.Levine, P.M.Stewart, L.Garcia, K.C.Baker, D.

(2024) Nat Chem Biol 20: 974-980

  • DOI: https://doi.org/10.1038/s41589-024-01632-2
  • Primary Citation of Related Structures:  
    8FRE, 8FRF

  • PubMed Abstract: 

    In natural proteins, structured loops have central roles in molecular recognition, signal transduction and enzyme catalysis. However, because of the intrinsic flexibility and irregularity of loop regions, organizing multiple structured loops at protein functional sites has been very difficult to achieve by de novo protein design. Here we describe a solution to this problem that designs tandem repeat proteins with structured loops (9-14 residues) buttressed by extensive hydrogen bonding interactions. Experimental characterization shows that the designs are monodisperse, highly soluble, folded and thermally stable. Crystal structures are in close agreement with the design models, with the loops structured and buttressed as designed. We demonstrate the functionality afforded by loop buttressing by designing and characterizing binders for extended peptides in which the loops form one side of an extended binding pocket. The ability to design multiple structured loops should contribute generally to efforts to design new protein functions.


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
RBL4
A, B
216synthetic 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

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.287α = 90
b = 215.442β = 90
c = 28.008γ = 90
Software Package:
Software NamePurpose
autoPROCdata reduction
PHENIXrefinement
PHASERphasing
Aimlessdata scaling

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Howard Hughes Medical Institute (HHMI)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2024-04-17
    Type: Initial release
  • Version 1.1: 2024-06-26
    Changes: Database references
  • Version 1.2: 2024-08-07
    Changes: Database references